================================================================================ ================================================================================ Starting configure run at Mon, 10 Oct 2022 16:49:43 -0700 Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-scalar-type=complex --with-mpi=1 --COPTFLAGS=-O3 --FOPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with-debugging=0 --prefix=/home/pesun/.emopt/ --download-scalapack --download-mumps --download-fblaslapack=1 --with-precision=single Working directory: /home/pesun/.emopt/build/petsc-3.12.1 Machine platform: uname_result(system='Linux', node='pesun-lt', release='5.15.0-48-generic', version='#54~20.04.1-Ubuntu SMP Thu Sep 1 16:17:26 UTC 2022', machine='x86_64', processor='x86_64') Python version: 3.8.13 (default, Mar 28 2022, 11:38:47) [GCC 7.5.0] ================================================================================ ================================================================================ TEST configureExternalPackagesDir from config.framework(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/framework.py:911) TESTING: configureExternalPackagesDir from config.framework(config/BuildSystem/config/framework.py:911) ================================================================================ TEST configureDebuggers from config.utilities.debuggers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/debuggers.py:21) TESTING: configureDebuggers from config.utilities.debuggers(config/BuildSystem/config/utilities/debuggers.py:21) Find a default debugger and determine its arguments Executing: uname -s stdout: Linux Checking for program /home/pesun/opt/openmpi/bin/gdb...not found Checking for program /home/pesun/anaconda3/bin/gdb...not found Checking for program /home/pesun/anaconda3/condabin/gdb...not found Checking for program /home/pesun/.local/bin/gdb...not found Checking for program /usr/local/sbin/gdb...not found Checking for program /usr/local/bin/gdb...not found Checking for program /usr/sbin/gdb...not found Checking for program /sbin/gdb...not found Checking for program /usr/games/gdb...not found Checking for program /usr/local/games/gdb...not found Checking for program /snap/bin/gdb...not found Checking for program /bin/gdb...found Defined make macro "GDB" to "/bin/gdb" Defined "USE_DEBUGGER" to ""gdb"" Executing: uname -s stdout: Linux Defined make macro "DSYMUTIL" to "true" child config.utilities.debuggers 0.004612 ================================================================================ TEST configureDirectories from PETSc.options.petscdir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/petscdir.py:23) TESTING: configureDirectories from PETSc.options.petscdir(config/PETSc/options/petscdir.py:23) Checks PETSC_DIR and sets if not set Version Information: #define PETSC_VERSION_RELEASE 1 #define PETSC_VERSION_MAJOR 3 #define PETSC_VERSION_MINOR 12 #define PETSC_VERSION_SUBMINOR 1 #define PETSC_VERSION_PATCH 0 #define PETSC_VERSION_DATE "Oct, 22, 2019" #define PETSC_VERSION_GIT "v3.12.1" #define PETSC_VERSION_DATE_GIT "2019-10-22 18:40:25 -0500" #define PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_ PETSC_VERSION_EQ #define PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ #define PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ child PETSc.options.petscdir 0.000878 ================================================================================ TEST getDatafilespath from PETSc.options.dataFilesPath(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/dataFilesPath.py:29) TESTING: getDatafilespath from PETSc.options.dataFilesPath(config/PETSc/options/dataFilesPath.py:29) Checks what DATAFILESPATH should be child PETSc.options.dataFilesPath 0.000087 ================================================================================ TEST configureGit from config.sourceControl(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/sourceControl.py:24) TESTING: configureGit from config.sourceControl(config/BuildSystem/config/sourceControl.py:24) Find the Git executable Checking for program /home/pesun/opt/openmpi/bin/git...not found Checking for program /home/pesun/anaconda3/bin/git...not found Checking for program /home/pesun/anaconda3/condabin/git...not found Checking for program /home/pesun/.local/bin/git...not found Checking for program /usr/local/sbin/git...not found Checking for program /usr/local/bin/git...not found Checking for program /usr/sbin/git...not found Checking for program /sbin/git...not found Checking for program /usr/games/git...not found Checking for program /usr/local/games/git...not found Checking for program /snap/bin/git...not found Checking for program /bin/git...found Defined make macro "GIT" to "git" Executing: git --version stdout: git version 2.25.1 child config.sourceControl 0.002723 ================================================================================ TEST configureInstallationMethod from PETSc.options.petscclone(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/petscclone.py:20) TESTING: configureInstallationMethod from PETSc.options.petscclone(config/PETSc/options/petscclone.py:20) This is a tarball installation child PETSc.options.petscclone 0.000384 ================================================================================ TEST setNativeArchitecture from PETSc.options.arch(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/arch.py:31) TESTING: setNativeArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:31) ================================================================================ TEST configureArchitecture from PETSc.options.arch(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/arch.py:43) TESTING: configureArchitecture from PETSc.options.arch(config/PETSc/options/arch.py:43) Checks PETSC_ARCH and sets if not set configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash does not match args: --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --download-fblaslapack=1 --download-mumps --download-scalapack --prefix=/home/pesun/.emopt/ --with-debugging=0 --with-mpi=1 --with-scalar-type=complex PATH=/home/pesun/opt/openmpi/bin:/home/pesun/anaconda3/bin:/home/pesun/anaconda3/condabin:/home/pesun/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/sbin:/usr/games:/usr/local/games:/snap/bin:/bin:/usr/bin:/usr/local/cuda-11.7/bin 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b config/PETSc/__init__.py 03cfd3351bf328e9fc8497df0272bfbf788218da7d5316ef5f5d85ec4e60b42f config/BuildSystem/config/packages/pnetcdf.py 049be0d9ca7d151e8caff1340662d97ee25bde73abb05986289188bc2f36241f config/BuildSystem/config/packages/openmp.py 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fb640bb9fcf78597d487715dc67dcb5d4bd38c6c8e7468590a0757f4a494606d config/BuildSystem/config/packages/strumpack.py fbb3e345e450de9321ccec4ad00e14dadaf5972678bfbe2f9071686ca33afd3e config/BuildSystem/config/packages/silo.py ffa9dbe18feaae9f9f6ac951ecadc05f1c24ecae5f77ed5d6bbd8be2eec0c25b config/BuildSystem/config/packages/mathlib.py need to run configure Setting hashfile: arch-linux-c-opt/lib/petsc/conf/configure-hash Deleting configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash Deleted configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash child PETSc.options.arch 0.003831 ================================================================================ TEST setInstallDir from PETSc.options.installDir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/installDir.py:35) TESTING: setInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:35) setup installDir to either prefix or if that is not set to PETSC_DIR/PETSC_ARCH Defined make macro "PREFIXDIR" to "/home/pesun/.emopt" ================================================================================ TEST saveReconfigure from PETSc.options.installDir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/installDir.py:79) TESTING: saveReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:79) ================================================================================ TEST cleanConfDir from PETSc.options.installDir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/installDir.py:72) TESTING: cleanConfDir from PETSc.options.installDir(config/PETSc/options/installDir.py:72) ================================================================================ TEST configureInstallDir from PETSc.options.installDir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/installDir.py:56) TESTING: configureInstallDir from PETSc.options.installDir(config/PETSc/options/installDir.py:56) Makes installDir subdirectories if it does not exist for both prefix install location and PETSc work install location Changed persistence directory to /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf ================================================================================ TEST restoreReconfigure from PETSc.options.installDir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/installDir.py:92) TESTING: restoreReconfigure from PETSc.options.installDir(config/PETSc/options/installDir.py:92) child PETSc.options.installDir 0.000545 ================================================================================ TEST setExternalPackagesDir from PETSc.options.externalpackagesdir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/externalpackagesdir.py:15) TESTING: setExternalPackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:15) ================================================================================ TEST cleanExternalpackagesDir from PETSc.options.externalpackagesdir(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/externalpackagesdir.py:22) TESTING: cleanExternalpackagesDir from PETSc.options.externalpackagesdir(config/PETSc/options/externalpackagesdir.py:22) child PETSc.options.externalpackagesdir 0.000102 ================================================================================ TEST configureCLanguage from PETSc.options.languages(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/languages.py:27) TESTING: configureCLanguage from PETSc.options.languages(config/PETSc/options/languages.py:27) Choose whether to compile the PETSc library using a C or C++ compiler C language is C Defined "CLANGUAGE_C" to "1" child PETSc.options.languages 0.000179 ================================================================================ TEST printEnvVariables from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1715) TESTING: printEnvVariables from config.setCompilers(config/BuildSystem/config/setCompilers.py:1715) **** printenv **** SHELL=/bin/bash SESSION_MANAGER=local/pesun-lt:@/tmp/.ICE-unix/2371,unix/pesun-lt:/tmp/.ICE-unix/2371 QT_ACCESSIBILITY=1 COLORTERM=truecolor XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg XDG_MENU_PREFIX=gnome- GNOME_DESKTOP_SESSION_ID=this-is-deprecated CONDA_EXE=/home/pesun/anaconda3/bin/conda _CE_M= GNOME_SHELL_SESSION_MODE=ubuntu SSH_AUTH_SOCK=/run/user/1000/keyring/ssh XMODIFIERS=@im=ibus DESKTOP_SESSION=ubuntu SSH_AGENT_PID=2333 GTK_MODULES=gail:atk-bridge ENV=/usr/share/modules/init/profile.sh PWD=/home/pesun/.emopt/build/petsc-3.12.1 LOGNAME=pesun XDG_SESSION_DESKTOP=ubuntu XDG_SESSION_TYPE=x11 CONDA_PREFIX=/home/pesun/anaconda3 MODULESHOME=/usr/share/modules MANPATH=: GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1 XAUTHORITY=/run/user/1000/gdm/Xauthority GJS_DEBUG_TOPICS=JS ERROR;JS LOG WINDOWPATH=2 HOME=/home/pesun USERNAME=pesun LANG=en_US.UTF-8 LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: XDG_CURRENT_DESKTOP=ubuntu:GNOME VTE_VERSION=6003 CONDA_PROMPT_MODIFIER=(base) GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/cca09c68_5015_4ae3_92ac_2f21a3c06d65 INVOCATION_ID=69b50ac7d3174bc4809e341dcc2ce7b3 MANAGERPID=2113 GJS_DEBUG_OUTPUT=stderr LESSCLOSE=/usr/bin/lesspipe %s %s MODULEPATH_modshare=/etc/environment-modules/modules:1:/usr/share/modules/$MODULE_VERSION/modulefiles:1:/usr/share/modules/modulefiles:1:/usr/share/modules/versions:1 XDG_SESSION_CLASS=user TERM=xterm-256color _CE_CONDA= LESSOPEN=| /usr/bin/lesspipe %s USER=pesun GNOME_TERMINAL_SERVICE=:1.107 CONDA_SHLVL=1 LOADEDMODULES= DISPLAY=:1 SHLVL=1 BASH_ENV=/usr/share/modules/init/bash QT_IM_MODULE=ibus CONDA_PYTHON_EXE=/home/pesun/anaconda3/bin/python LD_LIBRARY_PATH=/home/pesun/opt/openmpi/lib:/usr/local/cuda-11.7/lib64 XDG_RUNTIME_DIR=/run/user/1000 CONDA_DEFAULT_ENV=base OMP_NUM_THREADS=1 JOURNAL_STREAM=8:59561 XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop PATH=/home/pesun/opt/openmpi/bin:/home/pesun/anaconda3/bin:/home/pesun/anaconda3/condabin:/home/pesun/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/sbin:/usr/games:/usr/local/games:/snap/bin:/bin:/usr/bin:/usr/local/cuda-11.7/bin MODULEPATH=/etc/environment-modules/modules:/usr/share/modules/versions:/usr/share/modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles GDMSESSION=ubuntu DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus OLDPWD=/home/pesun/.emopt/build MODULES_CMD=/usr/lib/x86_64-linux-gnu/modulecmd.tcl _=./configure ================================================================================ TEST resetEnvCompilers from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1722) TESTING: resetEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1722) ================================================================================ TEST checkEnvCompilers from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1752) TESTING: checkEnvCompilers from config.setCompilers(config/BuildSystem/config/setCompilers.py:1752) ================================================================================ TEST checkMPICompilerOverride from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1685) TESTING: checkMPICompilerOverride from config.setCompilers(config/BuildSystem/config/setCompilers.py:1685) Check if --with-mpi-dir is used along with CC CXX or FC compiler options. This usually prevents mpi compilers from being used - so issue a warning ================================================================================ TEST requireMpiLdPath from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1706) TESTING: requireMpiLdPath from config.setCompilers(config/BuildSystem/config/setCompilers.py:1706) OpenMPI wrappers require LD_LIBRARY_PATH set ================================================================================ TEST checkInitialFlags from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:450) TESTING: checkInitialFlags from config.setCompilers(config/BuildSystem/config/setCompilers.py:450) Initialize the compiler and linker flags Initialized CFLAGS to Initialized CFLAGS to Initialized LDFLAGS to Initialized CUDAFLAGS to Initialized CUDAFLAGS to Initialized LDFLAGS to Initialized CXXFLAGS to Initialized CXX_CXXFLAGS to Initialized LDFLAGS to Initialized FFLAGS to Initialized FFLAGS to Initialized LDFLAGS to Initialized CPPFLAGS to Initialized FPPFLAGS to Initialized CUDAPPFLAGS to -Wno-deprecated-gpu-targets Initialized CXXPPFLAGS to Initialized CC_LINKER_FLAGS to [] Initialized CXX_LINKER_FLAGS to [] Initialized FC_LINKER_FLAGS to [] Initialized CUDAC_LINKER_FLAGS to [] Initialized sharedLibraryFlags to [] Initialized dynamicLibraryFlags to [] ================================================================================ TEST checkCCompiler from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:620) TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:620) Locate a functional C compiler Checking for program /home/pesun/opt/openmpi/bin/mpicc...found Defined make macro "CC" to "mpicc" All intermediate test results are stored in /tmp/petsc-xk72m0wq All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.setCompilers Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Testing executable /tmp/petsc-xk72m0wq/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: mpicc --version stdout: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCPreprocessor from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:657) TESTING: checkCPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:657) Locate a functional C preprocessor Checking for program /home/pesun/opt/openmpi/bin/mpicc...found Defined make macro "CPP" to "mpicc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCUDACompiler from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:695) TESTING: checkCUDACompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:695) Locate a functional CUDA compiler Checking for program /home/pesun/opt/openmpi/bin/nvcc...not found Checking for program /home/pesun/anaconda3/bin/nvcc...not found Checking for program /home/pesun/anaconda3/condabin/nvcc...not found Checking for program /home/pesun/.local/bin/nvcc...not found Checking for program /usr/local/sbin/nvcc...not found Checking for program /usr/local/bin/nvcc...not found Checking for program /usr/sbin/nvcc...not found Checking for program /sbin/nvcc...not found Checking for program /usr/games/nvcc...not found Checking for program /usr/local/games/nvcc...not found Checking for program /snap/bin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /usr/bin/nvcc...not found Checking for program /usr/local/cuda-11.7/bin/nvcc...found Defined make macro "CUDAC" to "nvcc" Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: nvcc --version stdout: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Tue_May__3_18:49:52_PDT_2022 Cuda compilation tools, release 11.7, V11.7.64 Build cuda_11.7.r11.7/compiler.31294372_0 ================================================================================ TEST checkCUDAPreprocessor from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:735) TESTING: checkCUDAPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:735) Locate a functional CUDA preprocessor Checking for program /home/pesun/opt/openmpi/bin/nvcc...not found Checking for program /home/pesun/anaconda3/bin/nvcc...not found Checking for program /home/pesun/anaconda3/condabin/nvcc...not found Checking for program /home/pesun/.local/bin/nvcc...not found Checking for program /usr/local/sbin/nvcc...not found Checking for program /usr/local/bin/nvcc...not found Checking for program /usr/sbin/nvcc...not found Checking for program /sbin/nvcc...not found Checking for program /usr/games/nvcc...not found Checking for program /usr/local/games/nvcc...not found Checking for program /snap/bin/nvcc...not found Checking for program /bin/nvcc...not found Checking for program /usr/bin/nvcc...not found Checking for program /usr/local/cuda-11.7/bin/nvcc...found Defined make macro "CUDAPP" to "nvcc -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include __global__ void testFunction() {return;}; Executing: nvcc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkCxxCompiler from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:835) TESTING: checkCxxCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:835) Locate a functional Cxx compiler Checking for program /home/pesun/opt/openmpi/bin/mpicxx...found Defined make macro "CXX" to "mpicxx" Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Testing executable /tmp/petsc-xk72m0wq/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: mpicxx --version stdout: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkCxxPreprocessor from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:877) TESTING: checkCxxPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:877) Locate a functional Cxx preprocessor Checking for program /home/pesun/opt/openmpi/bin/mpicxx...found Defined make macro "CXXPP" to "mpicxx -E" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicxx -E -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Preprocess stderr before filtering:: Preprocess stderr after filtering:: ================================================================================ TEST checkFortranCompiler from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:980) TESTING: checkFortranCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:980) Locate a functional Fortran compiler Checking for program /home/pesun/opt/openmpi/bin/mpif90...found Defined make macro "FC" to "mpif90" Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Testing executable /tmp/petsc-xk72m0wq/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: mpif90 --version stdout: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ================================================================================ TEST checkFortranPreprocessor from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1017) TESTING: checkFortranPreprocessor from config.setCompilers(config/BuildSystem/config/setCompilers.py:1017) Locate a functional Fortran preprocessor Checking for program /home/pesun/opt/openmpi/bin/mpif90...found Defined make macro "FPP" to "mpif90 -E" Deleting "FPP" Checking for program /home/pesun/opt/openmpi/bin/mpif90...found Defined make macro "FPP" to "mpif90 --use cpp32" Deleting "FPP" ================================================================================ TEST checkFortranComments from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1040) TESTING: checkFortranComments from config.setCompilers(config/BuildSystem/config/setCompilers.py:1040) Make sure fortran comment "!" works Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main ! comment end Fortran comments can use ! in column 1 ================================================================================ TEST checkLargeFileIO from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1171) TESTING: checkLargeFileIO from config.setCompilers(config/BuildSystem/config/setCompilers.py:1171) ================================================================================ TEST checkArchiver from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1270) TESTING: checkArchiver from config.setCompilers(config/BuildSystem/config/setCompilers.py:1270) Check that the archiver exists and can make a library usable by the compiler Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.34 Copyright (C) 2020 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.34 Copyright (C) 2020 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/pesun/opt/openmpi/bin/ar...not found Checking for program /home/pesun/anaconda3/bin/ar...not found Checking for program /home/pesun/anaconda3/condabin/ar...not found Checking for program /home/pesun/.local/bin/ar...not found Checking for program /usr/local/sbin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/sbin/ar...not found Checking for program /sbin/ar...not found Checking for program /usr/games/ar...not found Checking for program /usr/local/games/ar...not found Checking for program /snap/bin/ar...not found Checking for program /bin/ar...found Defined make macro "AR" to "/bin/ar" Checking for program /home/pesun/opt/openmpi/bin/ranlib...not found Checking for program /home/pesun/anaconda3/bin/ranlib...not found Checking for program /home/pesun/anaconda3/condabin/ranlib...not found Checking for program /home/pesun/.local/bin/ranlib...not found Checking for program /usr/local/sbin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/sbin/ranlib...not found Checking for program /sbin/ranlib...not found Checking for program /usr/games/ranlib...not found Checking for program /usr/local/games/ranlib...not found Checking for program /snap/bin/ranlib...not found Checking for program /bin/ranlib...found Defined make macro "RANLIB" to "/bin/ranlib -c" Executing: /bin/ar cr /tmp/petsc-xk72m0wq/config.setCompilers/libconf1.a /tmp/petsc-xk72m0wq/config.setCompilers/conf1.o Executing: /bin/ranlib -c /tmp/petsc-xk72m0wq/config.setCompilers/libconf1.a Possible ERROR while running ranlib: stderr: /bin/ranlib: invalid option -- 'c' Ranlib is not functional with your archiver. Try --with-ranlib=true if ranlib is unnecessary. Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.34 Copyright (C) 2020 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Executing: ar -V stdout: GNU ar (GNU Binutils for Ubuntu) 2.34 Copyright (C) 2020 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) any later version. This program has absolutely no warranty. Defined make macro "FAST_AR_FLAGS" to "Scq" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(int a) { return a+1; } Checking for program /home/pesun/opt/openmpi/bin/ar...not found Checking for program /home/pesun/anaconda3/bin/ar...not found Checking for program /home/pesun/anaconda3/condabin/ar...not found Checking for program /home/pesun/.local/bin/ar...not found Checking for program /usr/local/sbin/ar...not found Checking for program /usr/local/bin/ar...not found Checking for program /usr/sbin/ar...not found Checking for program /sbin/ar...not found Checking for program /usr/games/ar...not found Checking for program /usr/local/games/ar...not found Checking for program /snap/bin/ar...not found Checking for program /bin/ar...found Defined make macro "AR" to "/bin/ar" Checking for program /home/pesun/opt/openmpi/bin/ranlib...not found Checking for program /home/pesun/anaconda3/bin/ranlib...not found Checking for program /home/pesun/anaconda3/condabin/ranlib...not found Checking for program /home/pesun/.local/bin/ranlib...not found Checking for program /usr/local/sbin/ranlib...not found Checking for program /usr/local/bin/ranlib...not found Checking for program /usr/sbin/ranlib...not found Checking for program /sbin/ranlib...not found Checking for program /usr/games/ranlib...not found Checking for program /usr/local/games/ranlib...not found Checking for program /snap/bin/ranlib...not found Checking for program /bin/ranlib...found Defined make macro "RANLIB" to "/bin/ranlib" Executing: /bin/ar cr /tmp/petsc-xk72m0wq/config.setCompilers/libconf1.a /tmp/petsc-xk72m0wq/config.setCompilers/conf1.o Executing: /bin/ranlib /tmp/petsc-xk72m0wq/config.setCompilers/libconf1.a Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern int foo(int); int main() { int b = foo(1); if (b); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -L/tmp/petsc-xk72m0wq/config.setCompilers -lconf1 Defined make macro "AR_FLAGS" to "cr" Defined make macro "AR_LIB_SUFFIX" to "a" ================================================================================ TEST checkSharedLinker from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1384) TESTING: checkSharedLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1384) Check that the linker can produce shared libraries Executing: uname -s stdout: Linux Checking shared linker mpicc using flags ['-shared'] Checking for program /home/pesun/opt/openmpi/bin/mpicc...found Defined make macro "LD_SHARED" to "mpicc" Trying C compiler flag Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -shared /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected C compiler flag because it was not compatible with shared linker mpicc using flags ['-shared'] Executing: mpicc --help | head -n 20 stdout: Usage: gcc [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying C compiler flag -fPIC Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fPIC Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int foo(void); int main() { int ret = foo(); if (ret) {} ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -L/tmp/petsc-xk72m0wq/config.setCompilers -lconftest Using shared linker mpicc with flags ['-shared'] and library extension so Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux ================================================================================ TEST checkPIC from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1118) TESTING: checkPIC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1118) Determine the PIC option for each compiler Trying Cxx for PIC code without any compiler flag Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected Cxx compiler flag because shared linker cannot handle it Executing: mpicxx --help | head -n 20 stdout: Usage: g++ [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying Cxx compiler flag -fPIC for PIC code Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fPIC Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Accepted Cxx compiler flag -fPIC for PIC code Trying FC for PIC code without any compiler flag Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `xx_' can not be used when making a shared object; recompile with -fPIC /bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected FC compiler flag because shared linker cannot handle it Executing: mpif90 --help | head -n 20 stdout: Usage: gfortran [options] file... Options: -pass-exit-codes Exit with highest error code from a phase. --help Display this information. --target-help Display target specific command line options. --help={common|optimizers|params|target|warnings|[^]{joined|separate|undocumented}}[,...]. Display specific types of command line options. (Use '-v --help' to display command line options of sub-processes). --version Display compiler version information. -dumpspecs Display all of the built in spec strings. -dumpversion Display the version of the compiler. -dumpmachine Display the compiler's target processor. -print-search-dirs Display the directories in the compiler's search path. -print-libgcc-file-name Display the name of the compiler's companion library. -print-file-name= Display the full path to library . -print-prog-name= Display the full path to compiler component . -print-multiarch Display the target's normalized GNU triplet, used as a component in the library path. -print-multi-directory Display the root directory for versions of libgcc. -print-multi-lib Display the mapping between command line options and Trying FC compiler flag -fPIC for PIC code Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -fPIC Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: function foo(a) real:: a,x,bar common /xx/ x x=a foo = bar(x) end Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Accepted FC compiler flag -fPIC for PIC code Trying CUDA for PIC code without any compiler flag Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o: relocation R_X86_64_PC32 against symbol `fprintf_ptr' can not be used when making a shared object; recompile with -fPIC /bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status Rejected CUDA compiler flag because shared linker cannot handle it Trying CUDA compiler flag -Xcompiler -fPIC for PIC code Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added CUDA compiler flag -Xcompiler -fPIC Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int (*fprintf_ptr)(FILE*,const char*,...) = fprintf; void foo(void){ fprintf_ptr(stdout,"hello"); return; } void bar(void){foo();} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Accepted CUDA compiler flag -Xcompiler -fPIC for PIC code ================================================================================ TEST checkSharedLinkerPaths from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1496) TESTING: checkSharedLinkerPaths from config.setCompilers(config/BuildSystem/config/setCompilers.py:1496) Determine the shared linker path options - IRIX: -rpath - Linux, OSF: -Wl,-rpath, - Solaris: -R - FreeBSD: -Wl,-R, Executing: uname -s stdout: Linux Executing: mpicc -V Trying C linker flag -Wl,-rpath, Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid C linker flag -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 Executing: uname -s stdout: Linux Executing: mpicc -V Trying Cxx linker flag -Wl,-rpath, Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid Cxx linker flag -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 Executing: uname -s stdout: Linux Executing: mpicc -V Trying FC linker flag -Wl,-rpath, Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid FC linker flag -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 Executing: uname -s stdout: Linux Executing: mpicc -V Trying CUDA linker flag -Wl,-rpath, Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: nvcc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Xcompiler -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Valid CUDA linker flag -Wl,-rpath,/home/pesun/.emopt/build/petsc-3.12.1 ================================================================================ TEST checkLibC from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1531) TESTING: checkLibC from config.setCompilers(config/BuildSystem/config/setCompilers.py:1531) Test whether we need to explicitly include libc in shared linking - Mac OSX requires an explicit reference to libc for shared linking Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {void *chunk = malloc(31); free(chunk); return 0;} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o Shared linking does not require an explicit libc reference ================================================================================ TEST checkDynamicLinker from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1577) TESTING: checkDynamicLinker from config.setCompilers(config/BuildSystem/config/setCompilers.py:1577) Check that the linker can dynamicaly load shared libraries Checking for header: dlfcn.h All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.headers Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" Checking for functions [dlopen dlsym dlclose] in library ['dl'] [] All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.libraries Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -fPIC /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } char dlsym(); static void _check_dlsym() { dlsym(); } char dlclose(); static void _check_dlclose() { dlclose(); } int main() { _check_dlopen(); _check_dlsym(); _check_dlclose();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC /tmp/petsc-xk72m0wq/config.libraries/conftest.o -ldl Defined "HAVE_LIBDL" to "1" Adding ['dl'] to LIBS Executing: uname -s stdout: Linux Checking dynamic linker mpicc using flags ['-shared'] Checking for program /home/pesun/opt/openmpi/bin/mpicc...found Defined make macro "DYNAMICLINKER" to "mpicc" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -ldl Valid C linker flag -shared Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int foo(void) {printf("test");return 0;} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { void *handle = dlopen("/tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so", 0); int (*foo)(void) = (int (*)(void)) dlsym(handle, "foo"); if (!foo) { printf("Could not load symbol\n"); return -1; } if ((*foo)()) { printf("Invalid return from foo()\n"); return -1; } if (dlclose(handle)) { printf("Could not close library\n"); return -1; } ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -ldl Using dynamic linker mpicc with flags ['-shared'] and library extension so ================================================================================ TEST output from config.setCompilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/setCompilers.py:1626) TESTING: output from config.setCompilers(config/BuildSystem/config/setCompilers.py:1626) Output module data as defines and substitutions Substituting "CC" with "mpicc" Substituting "CFLAGS" with " -fPIC" Defined make macro "CC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "CPP" with "mpicc -E" Substituting "CPPFLAGS" with "" Substituting "CUDAC" with "nvcc" Substituting "CUDAFLAGS" with " -Xcompiler -fPIC" Substituting "CUDAPP" with "nvcc -E" Substituting "CUDAPPFLAGS" with "-Wno-deprecated-gpu-targets" Substituting "CXX" with "mpicxx" Substituting "CXX_CXXFLAGS" with " -fPIC" Substituting "CXXFLAGS" with "" Substituting "CXX_LINKER_SLFLAG" with "-Wl,-rpath," Substituting "CXXPP" with "mpicxx -E" Substituting "CXXPPFLAGS" with "" Substituting "FC" with "mpif90" Substituting "FFLAGS" with " -fPIC" Defined make macro "FC_LINKER_SLFLAG" to "-Wl,-rpath," Substituting "LDFLAGS" with "" Substituting "LIBS" with "-ldl " Substituting "SHARED_LIBRARY_FLAG" with "-shared" child config.setCompilers 3.843509 ================================================================================ TEST checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/sharedLibraries.py:36) TESTING: checkSharedDynamicPicOptions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:36) ================================================================================ TEST configureSharedLibraries from PETSc.options.sharedLibraries(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/sharedLibraries.py:52) TESTING: configureSharedLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:52) Checks whether shared libraries should be used, for which you must - Specify --with-shared-libraries - Have found a working shared linker Defines PETSC_USE_SHARED_LIBRARIES if they are used Executing: uname -s stdout: Linux Defined make rule "shared_arch" with dependencies "shared_linux" and code [] Defined make macro "SONAME_FUNCTION" to "$(1).so.$(2)" Defined make macro "SL_LINKER_FUNCTION" to "-shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2))" Defined make macro "BUILDSHAREDLIB" to "yes" Defined "USE_SHARED_LIBRARIES" to "1" ================================================================================ TEST configureDynamicLibraries from PETSc.options.sharedLibraries(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/sharedLibraries.py:94) TESTING: configureDynamicLibraries from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:94) Checks whether dynamic loading is available (with dlfcn.h and libdl) Defined "HAVE_DYNAMIC_LIBRARIES" to "1" ================================================================================ TEST configureSerializedFunctions from PETSc.options.sharedLibraries(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/sharedLibraries.py:100) TESTING: configureSerializedFunctions from PETSc.options.sharedLibraries(config/PETSc/options/sharedLibraries.py:100) Defines PETSC_SERIALIZE_FUNCTIONS if they are used Requires shared libraries child PETSc.options.sharedLibraries 0.003547 ================================================================================ TEST configureIndexSize from PETSc.options.indexTypes(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/indexTypes.py:30) TESTING: configureIndexSize from PETSc.options.indexTypes(config/PETSc/options/indexTypes.py:30) Defined make macro "PETSC_INDEX_SIZE" to "32" child PETSc.options.indexTypes 0.000308 ================================================================================ TEST configureCompilerFlags from config.compilerFlags(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilerFlags.py:72) TESTING: configureCompilerFlags from config.compilerFlags(config/BuildSystem/config/compilerFlags.py:72) Get the default compiler flags Defined make macro "C_VERSION" to "gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0" Defined make macro "MPICC_SHOW" to "gcc -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi" Trying C compiler flag -Wall Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wall Trying C compiler flag -Wwrite-strings Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wwrite-strings Trying C compiler flag -Wno-strict-aliasing Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-strict-aliasing Trying C compiler flag -Wno-unknown-pragmas Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -Wno-unknown-pragmas Trying C compiler flag -fstack-protector Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fstack-protector Trying C compiler flag -mfp16-format=ieee Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -mfp16-format=ieee /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option ���-mfp16-format=ieee��� Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gcc: error: unrecognized command line option ���-mfp16-format=ieee��� PETSc Error: No output file produced Rejected C compiler flag -mfp16-format=ieee Trying C compiler flag -fvisibility=hidden Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -fvisibility=hidden Trying C compiler flag -O3 Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added C compiler flag -O3 Defined make macro "Cxx_VERSION" to "g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0" Defined make macro "MPICXX_SHOW" to "g++ -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi" Trying Cxx compiler flag -Wall Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wall Trying Cxx compiler flag -Wwrite-strings Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wwrite-strings Trying Cxx compiler flag -Wno-strict-aliasing Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-strict-aliasing Trying Cxx compiler flag -Wno-unknown-pragmas Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -Wno-unknown-pragmas Trying Cxx compiler flag -fstack-protector Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fstack-protector Trying Cxx compiler flag -fvisibility=hidden Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -fvisibility=hidden Trying Cxx compiler flag -O3 Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added Cxx compiler flag -O3 Defined make macro "FC_VERSION" to "GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0" Defined make macro "MPIFC_SHOW" to "gfortran -I/home/pesun/opt/openmpi/include -pthread -I/home/pesun/opt/openmpi/lib -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi" Trying FC compiler flag -Wall Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wall Trying FC compiler flag -ffree-line-length-0 Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -ffree-line-length-0 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -ffree-line-length-0 Trying FC compiler flag -Wno-unused-dummy-argument Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -Wno-unused-dummy-argument Trying FC compiler flag -O3 Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Added FC compiler flag -O3 Defined make macro "CUDA_VERSION" to "nvcc: NVIDIA (R) Cuda compiler driver" Defined make macro "MPICC_SHOW" to "Unavailable" Defined make macro "MPICC_SHOW" to "Unavailable" Trying CUDA compiler flag -O Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -O -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Possible ERROR while running compiler: exit code 1 stderr: nvcc fatal : '-Wno-deprecated-gpu-targets': expected a number Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -O due to nonzero status from link Rejecting compiler flag -O due to nvcc fatal : '-Wno-deprecated-gpu-targets': expected a number PETSc Error: No output file produced Rejected CUDA compiler flag -O child config.compilerFlags 0.723888 ================================================================================ TEST checkRestrict from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.compilers Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.compilers/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.compilers/conftest.c:5:20: warning: unused variable ���x��� [-Wunused-variable] 5 | float * __restrict x;; | ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set C restrict keyword to __restrict Defined "C_RESTRICT" to "__restrict" ================================================================================ TEST checkCFormatting from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:391) TESTING: checkCFormatting from config.compilers(config/BuildSystem/config/compilers.py:391) Activate format string checking if using the GNU compilers ================================================================================ TEST checkCInline from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:108) TESTING: checkCInline from config.compilers(config/BuildSystem/config/compilers.py:108) Check for C inline keyword Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set C Inline keyword to inline Defined "C_INLINE" to "inline" ================================================================================ TEST checkDynamicLoadFlag from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:402) TESTING: checkDynamicLoadFlag from config.compilers(config/BuildSystem/config/compilers.py:402) Checks that dlopen() takes RTLD_XXX, and defines PETSC_HAVE_RTLD_XXX if it does Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include char *libname; int main() { dlopen(libname, RTLD_LAZY);dlopen(libname, RTLD_NOW);dlopen(libname, RTLD_LOCAL);dlopen(libname, RTLD_GLOBAL); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o -ldl Defined "HAVE_RTLD_LAZY" to "1" Defined "HAVE_RTLD_NOW" to "1" Defined "HAVE_RTLD_LOCAL" to "1" Defined "HAVE_RTLD_GLOBAL" to "1" ================================================================================ TEST checkCLibraries from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:202) TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py:202) Determines the libraries needed to link with C compiled code Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -ldl C libraries are not needed when using Fortran linker Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include void asub(void) {char s[16];printf("testing %s",s);} Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.compilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -ldl C libraries are not needed when using C++ linker ================================================================================ TEST checkDependencyGenerationFlag from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:1343) TESTING: checkDependencyGenerationFlag from config.compilers(config/BuildSystem/config/compilers.py:1343) Check if -MMD works for dependency generation, and add it if it does Trying C compiler flag -MMD -MP Defined make macro "C_DEPFLAGS" to "-MMD -MP" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -MMD -MP /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying Cxx compiler flag -MMD -MP Defined make macro "CXX_DEPFLAGS" to "-MMD -MP" Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC -MMD -MP /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Trying CUDA compiler flag -MMD -MP Defined make macro "CUDA_DEPFLAGS" to "-MMD -MP" Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -MMD -MP -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } ================================================================================ TEST checkC99Flag from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:1388) TESTING: checkC99Flag from config.compilers(config/BuildSystem/config/compilers.py:1388) Check for -std=c99 or equivalent flag Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c:7:11: warning: variable ���x��� set but not used [-Wunused-but-set-variable] 7 | float x[2],y; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { float x[2],y; y = FLT_ROUNDS; // c++ comment int j = 2; for (int i=0; i<2; i++){ x[i] = i*j*y; } ; return 0; } Accepted C99 compile flag: Defined "HAVE_C99" to "1" ================================================================================ TEST checkRestrict from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:138) TESTING: checkRestrict from config.compilers(config/BuildSystem/config/compilers.py:138) Check for the C/CXX restrict keyword Executing: mpicc -V Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.compilers/conftest.cc: In function ���int main()���: /tmp/petsc-xk72m0wq/config.compilers/conftest.cc:5:20: warning: unused variable ���x��� [-Wunused-variable] 5 | float * __restrict x;; | ^ Source: #include "confdefs.h" #include "conffix.h" int main() { float * __restrict x;; return 0; } compilers: Set Cxx restrict keyword to __restrict Defined "CXX_RESTRICT" to "__restrict" ================================================================================ TEST checkCxxOptionalExtensions from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:421) TESTING: checkCxxOptionalExtensions from config.compilers(config/BuildSystem/config/compilers.py:421) Check whether the C++ compiler (IBM xlC, OSF5) need special flag for .c files which contain C++ Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { class somename { int i; };; return 0; } ================================================================================ TEST checkCxxInline from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:123) TESTING: checkCxxInline from config.compilers(config/BuildSystem/config/compilers.py:123) Check for C++ inline keyword Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" static inline int foo(int a) {return a;} int main() { foo(1);; return 0; } compilers: Set Cxx Inline keyword to inline Defined "CXX_INLINE" to "inline" ================================================================================ TEST checkCxxLibraries from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:531) TESTING: checkCxxLibraries from config.compilers(config/BuildSystem/config/compilers.py:531) Determines the libraries needed to link with C++ from C and Fortran Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/confc.o: in function `asub()': conftest.cc:(.text.unlikely+0xb): undefined reference to `__cxa_allocate_exception' /bin/ld: conftest.cc:(.text.unlikely+0x12): undefined reference to `typeinfo for int' /bin/ld: conftest.cc:(.text.unlikely+0x22): undefined reference to `__cxa_throw' /bin/ld: conftest.cc:(.text.unlikely+0x33): undefined reference to `__cxa_begin_catch' /bin/ld: conftest.cc:(.text.unlikely+0x3a): undefined reference to `std::cout' /bin/ld: conftest.cc:(.text.unlikely+0x46): undefined reference to `std::basic_ostream >& std::operator<< >(std::basic_ostream >&, char const*)' /bin/ld: conftest.cc:(.text.unlikely+0x58): undefined reference to `__cxa_end_catch' /bin/ld: conftest.cc:(.text.unlikely+0x4c): undefined reference to `__cxa_end_catch' /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/confc.o: in function `_GLOBAL__sub_I_conftest.cc': conftest.cc:(.text.startup+0x10): undefined reference to `std::ios_base::Init::Init()' /bin/ld: conftest.cc:(.text.startup+0x17): undefined reference to `std::ios_base::Init::~Init()' /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/confc.o:(.data.rel.local.DW.ref._ZTIi[DW.ref._ZTIi]+0x0): undefined reference to `typeinfo for int' /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/confc.o:(.data.rel.local.DW.ref.__gxx_personality_v0[DW.ref.__gxx_personality_v0]+0x0): undefined reference to `__gxx_personality_v0' collect2: error: ld returned 1 exit status Executing: uname -s stdout: Linux Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl compilers: C++ requires -lstdc++ to link with C compiler Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void asub(void) {std::vector v; try { throw 20; } catch (int e) { std::cout << "An exception occurred"; }} Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main print*,'testing' stop end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl C++ libraries are not needed when using FC linker ================================================================================ TEST checkCxxDialect from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:449) TESTING: checkCxxDialect from config.compilers(config/BuildSystem/config/compilers.py:449) Determine the Cxx dialect supported by the compiler [and correspoding compiler option - if any]. -with-cxx-dialect can take options: auto: use highest dialect configure can determine cxx17: [future?] cxx14: gnu++14 or c++14 cxx11: gnu++11 or c++11 0: disable CxxDialect check and use compiler default checkCxxDialect: checking CXX14 with flag: Defined "HAVE_CXX_DIALECT_CXX14" to "1" Defined "HAVE_CXX_DIALECT_CXX11" to "1" Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include template constexpr T Cubed( T x ) { return x*x*x; } int main() { std::random_device rd; std::mt19937 mt(rd()); std::normal_distribution dist(0,1); const double x = dist(mt); std::cout << x; auto lambda = [](auto x, auto y) {return x + y;}; return lambda(3,4); ; return 0; } Executing: mpicxx -V ================================================================================ TEST checkFortranNameMangling from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:836) TESTING: checkFortranNameMangling from config.compilers(config/BuildSystem/config/compilers.py:836) Checks Fortran name mangling, and defines HAVE_FORTRAN_UNDERSCORE, HAVE_FORTRAN_NOUNDERSCORE, HAVE_FORTRAN_CAPS, or HAVE_FORTRAN_STDCALL Testing Fortran mangling type underscore with code void d1chk_(void){return;} Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1chk_(void){return;} Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran name mangling is underscore Defined "HAVE_FORTRAN_UNDERSCORE" to "1" Executing: mpif90 --version stdout: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Defined "FORTRAN_CHARLEN_T" to "size_t" ================================================================================ TEST checkFortranNameManglingDouble from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:877) TESTING: checkFortranNameManglingDouble from config.compilers(config/BuildSystem/config/compilers.py:877) Checks if symbols containing an underscore append an extra underscore, and defines HAVE_FORTRAN_UNDERSCORE_UNDERSCORE if necessary Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void d1_chk__(void){return;} Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main call d1_chk() end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/conftest.o: in function `main': conftest.F90:(.text.startup+0x1d): undefined reference to `d1_chk_' collect2: error: ld returned 1 exit status ================================================================================ TEST checkFortranLibraries from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:887) TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:887) Substitutes for FLIBS the libraries needed to link with Fortran This macro is intended to be used in those situations when it is necessary to mix, e.g. C++ and Fortran 77, source code into a single program or shared library. For example, if object files from a C++ and Fortran 77 compiler must be linked together, then the C++ compiler/linker must be used for linking (since special C++-ish things need to happen at link time like calling global constructors, instantiating templates, enabling exception support, etc.). However, the Fortran 77 intrinsic and run-time libraries must be linked in as well, but the C++ compiler/linker does not know how to add these Fortran 77 libraries. This code was translated from the autoconf macro which was packaged in its current form by Matthew D. Langston . However, nearly all of this macro came from the OCTAVE_FLIBS macro in octave-2.0.13/aclocal.m4, and full credit should go to John W. Eaton for writing this extremely useful macro. Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main #include call MPI_Allreduce() end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o -lstdc++ -ldl Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: subroutine asub() print*,'testing' call MPI_Allreduce() return end Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main(int argc,char **args) {return 0;} Executing: mpicc -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.compilers/confc.o: in function `asub_': conftest.F90:(.text+0x31): undefined reference to `_gfortran_st_write' /bin/ld: conftest.F90:(.text+0x45): undefined reference to `_gfortran_transfer_character_write' /bin/ld: conftest.F90:(.text+0x4d): undefined reference to `_gfortran_st_write_done' /bin/ld: conftest.F90:(.text+0x5c): undefined reference to `mpi_allreduce_' collect2: error: ld returned 1 exit status Fortran code cannot directly be linked with C linker, therefore will determine needed Fortran libraries Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: Driving: /bin/gfortran -o /tmp/petsc-xk72m0wq/config.compilers/conftest -v -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o -lstdc++ -ldl -I/home/pesun/opt/openmpi/include -pthread -I/home/pesun/opt/openmpi/lib -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -l gfortran -l m -shared-libgcc Using built-in specs. COLLECT_GCC=/bin/gfortran COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.1' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.1) Reading specs from /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.spec rename spec lib to liborig COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-xk72m0wq/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O3' '-I' '/home/pesun/opt/openmpi/include' '-pthread' '-I' '/home/pesun/opt/openmpi/lib' '-L/home/pesun/opt/openmpi/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-xk72m0wq/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O3' '-I' '/home/pesun/opt/openmpi/include' '-pthread' '-I' '/home/pesun/opt/openmpi/lib' '-L/home/pesun/opt/openmpi/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' /usr/lib/gcc/x86_64-linux-gnu/9/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/9/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper -plugin-opt=-fresolution=/tmp/cc9JxTpd.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lquadmath -plugin-opt=-pass-through=-lm -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lpthread -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o /tmp/petsc-xk72m0wq/config.compilers/conftest /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o -L/home/pesun/opt/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. /tmp/petsc-xk72m0wq/config.compilers/conftest.o -lstdc++ -ldl -rpath /home/pesun/opt/openmpi/lib --enable-new-dtags -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lpthread -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-o' '/tmp/petsc-xk72m0wq/config.compilers/conftest' '-v' '-fPIC' '-Wall' '-ffree-line-length-0' '-Wno-unused-dummy-argument' '-O3' '-I' '/home/pesun/opt/openmpi/include' '-pthread' '-I' '/home/pesun/opt/openmpi/lib' '-L/home/pesun/opt/openmpi/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' compilers: Checking arg Driving: compilers: Unknown arg Driving: compilers: Checking arg /bin/gfortran compilers: Unknown arg /bin/gfortran compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-xk72m0wq/config.compilers/conftest compilers: Unknown arg /tmp/petsc-xk72m0wq/config.compilers/conftest compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg -fPIC compilers: Unknown arg -fPIC compilers: Checking arg -Wall compilers: Unknown arg -Wall compilers: Checking arg -ffree-line-length-0 compilers: Unknown arg -ffree-line-length-0 compilers: Checking arg -Wno-unused-dummy-argument compilers: Unknown arg -Wno-unused-dummy-argument compilers: Checking arg -O3 compilers: Unknown arg -O3 compilers: Checking arg /tmp/petsc-xk72m0wq/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-xk72m0wq/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Found library: -lstdc++ compilers: Checking arg -ldl compilers: Found library: -ldl compilers: Checking arg -I/home/pesun/opt/openmpi/include compilers: Found include directory: /home/pesun/opt/openmpi/include compilers: Checking arg -pthread compilers: Unknown arg -pthread compilers: Checking arg -I/home/pesun/opt/openmpi/lib compilers: Found include directory: /home/pesun/opt/openmpi/lib compilers: Checking arg -Wl,-rpath compilers: Unknown arg -Wl,-rpath compilers: Checking arg -Wl,/home/pesun/opt/openmpi/lib compilers: Unknown arg -Wl,/home/pesun/opt/openmpi/lib compilers: Checking arg -Wl,--enable-new-dtags compilers: Unknown arg -Wl,--enable-new-dtags compilers: Checking arg -L/home/pesun/opt/openmpi/lib compilers: Found library directory: -L/home/pesun/opt/openmpi/lib compilers: Checking arg -lmpi_usempif08 compilers: Found library: -lmpi_usempif08 compilers: Checking arg -lmpi_usempi_ignore_tkr compilers: Found library: -lmpi_usempi_ignore_tkr compilers: Checking arg -lmpi_mpifh compilers: Found library: -lmpi_mpifh compilers: Checking arg -lmpi compilers: Found library: -lmpi compilers: Checking arg -l compilers: Found canonical library: -lgfortran compilers: Checking arg -l compilers: Found canonical library: -lm compilers: Checking arg -shared-libgcc compilers: Unknown arg -shared-libgcc compilers: Checking arg Using compilers: Unknown arg Using compilers: Checking arg built-in compilers: Unknown arg built-in compilers: Checking arg specs. compilers: Unknown arg specs. compilers: Checking arg COLLECT_GCC=/bin/gfortran compilers: Unknown arg COLLECT_GCC=/bin/gfortran compilers: Checking arg COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper compilers: Unknown arg COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper compilers: Checking arg OFFLOAD_TARGET_NAMES=nvptx-none:hsa compilers: Unknown arg OFFLOAD_TARGET_NAMES=nvptx-none:hsa compilers: Checking arg OFFLOAD_TARGET_DEFAULT=1 compilers: Unknown arg OFFLOAD_TARGET_DEFAULT=1 compilers: Checking arg Target: compilers: Unknown arg Target: compilers: Checking arg x86_64-linux-gnu compilers: Unknown arg x86_64-linux-gnu compilers: Checking arg Configured compilers: Unknown arg Configured compilers: Checking arg with: compilers: Unknown arg with: compilers: Checking arg ../src/configure compilers: Unknown arg ../src/configure compilers: Checking arg -v compilers: Unknown arg -v compilers: Checking arg --with-pkgversion= compilers: Unknown arg --with-pkgversion= compilers: Checking arg --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs compilers: Unknown arg --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs compilers: Checking arg --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 compilers: Unknown arg --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 compilers: Checking arg --prefix=/usr compilers: Unknown arg --prefix=/usr compilers: Checking arg --with-gcc-major-version-only compilers: Unknown arg --with-gcc-major-version-only compilers: Checking arg --program-suffix=-9 compilers: Unknown arg --program-suffix=-9 compilers: Checking arg --program-prefix=x86_64-linux-gnu- compilers: Unknown arg --program-prefix=x86_64-linux-gnu- compilers: Checking arg --enable-shared compilers: Unknown arg --enable-shared compilers: Checking arg --enable-linker-build-id compilers: Unknown arg --enable-linker-build-id compilers: Checking arg --libexecdir=/usr/lib compilers: Unknown arg --libexecdir=/usr/lib compilers: Checking arg --without-included-gettext compilers: Unknown arg --without-included-gettext compilers: Checking arg --enable-threads=posix compilers: Unknown arg --enable-threads=posix compilers: Checking arg --libdir=/usr/lib compilers: Unknown arg --libdir=/usr/lib compilers: Checking arg --enable-nls compilers: Unknown arg --enable-nls compilers: Checking arg --enable-clocale=gnu compilers: Unknown arg --enable-clocale=gnu compilers: Checking arg --enable-libstdcxx-debug compilers: Unknown arg --enable-libstdcxx-debug compilers: Checking arg --enable-libstdcxx-time=yes compilers: Unknown arg --enable-libstdcxx-time=yes compilers: Checking arg --with-default-libstdcxx-abi=new compilers: Unknown arg --with-default-libstdcxx-abi=new compilers: Checking arg --enable-gnu-unique-object compilers: Unknown arg --enable-gnu-unique-object compilers: Checking arg --disable-vtable-verify compilers: Unknown arg --disable-vtable-verify compilers: Checking arg --enable-plugin compilers: Unknown arg --enable-plugin compilers: Checking arg --enable-default-pie compilers: Unknown arg --enable-default-pie compilers: Checking arg --with-system-zlib compilers: Unknown arg --with-system-zlib compilers: Checking arg --with-target-system-zlib=auto compilers: Unknown arg --with-target-system-zlib=auto compilers: Checking arg --enable-objc-gc=auto compilers: Unknown arg --enable-objc-gc=auto compilers: Checking arg --enable-multiarch compilers: Unknown arg --enable-multiarch compilers: Checking arg --disable-werror compilers: Unknown arg --disable-werror compilers: Checking arg --with-arch-32=i686 compilers: Unknown arg --with-arch-32=i686 compilers: Checking arg --with-abi=m64 compilers: Unknown arg --with-abi=m64 compilers: Checking arg --with-multilib-list=m32,m64,mx32 compilers: Unknown arg --with-multilib-list=m32,m64,mx32 compilers: Checking arg --enable-multilib compilers: Unknown arg --enable-multilib compilers: Checking arg --with-tune=generic compilers: Unknown arg --with-tune=generic compilers: Checking arg --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa compilers: Unknown arg --enable-offload-targets=nvptx-none=/build/gcc-9-Av3uEd/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa compilers: Checking arg --without-cuda-driver compilers: Unknown arg --without-cuda-driver compilers: Checking arg --enable-checking=release compilers: Unknown arg --enable-checking=release compilers: Checking arg --build=x86_64-linux-gnu compilers: Unknown arg --build=x86_64-linux-gnu compilers: Checking arg --host=x86_64-linux-gnu compilers: Unknown arg --host=x86_64-linux-gnu compilers: Checking arg --target=x86_64-linux-gnu compilers: Unknown arg --target=x86_64-linux-gnu compilers: Checking arg Thread compilers: Unknown arg Thread compilers: Checking arg model: compilers: Unknown arg model: compilers: Checking arg posix compilers: Unknown arg posix compilers: Checking arg gcc compilers: Unknown arg gcc compilers: Checking arg version compilers: Unknown arg version compilers: Checking arg 9.4.0 compilers: Unknown arg 9.4.0 compilers: Checking arg (Ubuntu compilers: Unknown arg (Ubuntu compilers: Checking arg 9.4.0-1ubuntu1~20.04.1) compilers: Unknown arg 9.4.0-1ubuntu1~20.04.1) compilers: Checking arg Reading compilers: Unknown arg Reading compilers: Checking arg specs compilers: Unknown arg specs compilers: Checking arg from compilers: Unknown arg from compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.spec compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.spec compilers: Checking arg rename compilers: Unknown arg rename compilers: Checking arg spec compilers: Unknown arg spec compilers: Checking arg lib compilers: Unknown arg lib compilers: Checking arg to compilers: Unknown arg to compilers: Checking arg liborig compilers: Unknown arg liborig compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/ compilers: Skipping arg COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/ compilers: Checking arg LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../:/lib/:/usr/lib/ compilers: Skipping arg LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../:/lib/:/usr/lib/ compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/collect2 compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/collect2 compilers: Checking arg -plugin compilers: Unknown arg -plugin compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/liblto_plugin.so compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/liblto_plugin.so compilers: Checking arg -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper compilers: Unknown arg -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper compilers: Checking arg -plugin-opt=-fresolution=/tmp/cc9JxTpd.res compilers: Unknown arg -plugin-opt=-fresolution=/tmp/cc9JxTpd.res compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lquadmath compilers: Unknown arg -plugin-opt=-pass-through=-lquadmath compilers: Checking arg -plugin-opt=-pass-through=-lm compilers: Unknown arg -plugin-opt=-pass-through=-lm compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg -plugin-opt=-pass-through=-lpthread compilers: Unknown arg -plugin-opt=-pass-through=-lpthread compilers: Checking arg -plugin-opt=-pass-through=-lc compilers: Unknown arg -plugin-opt=-pass-through=-lc compilers: Checking arg -plugin-opt=-pass-through=-lgcc_s compilers: Unknown arg -plugin-opt=-pass-through=-lgcc_s compilers: Checking arg -plugin-opt=-pass-through=-lgcc compilers: Unknown arg -plugin-opt=-pass-through=-lgcc compilers: Checking arg --build-id compilers: Unknown arg --build-id compilers: Checking arg --eh-frame-hdr compilers: Unknown arg --eh-frame-hdr compilers: Checking arg -m compilers: Unknown arg -m compilers: Checking arg elf_x86_64 compilers: Unknown arg elf_x86_64 compilers: Checking arg --hash-style=gnu compilers: Unknown arg --hash-style=gnu compilers: Checking arg --as-needed compilers: Unknown arg --as-needed compilers: Checking arg -dynamic-linker compilers: Unknown arg -dynamic-linker compilers: Checking arg /lib64/ld-linux-x86-64.so.2 compilers: Unknown arg /lib64/ld-linux-x86-64.so.2 compilers: Checking arg -pie compilers: Unknown arg -pie compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg now compilers: Unknown arg now compilers: Checking arg -z compilers: Unknown arg -z compilers: Checking arg relro compilers: Unknown arg relro compilers: Checking arg -o compilers: Unknown arg -o compilers: Checking arg /tmp/petsc-xk72m0wq/config.compilers/conftest compilers: Unknown arg /tmp/petsc-xk72m0wq/config.compilers/conftest compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o compilers: Checking arg -L/home/pesun/opt/openmpi/lib compilers: Already in lflags so skipping: -L/home/pesun/opt/openmpi/lib compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/9 compilers: Found library directory: -L/usr/lib/gcc/x86_64-linux-gnu/9 compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu compilers: Found library directory: -L/usr/lib/x86_64-linux-gnu compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib compilers: Checking arg -L/lib/x86_64-linux-gnu compilers: Found library directory: -L/lib/x86_64-linux-gnu compilers: Checking arg -L/lib/../lib compilers: Checking arg -L/usr/lib/x86_64-linux-gnu compilers: Already in lflags so skipping: -L/usr/lib/x86_64-linux-gnu compilers: Checking arg -L/usr/lib/../lib compilers: Checking arg -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. compilers: Checking arg /tmp/petsc-xk72m0wq/config.compilers/conftest.o compilers: Unknown arg /tmp/petsc-xk72m0wq/config.compilers/conftest.o compilers: Checking arg -lstdc++ compilers: Already in lflags: -lstdc++ compilers: Checking arg -ldl compilers: Already in lflags: -ldl compilers: Checking arg -rpath compilers: Found -rpath library: /home/pesun/opt/openmpi/lib compilers: Checking arg --enable-new-dtags compilers: Unknown arg --enable-new-dtags compilers: Checking arg -lmpi_usempif08 compilers: Already in lflags: -lmpi_usempif08 compilers: Checking arg -lmpi_usempi_ignore_tkr compilers: Already in lflags: -lmpi_usempi_ignore_tkr compilers: Checking arg -lmpi_mpifh compilers: Already in lflags: -lmpi_mpifh compilers: Checking arg -lmpi compilers: Already in lflags: -lmpi compilers: Checking arg -lgfortran compilers: Found library: -lgfortran compilers: Checking arg -lm compilers: Found library: -lm compilers: Checking arg -lgcc_s compilers: Found library: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lquadmath compilers: Found library: -lquadmath compilers: Checking arg -lm compilers: Already in lflags: -lm compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg -lpthread compilers: Found library: -lpthread compilers: Checking arg -lc compilers: Found system library therefore skipping: -lc compilers: Checking arg -lgcc_s compilers: Already in lflags: -lgcc_s compilers: Checking arg -lgcc compilers: Found system library therefore skipping: -lgcc compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o compilers: Checking arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o compilers: Unknown arg /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o compilers: Checking arg COLLECT_GCC_OPTIONS= compilers: Unknown arg COLLECT_GCC_OPTIONS= compilers: Libraries needed to link Fortran code with the C linker: ['-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] compilers: Libraries needed to link Fortran main with the C linker: [] compilers: Check that Fortran libraries can be used with C as the linker Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest compilers: Check that Fortran libraries can be used with C++ as linker compilers: Fortran libraries can be used from C++ Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl -lpetsc-ufod4vtr9mqHvKIQiVAm Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lpetsc-ufod4vtr9mqHvKIQiVAm collect2: error: ld returned 1 exit status Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.setCompilers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest Executing: /tmp/petsc-xk72m0wq/config.setCompilers/conftest ================================================================================ TEST checkFortranLinkingCxx from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:1308) TESTING: checkFortranLinkingCxx from config.compilers(config/BuildSystem/config/compilers.py:1308) Check that Fortran can link C++ libraries Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void foo(void){d1chk_();} Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.compilers/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" extern "C" void d1chk_(void); void d1chk_(void){return;} Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.F90 Successful compile: Source: program main call d1chk() end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilers/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilers/conftest.o /tmp/petsc-xk72m0wq/config.compilers/cxxobj.o /tmp/petsc-xk72m0wq/config.compilers/confc.o -lstdc++ -ldl compilers: Fortran can link C++ functions ================================================================================ TEST setupFrameworkCompilers from config.compilers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilers.py:1453) TESTING: setupFrameworkCompilers from config.compilers(config/BuildSystem/config/compilers.py:1453) child config.compilers 2.562054 ================================================================================ TEST configureClosure from config.utilities.closure(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/closure.py:17) TESTING: configureClosure from config.utilities.closure(config/BuildSystem/config/utilities/closure.py:17) Determine if Apple ^close syntax is supported in C All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.utilities.closure Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.closure/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.closure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.utilities.closure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.utilities.closure/conftest.c:6:6: error: expected identifier or ���(��� before ���^��� token 6 | int (^closure)(int);; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int (^closure)(int);; return 0; } Compile failed inside link child config.utilities.closure 0.011875 ================================================================================ TEST checkFortranTypeSizes from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:56) TESTING: checkFortranTypeSizes from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:56) Check whether real*8 is supported and suggest flags which will allow support All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.compilersFortran Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90:2:21: 2 | real*8 variable | 1 Warning: Unused variable ���variable��� declared at (1) [-Wunused-variable] Source: program main real*8 variable end ================================================================================ TEST checkFortranPreprocessor from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:73) TESTING: checkFortranPreprocessor from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:73) Determine if Fortran handles preprocessing properly Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef dummy fooey #endif end compilers: Fortran uses preprocessor ================================================================================ TEST checkFortranDefineCompilerOption from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:96) TESTING: checkFortranDefineCompilerOption from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:96) Check if -WF,-Dfoobar or -Dfoobar is the compiler option to define a macro Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.setCompilers -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -DTesting /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main #define dummy dummy #ifndef Testing fooey #endif end Defined make macro "FC_DEFINE_FLAG" to "-D" compilers: Fortran uses -D for defining macro ================================================================================ TEST checkFortran90 from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:146) TESTING: checkFortran90 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:146) Determine whether the Fortran compiler handles F90 Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8) INTEGER (KIND=int) :: ierr ierr = 1 end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90" to "1" Fortran compiler supports F90 ================================================================================ TEST checkFortran90FreeForm from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:159) TESTING: checkFortran90FreeForm from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:159) Determine whether the Fortran compiler handles F90FreeForm We also require that the compiler handles lines longer than 132 characters Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main INTEGER, PARAMETER :: int = SELECTED_INT_KIND(8); INTEGER (KIND=int) :: ierr; ierr = 1 end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F90FREEFORM" to "1" Fortran compiler supports F90FreeForm ================================================================================ TEST checkFortran2003 from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:173) TESTING: checkFortran2003 from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:173) Determine whether the Fortran compiler handles F2003 Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: module Base_module type, public :: base_type integer :: A contains procedure, public :: Print => BasePrint end type base_type contains subroutine BasePrint(this) class(base_type) :: this end subroutine BasePrint end module Base_module program main use,intrinsic :: iso_c_binding Type(C_Ptr),Dimension(:),Pointer :: CArray character(kind=c_char),pointer :: nullc => null() character(kind=c_char,len=5),dimension(:),pointer::list1 allocate(list1(5)) CArray = (/(c_loc(list1(i)),i=1,5),c_loc(nullc)/) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "USING_F2003" to "1" Fortran compiler supports F2003 ================================================================================ TEST checkFortran90Array from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:208) TESTING: checkFortran90Array from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:208) Check for F90 array interfaces Executing: uname -s stdout: Linux Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include void f90arraytest_(void* a1, void* a2,void* a3, void* i) { printf("arrays [%p %p %p]\n",a1,a2,a3); fflush(stdout); return; } void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2, void* p3) { printf("arrays [%p %p %p]\n",a1,a2,a3); if ((p1 == p3) && (p1 != p2)) { printf("pointers match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); } else { printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2); fflush(stdout); exit(111); } return; } Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main Interface Subroutine f90ptrtest(p1,p2,p3,i) integer, pointer :: p1(:,:) integer, pointer :: p2(:,:) integer, pointer :: p3(:,:) integer i End Subroutine End Interface integer, pointer :: ptr1(:,:),ptr2(:,:) integer, target :: array(6:8,9:21) integer in in = 25 ptr1 => array ptr2 => array call f90arraytest(ptr1,ptr2,ptr1,in) call f90ptrtest(ptr1,ptr2,ptr1,in) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o /tmp/petsc-xk72m0wq/config.compilersFortran/fooobj.o -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.compilersFortran/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.compilersFortran/conftest Executing: /tmp/petsc-xk72m0wq/config.compilersFortran/conftest stdout: arrays [0x7fff7af9f470 0x7fff7af9f470 0x7fff7af9f470] arrays [0x7fff7af9f3b0 0x7fff7af9f410 0x7fff7af9f3b0] pointers do not match! [(nil) 0x7f7b4b06c420] [0x36] ERROR while running executable: Could not execute "['/tmp/petsc-xk72m0wq/config.compilersFortran/conftest']": arrays [0x7fff7af9f470 0x7fff7af9f470 0x7fff7af9f470] arrays [0x7fff7af9f3b0 0x7fff7af9f410 0x7fff7af9f3b0] pointers do not match! [(nil) 0x7f7b4b06c420] [0x36] compilers: F90 uses a single argument for array pointers ================================================================================ TEST checkFortranModuleInclude from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:295) TESTING: checkFortranModuleInclude from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:295) Figures out what flag is used to specify the include path for Fortran modules Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main use configtest write(*,*) testint end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -I/tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o /tmp/petsc-xk72m0wq/config.compilersFortran/configtest.o -lstdc++ -ldl compilers: Fortran module include flag -I found ================================================================================ TEST checkFortranModuleOutput from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:361) TESTING: checkFortranModuleOutput from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:361) Figures out what flag is used to specify the include path for Fortran modules Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -module /tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ���-module���; did you mean ���-fmodules���? Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module compile failed Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -module:/tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ���-module:/tmp/petsc-xk72m0wq/config.compilersFortran/confdir��� Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -module: compile failed Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fmod=/tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Possible ERROR while running compiler: stderr: f951: Warning: command line option ���-fmod=/tmp/petsc-xk72m0wq/config.compilersFortran/confdir��� is valid for Modula-2 but not for Fortran Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -fmod= failed Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -J/tmp/petsc-xk72m0wq/config.compilersFortran/confdir -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: module configtest integer testint parameter (testint = 42) end module configtest compilers: Fortran module output flag -J found ================================================================================ TEST checkFortranTypeStar from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:135) TESTING: checkFortranTypeStar from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:135) Determine whether the Fortran compiler handles type(*) Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main interface subroutine a(b) type(*) :: b(:) end subroutine end interface end Defined "HAVE_FORTRAN_TYPE_STAR" to "1" Fortran compiler supports type(*) ================================================================================ TEST checkFortranTypeInitialize from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:125) TESTING: checkFortranTypeInitialize from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:125) Determines if PETSc objects in Fortran are initialized by default (doesn't work with common blocks) Defined "FORTRAN_TYPE_INITIALIZE" to " = -2" Initializing Fortran objects ================================================================================ TEST configureFortranFlush from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:116) TESTING: configureFortranFlush from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:116) Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.F90 Successful compile: Source: program main call flush(6) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.compilersFortran/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.compilersFortran/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_FLUSH" to "1" ================================================================================ TEST checkDependencyGenerationFlag from config.compilersFortran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/compilersFortran.py:406) TESTING: checkDependencyGenerationFlag from config.compilersFortran(config/BuildSystem/config/compilersFortran.py:406) Check if -MMD works for dependency generation, and add it if it does Trying FC compiler flag -MMD -MP Defined make macro "FC_DEPFLAGS" to "-MMD -MP" Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -MMD -MP /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end child config.compilersFortran 0.656131 ================================================================================ TEST checkStdC from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:105) TESTING: checkStdC from config.headers(config/BuildSystem/config/headers.py:105) Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.headers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.headers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #define ISLOWER(c) ('a' <= (c) && (c) <= 'z') #define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main() { int i; for(i = 0; i < 256; i++) if (XOR(islower(i), ISLOWER(i)) || toupper(i) != TOUPPER(i)) exit(2); exit(0); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.headers/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.headers/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.headers/conftest Executing: /tmp/petsc-xk72m0wq/config.headers/conftest ================================================================================ TEST checkStat from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:138) TESTING: checkStat from config.headers(config/BuildSystem/config/headers.py:138) Checks whether stat file-mode macros are broken, and defines STAT_MACROS_BROKEN if they are Preprocessing source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(S_ISBLK) && defined(S_IFDIR) # if S_ISBLK (S_IFDIR) You lose. # endif #endif #if defined(S_ISBLK) && defined(S_IFCHR) # if S_ISBLK (S_IFCHR) You lose. # endif #endif #if defined(S_ISLNK) && defined(S_IFREG) # if S_ISLNK (S_IFREG) You lose. # endif #endif #if defined(S_ISSOCK) && defined(S_IFREG) # if S_ISSOCK (S_IFREG) You lose. # endif #endif Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c ================================================================================ TEST checkSysWait from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:173) TESTING: checkSysWait from config.headers(config/BuildSystem/config/headers.py:173) Check for POSIX.1 compatible sys/wait.h, and defines HAVE_SYS_WAIT_H if found Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.headers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #ifndef WEXITSTATUS #define WEXITSTATUS(stat_val) ((unsigned)(stat_val) >> 8) #endif #ifndef WIFEXITED #define WIFEXITED(stat_val) (((stat_val) & 255) == 0) #endif int main() { int s; wait (&s); s = WIFEXITED (s) ? WEXITSTATUS (s) : 1; ; return 0; } Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST checkTime from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:195) TESTING: checkTime from config.headers(config/BuildSystem/config/headers.py:195) Checks if you can safely include both and , and if so defines TIME_WITH_SYS_TIME Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" Checking for header: sys/time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIME_H" to "1" ================================================================================ TEST checkMath from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:201) TESTING: checkMath from config.headers(config/BuildSystem/config/headers.py:201) Checks for the math headers and defines Checking for header: math.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.headers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { double pi = M_PI; if (pi); ; return 0; } Found math #defines, like M_PI ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: setjmp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SETJMP_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: dos.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: dos.h: No such file or directory 3 | #include | ^~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: fcntl.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FCNTL_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: io.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: io.h: No such file or directory 3 | #include | ^~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: malloc.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_MALLOC_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pwd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PWD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: strings.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STRINGS_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: unistd.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_UNISTD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/sysinfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SYSINFO_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: machine/endian.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: machine/endian.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/param.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PARAM_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/procfs.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_PROCFS_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/resource.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_RESOURCE_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/systeminfo.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sys/systeminfo.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/times.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TIMES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/utsname.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_UTSNAME_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/socket.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_SOCKET_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/wait.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_WAIT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netinet/in.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETINET_IN_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: netdb.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_NETDB_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Direct.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Direct.h: No such file or directory 3 | #include | ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: time.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_TIME_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: Ws2tcpip.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: Ws2tcpip.h: No such file or directory 3 | #include | ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: sys/types.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_SYS_TYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: WindowsX.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: WindowsX.h: No such file or directory 3 | #include | ^~~~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: float.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_FLOAT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: ieeefp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: ieeefp.h: No such file or directory 3 | #include | ^~~~~~~~~~compilation terminated.: ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: stdint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_STDINT_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: pthread.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_PTHREAD_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: inttypes.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_INTTYPES_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: immintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_IMMINTRIN_H" to "1" ================================================================================ TEST check from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:77) TESTING: check from config.headers(config/BuildSystem/config/headers.py:77) Checks for "header", and defines HAVE_"header" if found Checking for header: zmmintrin.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: zmmintrin.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~compilation terminated.: ================================================================================ TEST checkRecursiveMacros from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:216) TESTING: checkRecursiveMacros from config.headers(config/BuildSystem/config/headers.py:216) Checks that the preprocessor allows recursive macros, and if not defines HAVE_BROKEN_RECURSIVE_MACRO Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.headers/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.headers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" void a(int i, int j) {} #define a(b) a(b,__LINE__) int main() { a(0); ; return 0; } child config.headers 1.374437 ================================================================================ TEST configureCacheDetails from config.utilities.cacheDetails(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/cacheDetails.py:78) TESTING: configureCacheDetails from config.utilities.cacheDetails(config/BuildSystem/config/utilities/cacheDetails.py:78) Try to determine the size and associativity of the cache. All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.utilities.cacheDetails Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include long getconf_LEVEL1_DCACHE_LINESIZE() { long val = sysconf(_SC_LEVEL1_DCACHE_LINESIZE); return (16 <= val && val <= 2147483647) ? val : 32; } int main() { FILE *output = fopen("conftestval","w"); if (!output) return 1; fprintf(output,"%ld",getconf_LEVEL1_DCACHE_LINESIZE()); fclose(output);; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest.o -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest Executing: /tmp/petsc-xk72m0wq/config.utilities.cacheDetails/conftest Defined "LEVEL1_DCACHE_LINESIZE" to "64" child config.utilities.cacheDetails 0.091178 ================================================================================ TEST check_struct_sigaction from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:43) TESTING: check_struct_sigaction from config.types(config/BuildSystem/config/types.py:43) Checks if "struct sigaction" exists in signal.h. This check is for C89 check. Checking for type: struct sigaction All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.types Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:18: warning: unused variable ���a��� [-Wunused-variable] 11 | struct sigaction a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { struct sigaction a;; return 0; } struct sigaction found Defined "HAVE_STRUCT_SIGACTION" to "1" ================================================================================ TEST check__int64 from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:49) TESTING: check__int64 from config.types(config/BuildSystem/config/types.py:49) Checks if __int64 exists. This is primarily for windows. Checking for type: __int64 Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:1: error: unknown type name ���__int64���; did you mean ���__int64_t���? 11 | __int64 a;; | ^~~~~~~ | __int64_t /tmp/petsc-xk72m0wq/config.types/conftest.c:11:9: warning: unused variable ���a��� [-Wunused-variable] 11 | __int64 a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { __int64 a;; return 0; } __int64 found ================================================================================ TEST checkSizeTypes from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:55) TESTING: checkSizeTypes from config.types(config/BuildSystem/config/types.py:55) Checks for types associated with sizes, such as size_t. Checking for type: size_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:8: warning: unused variable ���a��� [-Wunused-variable] 11 | size_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { size_t a;; return 0; } size_t found ================================================================================ TEST checkFileTypes from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:65) TESTING: checkFileTypes from config.types(config/BuildSystem/config/types.py:65) Checks for types associated with files, such as mode_t, off_t, etc. Checking for type: mode_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:8: warning: unused variable ���a��� [-Wunused-variable] 11 | mode_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { mode_t a;; return 0; } mode_t found Checking for type: off_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:7: warning: unused variable ���a��� [-Wunused-variable] 11 | off_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { off_t a;; return 0; } off_t found ================================================================================ TEST checkIntegerTypes from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:60) TESTING: checkIntegerTypes from config.types(config/BuildSystem/config/types.py:60) Checks for types associated with integers, such as int32_t. Checking for type: int32_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:9: warning: unused variable ���a��� [-Wunused-variable] 11 | int32_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found ================================================================================ TEST checkPID from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:71) TESTING: checkPID from config.types(config/BuildSystem/config/types.py:71) Checks for pid_t, and defines it if necessary Checking for type: pid_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:7: warning: unused variable ���a��� [-Wunused-variable] 11 | pid_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { pid_t a;; return 0; } pid_t found ================================================================================ TEST checkUID from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:75) TESTING: checkUID from config.types(config/BuildSystem/config/types.py:75) Checks for uid_t and gid_t, and defines them if necessary Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.types /tmp/petsc-xk72m0wq/config.types/conftest.c ================================================================================ TEST checkC99Complex from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:82) TESTING: checkC99Complex from config.types(config/BuildSystem/config/types.py:82) Check for complex numbers in in C99 std Note that since PETSc source code uses _Complex we test specifically for that, not complex Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:6:17: warning: variable ���x��� set but not used [-Wunused-but-set-variable] 6 | double _Complex x; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:6:17: warning: variable ���x��� set but not used [-Wunused-but-set-variable] 6 | double _Complex x; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double _Complex x; x = I; ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.types/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_C99_COMPLEX" to "1" ================================================================================ TEST checkCxxComplex from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:93) TESTING: checkCxxComplex from config.types(config/BuildSystem/config/types.py:93) Check for complex numbers in namespace std Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { std::complex x; ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.types/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.o -lstdc++ -ldl Defined "HAVE_CXX_COMPLEX" to "1" ================================================================================ TEST checkFortranKind from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:114) TESTING: checkFortranKind from config.types(config/BuildSystem/config/types.py:114) Checks whether selected_int_kind etc work USE_FORTRANKIND Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.types/conftest.F90 Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.F90:4:43: 4 | real(kind=selected_real_kind(10)) d | 1 Warning: Unused variable ���d��� declared at (1) [-Wunused-variable] /tmp/petsc-xk72m0wq/config.types/conftest.F90:3:45: 3 | integer(kind=selected_int_kind(10)) i | 1 Warning: Unused variable ���i��� declared at (1) [-Wunused-variable] Source: program main integer(kind=selected_int_kind(10)) i real(kind=selected_real_kind(10)) d end Defined "USE_FORTRANKIND" to "1" ================================================================================ TEST checkConst from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:126) TESTING: checkConst from config.types(config/BuildSystem/config/types.py:126) Checks for working const, and if not found defines it to empty string Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:25:5: warning: this ���if��� clause does not guard... [-Wmisleading-indentation] 25 | if (x[0]); | ^~ /tmp/petsc-xk72m0wq/config.types/conftest.c:26:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ���if��� 26 | { /* SCO 3.2v4 cc rejects this. */ | ^ /tmp/petsc-xk72m0wq/config.types/conftest.c:25:10: warning: ���x[0]��� is used uninitialized in this function [-Wuninitialized] 25 | if (x[0]); | ~^~~ /tmp/petsc-xk72m0wq/config.types/conftest.c:30:9: warning: ���t��� is used uninitialized in this function [-Wuninitialized] 30 | *t++ = 0; | ~^~ /tmp/petsc-xk72m0wq/config.types/conftest.c:46:25: warning: ���b��� is used uninitialized in this function [-Wuninitialized] 46 | struct s *b; b->j = 5; | ~~~~~^~~ Source: #include "confdefs.h" #include "conffix.h" int main() { /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; /* This section avoids unused variable warnings */ if (zero.x); if (x[0]); { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; if (*s); } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; /* Get rid of unused variable warning */ if (foo); } ; return 0; } ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: void * Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(void *)==8)*2-1]; Defined "SIZEOF_VOID_P" to "8" ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: short Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(short)==2)*2-1]; Defined "SIZEOF_SHORT" to "2" ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: int Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(int)==4)*2-1]; Defined "SIZEOF_INT" to "4" ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long)==8)*2-1]; Defined "SIZEOF_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: long long Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(long long)==8)*2-1]; Defined "SIZEOF_LONG_LONG" to "8" ================================================================================ TEST checkSizeof from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:182) TESTING: checkSizeof from config.types(config/BuildSystem/config/types.py:182) Determines the size of type "typeName", and defines SIZEOF_"typeName" to be the size Checking for size of type: size_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include char assert_sizeof[(sizeof(size_t)==8)*2-1]; Defined "SIZEOF_SIZE_T" to "8" ================================================================================ TEST checkVisibility from config.types(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/types.py:213) TESTING: checkVisibility from config.types(config/BuildSystem/config/types.py:213) Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_C" to "1" Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.types/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { __attribute__((visibility ("default"))) int foo(void);; return 0; } Defined "USE_VISIBILITY_CXX" to "1" child config.types 0.760350 ================================================================================ TEST configureMemAlign from PETSc.options.memAlign(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/memAlign.py:29) TESTING: configureMemAlign from PETSc.options.memAlign(config/PETSc/options/memAlign.py:29) Choose alignment Defined "MEMALIGN" to "16" Memory alignment is 16 child PETSc.options.memAlign 0.000642 ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [handle_sigfpes] in library ['fpe'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char handle_sigfpes(); static void _check_handle_sigfpes() { handle_sigfpes(); } int main() { _check_handle_sigfpes();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lfpe -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lfpe collect2: error: ld returned 1 exit status ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [socket] in library ['socket', 'nsl'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char socket(); static void _check_socket() { socket(); } int main() { _check_socket();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lsocket -lnsl -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: cannot find -lsocket collect2: error: ld returned 1 exit status ================================================================================ TEST checkMath from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:264) TESTING: checkMath from config.libraries(config/BuildSystem/config/libraries.py:264) Check for sin() in libm, the math library Checking for functions [sin floor log10 pow] in library [''] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_sin���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:6:40: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 6 | static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_floor���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:10:42: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 10 | static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_log10���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:14:42: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 14 | static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_pow���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:18:40: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 18 | static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); | ^~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0x26): undefined reference to `sin' /bin/ld: conftest.c:(.text.startup+0xd6): undefined reference to `log10' /bin/ld: conftest.c:(.text.startup+0x10c): undefined reference to `pow' collect2: error: ld returned 1 exit status Checking for functions [sin floor log10 pow] in library ['m'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_sin���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:6:40: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 6 | static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_floor���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:10:42: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 10 | static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_log10���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:14:42: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 14 | static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); | ^~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_pow���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:18:40: warning: ignoring return value of ���scanf���, declared with attribute warn_unused_result [-Wunused-result] 18 | static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); | ^~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include double sin(double); static void _check_sin() { double x,y; scanf("%lf",&x); y = sin(x); printf("%f",y); ; } #include double floor(double); static void _check_floor() { double x,y; scanf("%lf",&x); y = floor(x); printf("%f",y); ; } #include double log10(double); static void _check_log10() { double x,y; scanf("%lf",&x); y = log10(x); printf("%f",y); ; } #include double pow(double, double); static void _check_pow() { double x,y; scanf("%lf",&x); y = pow(x,x); printf("%f",y); ; } int main() { _check_sin(); _check_floor(); _check_log10(); _check_pow();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" CheckMath: using math library ['libm.a'] ================================================================================ TEST checkMathErf from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:283) TESTING: checkMathErf from config.libraries(config/BuildSystem/config/libraries.py:283) Check for erf() in libm, the math library Checking for functions [erf] in library ['libm.a'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_erf���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:5:74: warning: variable ���y��� set but not used [-Wunused-but-set-variable] 5 | static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } | ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_erf() { double (*checkErf)(double) = erf;double x = 0,y; y = (*checkErf)(x); } int main() { _check_erf();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" erf() found Defined "HAVE_ERF" to "1" ================================================================================ TEST checkMathTgamma from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:292) TESTING: checkMathTgamma from config.libraries(config/BuildSystem/config/libraries.py:292) Check for tgamma() in libm, the math library Checking for functions [tgamma] in library ['libm.a'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_tgamma���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:5:83: warning: variable ���y��� set but not used [-Wunused-but-set-variable] 5 | static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } | ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_tgamma() { double (*checkTgamma)(double) = tgamma;double x = 0,y; y = (*checkTgamma)(x); } int main() { _check_tgamma();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" tgamma() found Defined "HAVE_TGAMMA" to "1" ================================================================================ TEST checkMathFenv from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:301) TESTING: checkMathFenv from config.libraries(config/BuildSystem/config/libraries.py:301) Checks if can be used with FE_DFL_ENV Checking for functions [fesetenv] in library ['libm.a'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_fesetenv() { fesetenv(FE_DFL_ENV);; } int main() { _check_fesetenv();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" Defined "HAVE_FENV_H" to "1" ================================================================================ TEST checkMathLog2 from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:309) TESTING: checkMathLog2 from config.libraries(config/BuildSystem/config/libraries.py:309) Check for log2() in libm, the math library Checking for functions [log2] in library ['libm.a'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_log2���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:5:81: warning: unused variable ���y��� [-Wunused-variable] 5 | static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } | ^ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_log2() { double (*checkLog2)(double) = log2; double x = 2.5, y = (*checkLog2)(x); } int main() { _check_log2();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lm -lstdc++ -ldl Defined "HAVE_LIBM" to "1" log2() found Defined "HAVE_LOG2" to "1" ================================================================================ TEST checkRealtime from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:318) TESTING: checkRealtime from config.libraries(config/BuildSystem/config/libraries.py:318) Check for presence of clock_gettime() in realtime library (POSIX Realtime extensions) Checking for functions [clock_gettime] in library [''] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_clock_gettime() { struct timespec tp; clock_gettime(CLOCK_REALTIME,&tp);; } int main() { _check_clock_gettime();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lstdc++ -ldl realtime functions are linked in by default ================================================================================ TEST checkDynamic from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:334) TESTING: checkDynamic from config.libraries(config/BuildSystem/config/libraries.py:334) Check for the header and libraries necessary for dynamic library manipulation Checking for functions [dlopen] in library ['dl'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dlopen(); static void _check_dlopen() { dlopen(); } int main() { _check_dlopen();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -ldl -lstdc++ -ldl Defined "HAVE_LIBDL" to "1" Checking for header: dlfcn.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Defined "HAVE_DLFCN_H" to "1" child config.libraries 0.677795 ================================================================================ TEST configureLibraryOptions from PETSc.options.libraryOptions(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/libraryOptions.py:37) TESTING: configureLibraryOptions from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:37) Sets PETSC_USE_DEBUG, PETSC_USE_INFO, PETSC_USE_LOG, PETSC_USE_CTABLE, PETSC_USE_FORTRAN_KERNELS, and PETSC_USE_AVX512_KERNELS Defined "USE_LOG" to "1" Executing: mpicc -qversion Defined "USE_MALLOC_COALESCED" to "1" Defined "USE_INFO" to "1" Defined "USE_CTABLE" to "1" Defined "USE_BACKWARD_LOOP" to "1" **********Checking if running on BGL/IBM detected Checking for functions [bgl_perfctr_void] in library [''] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char bgl_perfctr_void(); static void _check_bgl_perfctr_void() { bgl_perfctr_void(); } int main() { _check_bgl_perfctr_void();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `bgl_perfctr_void' collect2: error: ld returned 1 exit status Checking for functions [ADIOI_BGL_Open] in library [''] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char ADIOI_BGL_Open(); static void _check_ADIOI_BGL_Open() { ADIOI_BGL_Open(); } int main() { _check_ADIOI_BGL_Open();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `ADIOI_BGL_Open' collect2: error: ld returned 1 exit status *********BGL/IBM test failure Defined "USE_AVX512_KERNELS" to "1" Defined "Alignx(a,b)" to " " ================================================================================ TEST configureISColorValueType from PETSc.options.libraryOptions(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/libraryOptions.py:95) TESTING: configureISColorValueType from PETSc.options.libraryOptions(config/PETSc/options/libraryOptions.py:95) Sets PETSC_IS_COLOR_VALUE_TYPE, MPIU_COLORING_VALUE, IS_COLORING_MAX required by ISColor Defined "MPIU_COLORING_VALUE" to "MPI_UNSIGNED_SHORT" Defined "IS_COLORING_MAX" to "USHRT_MAX" Defined "IS_COLOR_VALUE_TYPE" to "short" Defined "IS_COLOR_VALUE_TYPE_F" to "integer2" child PETSc.options.libraryOptions 0.109818 child config.atomics 0.000004 ================================================================================ TEST checkSysinfo from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:106) TESTING: checkSysinfo from config.functions(config/BuildSystem/config/functions.py:106) Check whether sysinfo takes three arguments, and if it does define HAVE_SYSINFO_3ARG Checking for functions [sysinfo] All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.functions Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sysinfo(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sysinfo) || defined (__stub___sysinfo) sysinfo_will_always_fail_with_ENOSYS(); #else sysinfo(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SYSINFO" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.functions/conftest.c:9:4: error: #error "Cannot check sysinfo without special headers" 9 | # error "Cannot check sysinfo without special headers" | ^~~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.functions/conftest.c:13:30: warning: implicit declaration of function ���sysinfo��� [-Wimplicit-function-declaration] 13 | char buf[10]; long count=10; sysinfo(1, buf, count); | ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #ifdef HAVE_SYS_SYSINFO_H # include #elif defined(HAVE_SYS_SYSTEMINFO_H) # include #else # error "Cannot check sysinfo without special headers" #endif int main() { char buf[10]; long count=10; sysinfo(1, buf, count); ; return 0; } Compile failed inside link ================================================================================ TEST checkVPrintf from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:125) TESTING: checkVPrintf from config.functions(config/BuildSystem/config/functions.py:125) Checks whether vprintf requires a char * last argument, and if it does defines HAVE_VPRINTF_CHAR Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vprintf( "%d", Argp ); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVFPrintf from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:131) TESTING: checkVFPrintf from config.functions(config/BuildSystem/config/functions.py:131) Checks whether vfprintf requires a char * last argument, and if it does defines HAVE_VFPRINTF_CHAR Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp; vfprintf(stdout, "%d", Argp ); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl ================================================================================ TEST checkVSNPrintf from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:137) TESTING: checkVSNPrintf from config.functions(config/BuildSystem/config/functions.py:137) Checks whether vsnprintf requires a char * last argument, and if it does defines HAVE_VSNPRINTF_CHAR Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { va_list Argp;char str[6]; vsnprintf(str,5, "%d", Argp ); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VSNPRINTF" to "1" ================================================================================ TEST checkNanosleep from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:167) TESTING: checkNanosleep from config.functions(config/BuildSystem/config/functions.py:167) Check for functional nanosleep() - as time.h behaves differently for different compiler flags - like -std=c89 Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { struct timespec tp; tp.tv_sec = 0; tp.tv_nsec = (long)(1e9); nanosleep(&tp,0); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_NANOSLEEP" to "1" ================================================================================ TEST checkMemmove from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:173) TESTING: checkMemmove from config.functions(config/BuildSystem/config/functions.py:173) Check for functional memmove() - as MS VC requires correct includes to for this test Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char c1[1], c2[1] = "c"; size_t n=1; memmove(c1,c2,n); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MEMMOVE" to "1" ================================================================================ TEST checkSignalHandlerType from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:143) TESTING: checkSignalHandlerType from config.functions(config/BuildSystem/config/functions.py:143) Checks the type of C++ signals handlers, and defines SIGNAL_CAST to the correct value Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.functions/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include static void myhandler(int sig) {} int main() { signal(SIGFPE,myhandler); ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.functions/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "SIGNAL_CAST" to " " ================================================================================ TEST checkFreeReturnType from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:153) TESTING: checkFreeReturnType from config.functions(config/BuildSystem/config/functions.py:153) Checks whether free returns void or int, and defines HAVE_FREE_RETURN_INT Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.functions/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.functions/conftest.c:6:25: error: void value not ignored as it ought to be 6 | int ierr; void *p; ierr = free(p); return 0; | ^ /tmp/petsc-xk72m0wq/config.functions/conftest.c:6:5: warning: variable ���ierr��� set but not used [-Wunused-but-set-variable] 6 | int ierr; void *p; ierr = free(p); return 0; | ^~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int ierr; void *p; ierr = free(p); return 0; ; return 0; } Compile failed inside link ================================================================================ TEST checkVariableArgumentLists from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:159) TESTING: checkVariableArgumentLists from config.functions(config/BuildSystem/config/functions.py:159) Checks whether the variable argument list functionality is working Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { va_list l1, l2; va_copy(l1, l2); return 0; ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_VA_COPY" to "1" ================================================================================ TEST checkClassify from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:85) TESTING: checkClassify from config.functions(config/BuildSystem/config/functions.py:85) Recursive decompose to rapidly classify functions as found or missing To confirm that a function is missing, we require a compile/link failure with only that function in a compilation unit. In contrast, we can confirm that many functions are present by compiling them all together in a large compilation unit. We optimistically compile everything together, then trim all functions that were named in the error message and bisect the result. The trimming is only an optimization to increase the likelihood of a big-batch compile succeeding; we do not rely on the compiler naming missing functions. Checking for functions [popen dlsym getcwd getrusage gethostname _sleep time _set_output_format _getcwd PXFGETARG _snprintf getwd getdomainname usleep dlclose _mkdir _access rand sbreak stricmp sleep uname dlopen snprintf lseek getpagesize _lseek bzero memalign access realpath readlink fork socket dlerror clock gethostbyname drand48 strcasecmp] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.functions/conftest.c:36:6: warning: conflicting types for built-in function ���snprintf���; expected ���int(char *, long unsigned int, const char *, ...)��� [-Wbuiltin-declaration-mismatch] 36 | char snprintf(); | ^~~~~~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:6:1: note: ���snprintf��� is declared in header ������ 5 | #include +++ |+#include 6 | /* Override any gcc2 internal prototype to avoid an error. */ /tmp/petsc-xk72m0wq/config.functions/conftest.c:40:6: warning: conflicting types for built-in function ���bzero���; expected ���void(void *, long unsigned int)��� [-Wbuiltin-declaration-mismatch] 40 | char bzero(); | ^~~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:45:6: warning: conflicting types for built-in function ���fork���; expected ���int(void)��� [-Wbuiltin-declaration-mismatch] 45 | char fork(); | ^~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:51:6: warning: conflicting types for built-in function ���strcasecmp���; expected ���int(const char *, const char *)��� [-Wbuiltin-declaration-mismatch] 51 | char strcasecmp(); | ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char popen(); char dlsym(); char getcwd(); char getrusage(); char gethostname(); char _sleep(); char time(); char _set_output_format(); char _getcwd(); char PXFGETARG(); char _snprintf(); char getwd(); char getdomainname(); char usleep(); char dlclose(); char _mkdir(); char _access(); char rand(); char sbreak(); char stricmp(); char sleep(); char uname(); char dlopen(); char snprintf(); char lseek(); char getpagesize(); char _lseek(); char bzero(); char memalign(); char access(); char realpath(); char readlink(); char fork(); char socket(); char dlerror(); char clock(); char gethostbyname(); char drand48(); char strcasecmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0x58): warning: the `getwd' function is dangerous and should not be used. /bin/ld: conftest.c:(.text.startup+0x2e): undefined reference to `_sleep' /bin/ld: conftest.c:(.text.startup+0x3c): undefined reference to `_set_output_format' /bin/ld: conftest.c:(.text.startup+0x43): undefined reference to `_getcwd' /bin/ld: conftest.c:(.text.startup+0x4a): undefined reference to `PXFGETARG' /bin/ld: conftest.c:(.text.startup+0x51): undefined reference to `_snprintf' /bin/ld: conftest.c:(.text.startup+0x74): undefined reference to `_mkdir' /bin/ld: conftest.c:(.text.startup+0x7b): undefined reference to `_access' /bin/ld: conftest.c:(.text.startup+0x89): undefined reference to `sbreak' /bin/ld: conftest.c:(.text.startup+0x90): undefined reference to `stricmp' /bin/ld: conftest.c:(.text.startup+0xc1): undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [popen dlsym getrusage gethostname time getdomainname usleep dlclose rand uname dlopen] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char popen(); char dlsym(); char getrusage(); char gethostname(); char time(); char getdomainname(); char usleep(); char dlclose(); char rand(); char uname(); char dlopen(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_popen) || defined (__stub___popen) popen_will_always_fail_with_ENOSYS(); #else popen(); #endif #if defined (__stub_dlsym) || defined (__stub___dlsym) dlsym_will_always_fail_with_ENOSYS(); #else dlsym(); #endif #if defined (__stub_getrusage) || defined (__stub___getrusage) getrusage_will_always_fail_with_ENOSYS(); #else getrusage(); #endif #if defined (__stub_gethostname) || defined (__stub___gethostname) gethostname_will_always_fail_with_ENOSYS(); #else gethostname(); #endif #if defined (__stub_time) || defined (__stub___time) time_will_always_fail_with_ENOSYS(); #else time(); #endif #if defined (__stub_getdomainname) || defined (__stub___getdomainname) getdomainname_will_always_fail_with_ENOSYS(); #else getdomainname(); #endif #if defined (__stub_usleep) || defined (__stub___usleep) usleep_will_always_fail_with_ENOSYS(); #else usleep(); #endif #if defined (__stub_dlclose) || defined (__stub___dlclose) dlclose_will_always_fail_with_ENOSYS(); #else dlclose(); #endif #if defined (__stub_rand) || defined (__stub___rand) rand_will_always_fail_with_ENOSYS(); #else rand(); #endif #if defined (__stub_uname) || defined (__stub___uname) uname_will_always_fail_with_ENOSYS(); #else uname(); #endif #if defined (__stub_dlopen) || defined (__stub___dlopen) dlopen_will_always_fail_with_ENOSYS(); #else dlopen(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_POPEN" to "1" Defined "HAVE_DLSYM" to "1" Defined "HAVE_GETRUSAGE" to "1" Defined "HAVE_GETHOSTNAME" to "1" Defined "HAVE_TIME" to "1" Defined "HAVE_GETDOMAINNAME" to "1" Defined "HAVE_USLEEP" to "1" Defined "HAVE_DLCLOSE" to "1" Defined "HAVE_RAND" to "1" Defined "HAVE_UNAME" to "1" Defined "HAVE_DLOPEN" to "1" Checking for functions [getpagesize bzero memalign realpath readlink fork socket dlerror clock gethostbyname drand48 strcasecmp] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.functions/conftest.c:14:6: warning: conflicting types for built-in function ���bzero���; expected ���void(void *, long unsigned int)��� [-Wbuiltin-declaration-mismatch] 14 | char bzero(); | ^~~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:18:6: warning: conflicting types for built-in function ���fork���; expected ���int(void)��� [-Wbuiltin-declaration-mismatch] 18 | char fork(); | ^~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:24:6: warning: conflicting types for built-in function ���strcasecmp���; expected ���int(const char *, const char *)��� [-Wbuiltin-declaration-mismatch] 24 | char strcasecmp(); | ^~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getpagesize(); char bzero(); char memalign(); char realpath(); char readlink(); char fork(); char socket(); char dlerror(); char clock(); char gethostbyname(); char drand48(); char strcasecmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getpagesize) || defined (__stub___getpagesize) getpagesize_will_always_fail_with_ENOSYS(); #else getpagesize(); #endif #if defined (__stub_bzero) || defined (__stub___bzero) bzero_will_always_fail_with_ENOSYS(); #else bzero(); #endif #if defined (__stub_memalign) || defined (__stub___memalign) memalign_will_always_fail_with_ENOSYS(); #else memalign(); #endif #if defined (__stub_realpath) || defined (__stub___realpath) realpath_will_always_fail_with_ENOSYS(); #else realpath(); #endif #if defined (__stub_readlink) || defined (__stub___readlink) readlink_will_always_fail_with_ENOSYS(); #else readlink(); #endif #if defined (__stub_fork) || defined (__stub___fork) fork_will_always_fail_with_ENOSYS(); #else fork(); #endif #if defined (__stub_socket) || defined (__stub___socket) socket_will_always_fail_with_ENOSYS(); #else socket(); #endif #if defined (__stub_dlerror) || defined (__stub___dlerror) dlerror_will_always_fail_with_ENOSYS(); #else dlerror(); #endif #if defined (__stub_clock) || defined (__stub___clock) clock_will_always_fail_with_ENOSYS(); #else clock(); #endif #if defined (__stub_gethostbyname) || defined (__stub___gethostbyname) gethostbyname_will_always_fail_with_ENOSYS(); #else gethostbyname(); #endif #if defined (__stub_drand48) || defined (__stub___drand48) drand48_will_always_fail_with_ENOSYS(); #else drand48(); #endif #if defined (__stub_strcasecmp) || defined (__stub___strcasecmp) strcasecmp_will_always_fail_with_ENOSYS(); #else strcasecmp(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETPAGESIZE" to "1" Defined "HAVE_BZERO" to "1" Defined "HAVE_MEMALIGN" to "1" Defined "HAVE_REALPATH" to "1" Defined "HAVE_READLINK" to "1" Defined "HAVE_FORK" to "1" Defined "HAVE_SOCKET" to "1" Defined "HAVE_DLERROR" to "1" Defined "HAVE_CLOCK" to "1" Defined "HAVE_GETHOSTBYNAME" to "1" Defined "HAVE_DRAND48" to "1" Defined "HAVE_STRCASECMP" to "1" Checking for functions [getcwd] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getcwd) || defined (__stub___getcwd) getcwd_will_always_fail_with_ENOSYS(); #else getcwd(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_GETCWD" to "1" Checking for functions [_sleep] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__sleep) || defined (__stub____sleep) _sleep_will_always_fail_with_ENOSYS(); #else _sleep(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_sleep' collect2: error: ld returned 1 exit status Checking for functions [_set_output_format] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _set_output_format(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__set_output_format) || defined (__stub____set_output_format) _set_output_format_will_always_fail_with_ENOSYS(); #else _set_output_format(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_set_output_format' collect2: error: ld returned 1 exit status Checking for functions [_getcwd] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _getcwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__getcwd) || defined (__stub____getcwd) _getcwd_will_always_fail_with_ENOSYS(); #else _getcwd(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_getcwd' collect2: error: ld returned 1 exit status Checking for functions [PXFGETARG] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char PXFGETARG(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_PXFGETARG) || defined (__stub___PXFGETARG) PXFGETARG_will_always_fail_with_ENOSYS(); #else PXFGETARG(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `PXFGETARG' collect2: error: ld returned 1 exit status Checking for functions [_snprintf] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__snprintf) || defined (__stub____snprintf) _snprintf_will_always_fail_with_ENOSYS(); #else _snprintf(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_snprintf' collect2: error: ld returned 1 exit status Checking for functions [getwd] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char getwd(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_getwd) || defined (__stub___getwd) getwd_will_always_fail_with_ENOSYS(); #else getwd(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): warning: the `getwd' function is dangerous and should not be used. Defined "HAVE_GETWD" to "1" Checking for functions [_mkdir] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _mkdir(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__mkdir) || defined (__stub____mkdir) _mkdir_will_always_fail_with_ENOSYS(); #else _mkdir(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_mkdir' collect2: error: ld returned 1 exit status Checking for functions [_access] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__access) || defined (__stub____access) _access_will_always_fail_with_ENOSYS(); #else _access(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_access' collect2: error: ld returned 1 exit status Checking for functions [sbreak] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sbreak(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sbreak) || defined (__stub___sbreak) sbreak_will_always_fail_with_ENOSYS(); #else sbreak(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `sbreak' collect2: error: ld returned 1 exit status Checking for functions [stricmp] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char stricmp(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_stricmp) || defined (__stub___stricmp) stricmp_will_always_fail_with_ENOSYS(); #else stricmp(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `stricmp' collect2: error: ld returned 1 exit status Checking for functions [sleep] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char sleep(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_sleep) || defined (__stub___sleep) sleep_will_always_fail_with_ENOSYS(); #else sleep(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SLEEP" to "1" Checking for functions [snprintf] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.functions/conftest.c:13:6: warning: conflicting types for built-in function ���snprintf���; expected ���int(char *, long unsigned int, const char *, ...)��� [-Wbuiltin-declaration-mismatch] 13 | char snprintf(); | ^~~~~~~~ /tmp/petsc-xk72m0wq/config.functions/conftest.c:6:1: note: ���snprintf��� is declared in header ������ 5 | #include +++ |+#include 6 | /* Override any gcc2 internal prototype to avoid an error. */ Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char snprintf(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_snprintf) || defined (__stub___snprintf) snprintf_will_always_fail_with_ENOSYS(); #else snprintf(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_SNPRINTF" to "1" Checking for functions [lseek] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_lseek) || defined (__stub___lseek) lseek_will_always_fail_with_ENOSYS(); #else lseek(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_LSEEK" to "1" Checking for functions [_lseek] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char _lseek(); #ifdef __cplusplus } #endif int main() { #if defined (__stub__lseek) || defined (__stub____lseek) _lseek_will_always_fail_with_ENOSYS(); #else _lseek(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.functions/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `_lseek' collect2: error: ld returned 1 exit status Checking for functions [access] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* System header to define __stub macros and hopefully no other prototypes since they would conflict with our 'char funcname()' declaration below. */ #include /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char access(); #ifdef __cplusplus } #endif int main() { #if defined (__stub_access) || defined (__stub___access) access_will_always_fail_with_ENOSYS(); #else access(); #endif ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_ACCESS" to "1" ================================================================================ TEST checkMmap from config.functions(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/functions.py:179) TESTING: checkMmap from config.functions(config/BuildSystem/config/functions.py:179) Check for functional mmap() to allocate shared memory and define HAVE_MMAP Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.functions/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { int fd; fd=open("/tmp/file",O_RDWR); mmap((void*)0,100,PROT_READ|PROT_WRITE,MAP_SHARED,fd,0); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.functions/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.functions/conftest.o -lstdc++ -ldl Defined "HAVE_MMAP" to "1" child config.functions 1.550032 ================================================================================ TEST configureMemorySize from config.utilities.getResidentSetSize(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/getResidentSetSize.py:31) TESTING: configureMemorySize from config.utilities.getResidentSetSize(config/BuildSystem/config/utilities/getResidentSetSize.py:31) Try to determine how to measure the memory usage Defined "USE_PROC_FOR_SIZE" to "1" Using /proc for PetscMemoryGetCurrentUsage() child config.utilities.getResidentSetSize 0.000390 ================================================================================ TEST configureFortranCommandLine from config.utilities.fortranCommandLine(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/fortranCommandLine.py:27) TESTING: configureFortranCommandLine from config.utilities.fortranCommandLine(config/BuildSystem/config/utilities/fortranCommandLine.py:27) Check for the mechanism to retrieve command line arguments in Fortran Checking for functions [] in library [''] [] Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.F90 Successful compile: Source: program main integer i character*(80) arg i = command_argument_count() call get_command_argument(i,arg) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lstdc++ -ldl Defined "HAVE_FORTRAN_GET_COMMAND_ARGUMENT" to "1" child config.utilities.fortranCommandLine 0.057120 ================================================================================ TEST configureFeatureTestMacros from config.utilities.featureTestMacros(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/featureTestMacros.py:13) TESTING: configureFeatureTestMacros from config.utilities.featureTestMacros(config/BuildSystem/config/utilities/featureTestMacros.py:13) Checks if certain feature test macros are support All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c:4:10: fatal error: sysctl.h: No such file or directory 4 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c Possible ERROR while running compiler: stderr: In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdlib.h:25, from /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c:4: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #include int main() { ; return 0; } Defined "_BSD_SOURCE" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _DEFAULT_SOURCE #include int main() { ; return 0; } Defined "_DEFAULT_SOURCE" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to "1" child config.utilities.featureTestMacros 0.091285 ================================================================================ TEST configureMissingUtypeTypedefs from config.utilities.missing(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/missing.py:55) TESTING: configureMissingUtypeTypedefs from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:55) Checks if u_short is undefined All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.utilities.missing Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c:6:9: warning: unused variable ���foo��� [-Wunused-variable] 6 | u_short foo; | ^~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { u_short foo; ; return 0; } ================================================================================ TEST configureMissingFunctions from config.utilities.missing(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/missing.py:61) TESTING: configureMissingFunctions from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:61) Checks for SOCKETS ================================================================================ TEST configureMissingSignals from config.utilities.missing(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/missing.py:79) TESTING: configureMissingSignals from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:79) Check for missing signals, and define MISSING_ if necessary Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGABRT; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGALRM; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGBUS; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCHLD; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGCONT; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGFPE; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGHUP; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGILL; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGINT; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGKILL; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGPIPE; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGQUIT; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSEGV; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSTOP; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGSYS; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTERM; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTRAP; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGTSTP; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGURG; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR1; if (i); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int i=SIGUSR2; if (i); ; return 0; } ================================================================================ TEST configureMissingGetdomainnamePrototype from config.utilities.missing(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/missing.py:96) TESTING: configureMissingGetdomainnamePrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:96) Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #ifdef PETSC_HAVE_UNISTD_H #include #endif #ifdef PETSC_HAVE_NETDB_H #include #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -lstdc++ -ldl ================================================================================ TEST configureMissingSrandPrototype from config.utilities.missing(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/missing.py:121) TESTING: configureMissingSrandPrototype from config.utilities.missing(config/BuildSystem/config/utilities/missing.py:121) Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.missing -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" #if !defined(_BSD_SOURCE) #define _BSD_SOURCE #endif #if !defined(_DEFAULT_SOURCE) #define _DEFAULT_SOURCE #endif #if !defined(_GNU_SOURCE) #define _GNU_SOURCE #endif #include int main() { double (*drand48_ptr)(void) = drand48; void (*srand48_ptr)(long int) = srand48; long int seed=10; srand48_ptr(seed); if (drand48_ptr() > 0.5) return 1; ; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.utilities.missing/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.utilities.missing/conftest.o -lstdc++ -ldl child config.utilities.missing 0.845381 ================================================================================ TEST configureFPTrap from config.utilities.FPTrap(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/utilities/FPTrap.py:27) TESTING: configureFPTrap from config.utilities.FPTrap(config/BuildSystem/config/utilities/FPTrap.py:27) Checking the handling of floating point traps Checking for header: sigfpe.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory 3 | #include | ^~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: sigfpe.h: No such file or directory 3 | #include | ^~~~~~~~~~compilation terminated.: Checking for header: fpxcp.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory 3 | #include | ^~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory 3 | #include | ^~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: fpxcp.h: No such file or directory 3 | #include | ^~~~~~~~~compilation terminated.: Checking for header: floatingpoint.h Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: floatingpoint.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~compilation terminated.: child config.utilities.FPTrap 0.025237 ================================================================================ TEST configureScalarType from PETSc.options.scalarTypes(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/scalarTypes.py:40) TESTING: configureScalarType from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:40) Choose between real and complex numbers Defined "USE_COMPLEX" to "1" Scalar type is complex All intermediate test results are stored in /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ���a��� [-Wunused-variable] 6 | double b = 2.0; int a = isnormal(b); | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnormal(b); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNORMAL" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ���a��� [-Wunused-variable] 6 | double b = 2.0; int a = isnan(b); | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isnan(b); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISNAN" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.c:6:21: warning: unused variable ���a��� [-Wunused-variable] 6 | double b = 2.0; int a = isinf(b); | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { double b = 2.0; int a = isinf(b); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.options.scalarTypes/conftest.o -lstdc++ -ldl Defined "HAVE_ISINF" to "1" ================================================================================ TEST configurePrecision from PETSc.options.scalarTypes(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/options/scalarTypes.py:81) TESTING: configurePrecision from PETSc.options.scalarTypes(config/PETSc/options/scalarTypes.py:81) Set the default real number precision for PETSc objects Checking C compiler works with __float128 Checking for functions [logq] in library ['quadmath'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_logq���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:5:43: warning: ���f��� is used uninitialized in this function [-Wuninitialized] 5 | static void _check_logq() { __float128 f; logq(f);; } | ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" C compiler with quadmath library Checking Fortran works with quadmath library Checking for functions [ ] in library ['quadmath'] [] Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.F90 Successful compile: Source: program main real*16 s,w; w = 2.0 ;s = cos(w) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Fortran works with quadmath library Checking for functions [logq] in library ['quadmath'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c: In function ���_check_logq���: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:5:43: warning: ���f��� is used uninitialized in this function [-Wuninitialized] 5 | static void _check_logq() { __float128 f; logq(f);; } | ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_logq() { __float128 f; logq(f);; } int main() { _check_logq();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_LIBQUADMATH" to "1" Adding ['quadmath'] to LIBS Defined "HAVE_REAL___FLOAT128" to "1" Defined "USE_REAL_SINGLE" to "1" Defined make macro "PETSC_SCALAR_SIZE" to "32" Precision is single child PETSc.options.scalarTypes 0.333804 ================================================================================ TEST configureMkdir from config.programs(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/programs.py:22) TESTING: configureMkdir from config.programs(config/BuildSystem/config/programs.py:22) Make sure we can have mkdir automatically make intermediate directories Checking for program /home/pesun/opt/openmpi/bin/mkdir...not found Checking for program /home/pesun/anaconda3/bin/mkdir...not found Checking for program /home/pesun/anaconda3/condabin/mkdir...not found Checking for program /home/pesun/.local/bin/mkdir...not found Checking for program /usr/local/sbin/mkdir...not found Checking for program /usr/local/bin/mkdir...not found Checking for program /usr/sbin/mkdir...not found Checking for program /sbin/mkdir...not found Checking for program /usr/games/mkdir...not found Checking for program /usr/local/games/mkdir...not found Checking for program /snap/bin/mkdir...not found Checking for program /bin/mkdir...found Executing: /bin/mkdir -p .conftest/tmp Adding -p flag to /bin/mkdir -p to automatically create directories Defined make macro "MKDIR" to "/bin/mkdir -p" ================================================================================ TEST configureAutoreconf from config.programs(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/programs.py:44) TESTING: configureAutoreconf from config.programs(config/BuildSystem/config/programs.py:44) Check for autoreconf Checking for program /home/pesun/opt/openmpi/bin/autoreconf...not found Checking for program /home/pesun/anaconda3/bin/autoreconf...not found Checking for program /home/pesun/anaconda3/condabin/autoreconf...not found Checking for program /home/pesun/.local/bin/autoreconf...not found Checking for program /usr/local/sbin/autoreconf...not found Checking for program /usr/local/bin/autoreconf...not found Checking for program /usr/sbin/autoreconf...not found Checking for program /sbin/autoreconf...not found Checking for program /usr/games/autoreconf...not found Checking for program /usr/local/games/autoreconf...not found Checking for program /snap/bin/autoreconf...not found Checking for program /bin/autoreconf...found All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.programs Executing: ['/bin/autoreconf'] autoreconf test successful! Checking for program /home/pesun/opt/openmpi/bin/libtoolize...not found Checking for program /home/pesun/anaconda3/bin/libtoolize...not found Checking for program /home/pesun/anaconda3/condabin/libtoolize...not found Checking for program /home/pesun/.local/bin/libtoolize...not found Checking for program /usr/local/sbin/libtoolize...not found Checking for program /usr/local/bin/libtoolize...not found Checking for program /usr/sbin/libtoolize...not found Checking for program /sbin/libtoolize...not found Checking for program /usr/games/libtoolize...not found Checking for program /usr/local/games/libtoolize...not found Checking for program /snap/bin/libtoolize...not found Checking for program /bin/libtoolize...found ================================================================================ TEST configurePrograms from config.programs(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/programs.py:71) TESTING: configurePrograms from config.programs(config/BuildSystem/config/programs.py:71) Check for the programs needed to build and run PETSc Checking for program /home/pesun/opt/openmpi/bin/sh...not found Checking for program /home/pesun/anaconda3/bin/sh...not found Checking for program /home/pesun/anaconda3/condabin/sh...not found Checking for program /home/pesun/.local/bin/sh...not found Checking for program /usr/local/sbin/sh...not found Checking for program /usr/local/bin/sh...not found Checking for program /usr/sbin/sh...not found Checking for program /sbin/sh...not found Checking for program /usr/games/sh...not found Checking for program /usr/local/games/sh...not found Checking for program /snap/bin/sh...not found Checking for program /bin/sh...found Defined make macro "SHELL" to "/bin/sh" Checking for program /home/pesun/opt/openmpi/bin/sed...not found Checking for program /home/pesun/anaconda3/bin/sed...not found Checking for program /home/pesun/anaconda3/condabin/sed...not found Checking for program /home/pesun/.local/bin/sed...not found Checking for program /usr/local/sbin/sed...not found Checking for program /usr/local/bin/sed...not found Checking for program /usr/sbin/sed...not found Checking for program /sbin/sed...not found Checking for program /usr/games/sed...not found Checking for program /usr/local/games/sed...not found Checking for program /snap/bin/sed...not found Checking for program /bin/sed...found Defined make macro "SED" to "/bin/sed" Executing: /bin/sed -i s/sed/sd/g "/tmp/petsc-xk72m0wq/config.programs/sed1" Adding SEDINPLACE cmd: /bin/sed -i Defined make macro "SEDINPLACE" to "/bin/sed -i" Checking for program /home/pesun/opt/openmpi/bin/mv...not found Checking for program /home/pesun/anaconda3/bin/mv...not found Checking for program /home/pesun/anaconda3/condabin/mv...not found Checking for program /home/pesun/.local/bin/mv...not found Checking for program /usr/local/sbin/mv...not found Checking for program /usr/local/bin/mv...not found Checking for program /usr/sbin/mv...not found Checking for program /sbin/mv...not found Checking for program /usr/games/mv...not found Checking for program /usr/local/games/mv...not found Checking for program /snap/bin/mv...not found Checking for program /bin/mv...found Defined make macro "MV" to "/bin/mv" Checking for program /home/pesun/opt/openmpi/bin/cp...not found Checking for program /home/pesun/anaconda3/bin/cp...not found Checking for program /home/pesun/anaconda3/condabin/cp...not found Checking for program /home/pesun/.local/bin/cp...not found Checking for program /usr/local/sbin/cp...not found Checking for program /usr/local/bin/cp...not found Checking for program /usr/sbin/cp...not found Checking for program /sbin/cp...not found Checking for program /usr/games/cp...not found Checking for program /usr/local/games/cp...not found Checking for program /snap/bin/cp...not found Checking for program /bin/cp...found Defined make macro "CP" to "/bin/cp" Checking for program /home/pesun/opt/openmpi/bin/grep...not found Checking for program /home/pesun/anaconda3/bin/grep...not found Checking for program /home/pesun/anaconda3/condabin/grep...not found Checking for program /home/pesun/.local/bin/grep...not found Checking for program /usr/local/sbin/grep...not found Checking for program /usr/local/bin/grep...not found Checking for program /usr/sbin/grep...not found Checking for program /sbin/grep...not found Checking for program /usr/games/grep...not found Checking for program /usr/local/games/grep...not found Checking for program /snap/bin/grep...not found Checking for program /bin/grep...found Defined make macro "GREP" to "/bin/grep" Checking for program /home/pesun/opt/openmpi/bin/rm...not found Checking for program /home/pesun/anaconda3/bin/rm...not found Checking for program /home/pesun/anaconda3/condabin/rm...not found Checking for program /home/pesun/.local/bin/rm...not found Checking for program /usr/local/sbin/rm...not found Checking for program /usr/local/bin/rm...not found Checking for program /usr/sbin/rm...not found Checking for program /sbin/rm...not found Checking for program /usr/games/rm...not found Checking for program /usr/local/games/rm...not found Checking for program /snap/bin/rm...not found Checking for program /bin/rm...found Defined make macro "RM" to "/bin/rm -f" Checking for program /home/pesun/opt/openmpi/bin/diff...not found Checking for program /home/pesun/anaconda3/bin/diff...not found Checking for program /home/pesun/anaconda3/condabin/diff...not found Checking for program /home/pesun/.local/bin/diff...not found Checking for program /usr/local/sbin/diff...not found Checking for program /usr/local/bin/diff...not found Checking for program /usr/sbin/diff...not found Checking for program /sbin/diff...not found Checking for program /usr/games/diff...not found Checking for program /usr/local/games/diff...not found Checking for program /snap/bin/diff...not found Checking for program /bin/diff...found Executing: "/bin/diff" -w "/tmp/petsc-xk72m0wq/config.programs/diff1" "/tmp/petsc-xk72m0wq/config.programs/diff2" Defined make macro "DIFF" to "/bin/diff -w" Checking for program /usr/ucb/ps...not found Checking for program /usr/usb/ps...not found Checking for program /home/pesun/.emopt/build/petsc-3.12.1/lib/petsc/bin/win32fe/ps...not found Defined make macro "PYTHON" to "/home/pesun/anaconda3/bin/python" Checking for program /home/pesun/opt/openmpi/bin/m4...not found Checking for program /home/pesun/anaconda3/bin/m4...not found Checking for program /home/pesun/anaconda3/condabin/m4...not found Checking for program /home/pesun/.local/bin/m4...not found Checking for program /usr/local/sbin/m4...not found Checking for program /usr/local/bin/m4...not found Checking for program /usr/sbin/m4...not found Checking for program /sbin/m4...not found Checking for program /usr/games/m4...not found Checking for program /usr/local/games/m4...not found Checking for program /snap/bin/m4...not found Checking for program /bin/m4...found Defined make macro "M4" to "/bin/m4" child config.programs 1.454097 ================================================================================ TEST configureMake from config.packages.make(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/make.py:87) TESTING: configureMake from config.packages.make(config/BuildSystem/config/packages/make.py:87) Check Guesses for GNU make Executing: gmake --version GNUMake check failed: Could not execute "['gmake --version']": /bin/sh: 1: gmake: not found Executing: make --version stdout: GNU Make 4.2.1 Built for x86_64-pc-linux-gnu Copyright (C) 1988-2016 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Checking for program /home/pesun/opt/openmpi/bin/make...not found Checking for program /home/pesun/anaconda3/bin/make...not found Checking for program /home/pesun/anaconda3/condabin/make...not found Checking for program /home/pesun/.local/bin/make...not found Checking for program /usr/local/sbin/make...not found Checking for program /usr/local/bin/make...not found Checking for program /usr/sbin/make...not found Checking for program /sbin/make...not found Checking for program /usr/games/make...not found Checking for program /usr/local/games/make...not found Checking for program /snap/bin/make...not found Checking for program /bin/make...found Defined make macro "MAKE" to "/bin/make" ================================================================================ TEST setupGNUMake from config.packages.make(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/make.py:121) TESTING: setupGNUMake from config.packages.make(config/BuildSystem/config/packages/make.py:121) Setup other GNU make stuff Executing: uname -s stdout: Linux Executing: uname -s stdout: Linux Defined make rule "libc" with dependencies "${LIBNAME}(${OBJSC})" and code [] Defined make rule "libcxx" with dependencies "${LIBNAME}(${OBJSCXX})" and code [] Defined make rule "libcu" with dependencies "${LIBNAME}(${OBJSCU})" and code [] Defined make rule "libf" with dependencies "${OBJSF}" and code -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} Defined make macro "OMAKE_PRINTDIR " to "/bin/make --print-directory" Defined make macro "OMAKE" to "/bin/make --no-print-directory" Defined make macro "MAKE_PAR_OUT_FLG" to "--output-sync=recurse" ================================================================================ TEST configureMakeNP from config.packages.make(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/make.py:168) TESTING: configureMakeNP from config.packages.make(config/BuildSystem/config/packages/make.py:168) check no of cores on the build machine [perhaps to do make '-j ncores'] module multiprocessing found 16 cores: using make_np = 13 Defined make macro "MAKE_NP" to "13" Defined make macro "MAKE_TEST_NP" to "8" Defined make macro "MAKE_LOAD" to "24.0" Defined make macro "NPMAX" to "16" child config.packages.make 0.010602 ================================================================================ TEST alternateConfigureLibrary from config.packages.OpenMPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.OpenMPI(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.OpenMPI 0.000229 Executing: uname -s stdout: Linux ================================================================================ TEST alternateConfigureLibrary from config.packages.MPICH(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.MPICH(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.MPICH 0.001961 ================================================================================ TEST checkDependencies from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.MPI(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:581) TESTING: configureLibrary from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:581) ================================================================================== Checking for a functional MPI Checking for library in Compiler specific search MPI: [] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [MPI_Init MPI_Comm_create] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Init(); static void _check_MPI_Init() { MPI_Init(); } char MPI_Comm_create(); static void _check_MPI_Comm_create() { MPI_Comm_create(); } int main() { _check_MPI_Init(); _check_MPI_Comm_create();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl No functions to check for in library [] [] Checking for headers Compiler specific search MPI: ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['mpi.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['mpi.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkMPICHorOpenMPI from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:468) TESTING: checkMPICHorOpenMPI from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:468) Determine if MPICH_NUMVERSION or OMPI_MAJOR_VERSION exist in mpi.h Used for consistency checking of MPI installation at compile time All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.packages.MPI Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:4:25: error: ���I_MPI_VERSION��� undeclared here (not in a function); did you mean ���MPI_VERSION���? 4 | const char *mpich_ver = I_MPI_VERSION; | ^~~~~~~~~~~~~ | MPI_VERSION Source: #include "confdefs.h" #include "conffix.h" #include const char *mpich_ver = I_MPI_VERSION; int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:4:17: error: ���I_MPI_NUMVERSION��� undeclared here (not in a function); did you mean ���MPI_SUBVERSION���? 4 | int mpich_ver = I_MPI_NUMVERSION; | ^~~~~~~~~~~~~~~~ | MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = I_MPI_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:4:17: error: ���MVAPICH2_NUMVERSION��� undeclared here (not in a function); did you mean ���MPI_SUBVERSION���? 4 | int mpich_ver = MVAPICH2_NUMVERSION; | ^~~~~~~~~~~~~~~~~~~ | MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MVAPICH2_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:4:17: error: ���MPICH_NUMVERSION��� undeclared here (not in a function); did you mean ���MPI_SUBVERSION���? 4 | int mpich_ver = MPICH_NUMVERSION; | ^~~~~~~~~~~~~~~~ | MPI_SUBVERSION Source: #include "confdefs.h" #include "conffix.h" #include int mpich_ver = MPICH_NUMVERSION; int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int ompi_major = OMPI_MAJOR_VERSION; int ompi_minor = OMPI_MINOR_VERSION; int ompi_release = OMPI_RELEASE_VERSION; int main() { ; return 0; } Preprocessing source: #include "confdefs.h" #include "conffix.h" #include int ompi_major = OMPI_MAJOR_VERSION; int ompi_minor = OMPI_MINOR_VERSION; int ompi_release = OMPI_RELEASE_VERSION; Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Defined "HAVE_OMPI_MAJOR_VERSION" to "4" Defined "HAVE_OMPI_MINOR_VERSION" to "0" Defined "HAVE_OMPI_RELEASE_VERSION" to "3" Executing: uname -s stdout: Linux ================================================================================ TEST configureMPI2 from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:250) TESTING: configureMPI2 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:250) Check for functions added to the interface in MPI-2 Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int flag;if (MPI_Finalized(&flag)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_FINALIZED" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Allreduce(MPI_IN_PLACE,0, 1, MPI_INT, MPI_SUM, MPI_COMM_SELF)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_IN_PLACE" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:94: warning: initialization of ���struct ompi_datatype_t *��� from ���int��� makes pointer from integer without a cast [-Wint-conversion] 6 | int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; | ^ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:94: note: (near initialization for ���old_types[1]���) Source: #include "confdefs.h" #include "conffix.h" #include int main() { int count=2; int blocklens[2]={0,1}; MPI_Aint indices[2]={0,1}; MPI_Datatype old_types[2]={0,1}; MPI_Datatype *newtype = 0; if (MPI_Type_create_struct(count, blocklens, indices, old_types, newtype)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:1: warning: ���MPI_Comm_errhandler_fn��� is deprecated: MPI_Comm_errhandler_fn was deprecated in MPI-2.2; use MPI_Comm_errhandler_function instead [-Wdeprecated-declarations] 6 | MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); | ^~~~~~~~~~~~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm_errhandler_fn * p_err_fun = 0; MPI_Errhandler * p_errhandler = 0; if (MPI_Comm_create_errhandler(p_err_fun,p_errhandler)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Comm_set_errhandler(MPI_COMM_WORLD,MPI_ERRORS_RETURN)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { if (MPI_Reduce_local(0, 0, 0, MPI_INT, MPI_SUM));; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_REDUCE_LOCAL" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { char version[MPI_MAX_LIBRARY_VERSION_STRING];int verlen;if (MPI_Get_library_version(version,&verlen)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_GET_LIBRARY_VERSION" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int base[100]; MPI_Win win; if (MPI_Win_create(base,100,4,MPI_INFO_NULL,MPI_COMM_WORLD,&win)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_WIN_CREATE" to "1" ================================================================================ TEST configureMPI3 from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:292) TESTING: configureMPI3 from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:292) Check for functions added to the interface in MPI-3 Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm scomm; MPI_Aint size=128; int disp_unit=8,*baseptr; MPI_Win win; if (MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &scomm)); if (MPI_Win_allocate_shared(size,disp_unit,MPI_INFO_NULL,MPI_COMM_WORLD,&baseptr,&win)); if (MPI_Win_shared_query(win,0,&size,&disp_unit,&baseptr)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_PROCESS_SHARED_MEMORY" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:7:24: warning: this ���if��� clause does not guard... [-Wmisleading-indentation] 7 | if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:8:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ���if��� 8 | if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); | ^~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int send=0,recv,counts[2]={1,1},displs[2]={1,2}; MPI_Request req; if (MPI_Iscatter(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iscatterv(&send,counts,displs,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igather(&send,1,MPI_INT,&recv,1,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Igatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,0,MPI_COMM_WORLD,&req)); if (MPI_Iallgather(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Iallgatherv(&send,1,MPI_INT,&recv,counts,displs,MPI_INT,MPI_COMM_WORLD,&req)); if (MPI_Ialltoall(&send,1,MPI_INT,&recv,1,MPI_INT,MPI_COMM_WORLD,&req)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NONBLOCKING_COLLECTIVES" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Comm distcomm; MPI_Request req; if (MPI_Dist_graph_create_adjacent(MPI_COMM_WORLD,0,0,MPI_WEIGHTS_EMPTY,0,0,MPI_WEIGHTS_EMPTY,MPI_INFO_NULL,0,&distcomm)); if (MPI_Neighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm)); if (MPI_Ineighbor_alltoallv(0,0,0,MPI_INT,0,0,0,MPI_INT,distcomm,&req)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_NEIGHBORHOOD_COLLECTIVES" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:7:3: error: #error This OpenMPI is not CUDA-aware 7 | #error This OpenMPI is not CUDA-aware | ^~~~~ Source: #include "confdefs.h" #include "conffix.h" #include #include #if defined(MPIX_CUDA_AWARE_SUPPORT) && MPIX_CUDA_AWARE_SUPPORT #else #error This OpenMPI is not CUDA-aware #endif int main() { ; return 0; } ================================================================================ TEST configureMPITypes from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:335) TESTING: configureMPITypes from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:335) Checking for MPI Datatype handles Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_LONG_DOUBLE, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.MPI/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Defined "HAVE_MPI_LONG_DOUBLE" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_INT64_T, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.MPI/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Defined "HAVE_MPI_INT64_T" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int size; int ierr; MPI_Init(0,0); ierr = MPI_Type_size(MPI_C_DOUBLE_COMPLEX, &size); if(ierr || (size == 0)) exit(1); MPI_Finalize(); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.MPI/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Executing: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Defined "HAVE_MPI_C_DOUBLE_COMPLEX" to "1" ================================================================================ TEST SGIMPICheck from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:396) TESTING: SGIMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:396) Returns true if SGI MPI is used Checking for functions [MPI_SGI_barrier] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_SGI_barrier(); static void _check_MPI_SGI_barrier() { MPI_SGI_barrier(); } int main() { _check_MPI_SGI_barrier();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `MPI_SGI_barrier' collect2: error: ld returned 1 exit status SGI MPI test failure ================================================================================ TEST CxxMPICheck from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:406) TESTING: CxxMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:406) Make sure C++ can compile and link Checking for header mpi.h Checking for C++ MPI_Finalize() Checking for functions [MPI_Finalize] in library [] [] Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/config.libraries/conftest.cc Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.cc: In function ���void _check_MPI_Finalize()���: /tmp/petsc-xk72m0wq/config.libraries/conftest.cc:5:41: warning: variable ���ierr��� set but not used [-Wunused-but-set-variable] 5 | static void _check_MPI_Finalize() { int ierr; | ^~~~ Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_MPI_Finalize() { int ierr; ierr = MPI_Finalize();; } int main() { _check_MPI_Finalize();; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/config.libraries/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl ================================================================================ TEST FortranMPICheck from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:422) TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:422) Make sure fortran include [mpif.h] and library symbols are found Checking for fortran mpi_init() Checking for functions [] in library [] [] Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.F90 Successful compile: Source: program main #include "mpif.h" integer ierr call mpi_init(ierr) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Checking for mpi.mod Checking for functions [] in library [] [] Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.F90 Successful compile: Source: program main use mpi integer ierr,rank call mpi_init(ierr) call mpi_comm_rank(MPI_COMM_WORLD,rank,ierr) end Executing: mpif90 -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_F90MODULE" to "1" ================================================================================ TEST configureIO from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:444) TESTING: configureIO from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:444) Check for the functions in MPI/IO - Define HAVE_MPIIO if they are present - Some older MPI 1 implementations are missing these Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:7:1: warning: this ���if��� clause does not guard... [-Wmisleading-indentation] 7 | if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:9:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ���if��� 9 | MPI_File fh; | ^~~~~~~~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:12:1: warning: this ���if��� clause does not guard... [-Wmisleading-indentation] 12 | if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:14:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ���if��� 14 | if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:18:1: warning: this ���if��� clause does not guard... [-Wmisleading-indentation] 18 | if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:20:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ���if��� 20 | if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); | ^~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:12:5: warning: ���buf��� is used uninitialized in this function [-Wuninitialized] 12 | if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:18:5: warning: ���disp��� is used uninitialized in this function [-Wuninitialized] 18 | if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:18:5: warning: ���info��� is used uninitialized in this function [-Wuninitialized] Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Aint lb, extent; if (MPI_Type_get_extent(MPI_INT, &lb, &extent)); MPI_File fh; void *buf; MPI_Status status; if (MPI_File_write_all(fh, buf, 1, MPI_INT, &status)); if (MPI_File_read_all(fh, buf, 1, MPI_INT, &status)); MPI_Offset disp; MPI_Info info; if (MPI_File_set_view(fh, disp, MPI_INT, MPI_INT, "", info)); if (MPI_File_open(MPI_COMM_SELF, "", 0, info, &fh)); if (MPI_File_close(&fh)); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPIIO" to "1" ================================================================================ TEST findMPIInc from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:522) TESTING: findMPIInc from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:522) Find MPI include paths from "mpicc -show" and use with CUDAC_FLAGS Executing: mpicc -show stdout: gcc -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi compilers: Checking arg gcc compilers: Checking arg -I/home/pesun/opt/openmpi/include compilers: Found include option: -I/home/pesun/opt/openmpi/include Executing: nvcc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -Xcompiler -fPIC -I/home/pesun/opt/openmpi/include -Wno-deprecated-gpu-targets /tmp/petsc-xk72m0wq/config.setCompilers/conftest.cu Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Added CUDA compiler flag -I/home/pesun/opt/openmpi/include compilers: Checking arg -pthread compilers: Checking arg -Wl,-rpath compilers: Checking arg -Wl,/home/pesun/opt/openmpi/lib compilers: Checking arg -Wl,--enable-new-dtags compilers: Checking arg -L/home/pesun/opt/openmpi/lib compilers: Checking arg -lmpi ================================================================================ TEST PetscArchMPICheck from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:556) TESTING: PetscArchMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:556) ================================================================================ TEST configureMPIEXEC from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MPI.py:174) TESTING: configureMPIEXEC from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:174) Checking for location of mpiexec Checking for program /home/pesun/opt/openmpi/bin/mpiexec...found Executing: mpiexec -help all stdout: mpiexec (OpenRTE) 4.0.3 Usage: mpiexec [OPTION]... [PROGRAM]... Start the given program using Open RTE -allow-run-as-root|--allow-run-as-root Allow execution as root (STRONGLY DISCOURAGED) -am Aggregate MCA parameter set file list --app Provide an appfile; ignore all other command line options --bind-to Policy for binding processes. Allowed values: none, hwthread, core, l1cache, l2cache, l3cache, socket, numa, board, cpu-list ("none" is the default when oversubscribed, "core" is the default when np<=2, and "socket" is the default when np>2). Allowed qualifiers: overload-allowed, if-supported, ordered -bind-to-core|--bind-to-core Bind processes to cores -bind-to-socket|--bind-to-socket Bind processes to sockets -bycore|--bycore Whether to map and rank processes round-robin by core -bynode|--bynode Whether to map and rank processes round-robin by node -byslot|--byslot Whether to map and rank processes round-robin by slot -c|-np|--np Number of processes to run -cf|--cartofile Provide a cartography file -continuous|--continuous Job is to run until explicitly terminated -cpu-list|--cpu-list List of processor IDs to bind processes to [default=NULL] -cpu-set|--cpu-set Comma-separated list of ranges specifying logical cpus allocated to this job [default: none] -cpus-per-proc|--cpus-per-proc Number of cpus to use for each process [default=1] -cpus-per-rank|--cpus-per-rank Synonym for cpus-per-proc -d|-debug-devel|--debug-devel Enable debugging of OpenRTE -debug|--debug Invoke the user-level debugger indicated by the orte_base_user_debugger MCA parameter -debug-daemons|--debug-daemons Enable debugging of any OpenRTE daemons used by this application -debug-daemons-file|--debug-daemons-file Enable debugging of any OpenRTE daemons used by this application, storing output in files -debugger|--debugger Sequence of debuggers to search for when "--debug" is used -default-hostfile|--default-hostfile Provide a default hostfile -disable-recovery|--disable-recovery Disable recovery (resets all recovery options to off) -display-allocation|--display-allocation Display the allocation being used by this job -display-devel-allocation|--display-devel-allocation Display a detailed list (mostly intended for developers) of the allocation being used by this job -display-devel-map|--display-devel-map Display a detailed process map (mostly intended for developers) just before launch -display-diffable-map|--display-diffable-map Display a diffable process map (mostly intended for developers) just before launch -display-map|--display-map Display the process map just before launch -display-topo|--display-topo Display the topology as part of the process map (mostly intended for developers) just before launch -do-not-launch|--do-not-launch Perform all necessary operations to prepare to launch the application, but do not actually launch it -do-not-resolve|--do-not-resolve Do not attempt to resolve interfaces -dvm|--dvm Create a persistent distributed virtual machine (DVM) -enable-instant-on-support|--enable-instant-on-support Enable PMIx-based instant on launch support (experimental) -enable-recovery|--enable-recovery Enable recovery from process failure [Default = disabled] -fwd-mpirun-port|--fwd-mpirun-port Forward mpirun port to compute node daemons so all will use it -get-stack-traces|--get-stack-traces Get stack traces of all application procs on timeout -gmca|--gmca Pass global MCA parameters that are applicable to all contexts (arg0 is the parameter name; arg1 is the parameter value) -h|--help This help message -H|-host|--host List of hosts to invoke processes on -hnp|--hnp Specify the URI of the HNP, or the name of the file (specified as file:filename) that contains that info -hostfile|--hostfile Provide a hostfile -index-argv-by-rank|--index-argv-by-rank Uniquely index argv[0] for each process using its rank -launch-agent|--launch-agent Command used to start processes on remote nodes (default: orted) -leave-session-attached|--leave-session-attached Enable debugging of OpenRTE -machinefile|--machinefile Provide a hostfile --map-by Mapping Policy [slot | hwthread | core | socket (default) | numa | board | node] -max-restarts|--max-restarts Max number of times to restart a failed process -max-vm-size|--max-vm-size Number of processes to run -mca|--mca Pass context-specific MCA parameters; they are considered global if --gmca is not used and only one context is specified (arg0 is the parameter name; arg1 is the parameter value) -merge-stderr-to-stdout|--merge-stderr-to-stdout Merge stderr to stdout for each process -N Launch n processes per node on all allocated nodes (synonym for 'map-by node') -n|--n Number of processes to run -nolocal|--nolocal Do not run any MPI applications on the local node -nooversubscribe|--nooversubscribe Nodes are not to be oversubscribed, even if the system supports such operation --noprefix Disable automatic --prefix behavior -novm|--novm Execute without creating an allocation-spanning virtual machine (only start daemons on nodes hosting application procs) -npernode|--npernode Launch n processes per node on all allocated nodes -npersocket|--npersocket Launch n processes per socket on all allocated nodes -ompi-server|--ompi-server Specify the URI of the publish/lookup server, or the name of the file (specified as file:filename) that contains that info -output-filename|--output-filename Redirect output from application processes into filename/job/rank/std[out,err,diag]. A relative path value will be converted to an absolute path -output-proctable|--output-proctable Output the debugger proctable after launch -oversubscribe|--oversubscribe Nodes are allowed to be oversubscribed, even on a managed system, and overloading of processing elements -path|--path PATH to be used to look for executables to start processes -pernode|--pernode Launch one process per available node -personality|--personality Comma-separated list of programming model, languages, and containers being used (default="ompi") --ppr Comma-separated list of number of processes on a given resource type [default: none] --prefix Prefix where Open MPI is installed on remote nodes --preload-files Preload the comma separated list of files to the remote machines current working directory before starting the remote process. -q|--quiet Suppress helpful messages --rank-by Ranking Policy [slot (default) | hwthread | core | socket | numa | board | node] -report-bindings|--report-bindings Whether to report process bindings to stderr -report-child-jobs-separately|--report-child-jobs-separately Return the exit status of the primary job only -report-events|--report-events Report events to a tool listening at the specified URI -report-pid|--report-pid Printout pid on stdout [-], stderr [+], or a file [anything else] -report-state-on-timeout|--report-state-on-timeout Report all job and process states upon timeout -report-uri|--report-uri Printout URI on stdout [-], stderr [+], or a file [anything else] -rf|--rankfile Provide a rankfile file -s|--preload-binary Preload the binary on the remote machine before starting the remote process. -set-cwd-to-session-dir|--set-cwd-to-session-dir Set the working directory of the started processes to their session directory -show-progress|--show-progress Output a brief periodic report on launch progress -stdin|--stdin Specify procs to receive stdin [rank, all, none] (default: 0, indicating rank 0) -tag-output|--tag-output Tag all output with [job,rank] -timeout|--timeout Timeout the job after the specified number of seconds -timestamp-output|--timestamp-output Timestamp all application process output -tune Application profile options file list -tv|--tv Deprecated backwards compatibility flag; synonym for "--debug" -use-hwthread-cpus|--use-hwthread-cpus Use hardware threads as independent cpus -use-regexp|--use-regexp Use regular expressions for launch -v|--verbose Be verbose -V|--version Print version and exit -wd|--wd Synonym for --wdir -wdir|--wdir Set the working directory of the started processes -x Export an environment variable, optionally specifying a value (e.g., "-x foo" exports the environment variable foo and takes its value from the current environment; "-x foo=bar" exports the environment variable name foo and sets its value to "bar" in the started processes) -xml|--xml Provide all output in XML format -xml-file|--xml-file Provide all output in XML format to the specified file -xterm|--xterm Create a new xterm window and display output from the specified ranks there For additional mpirun arguments, run 'mpirun --help ' The following categories exist: general (Defaults to this option), debug, output, input, mapping, ranking, binding, devel (arguments useful to OMPI Developers), compatibility (arguments supported for backwards compatibility), launch (arguments to modify launch options), and dvm (Distributed Virtual Machine arguments). Report bugs to http://www.open-mpi.org/community/help/ Executing: mpiexec --oversubscribe -n 1 printenv stdout: OMPI_MCA_rmaps_base_oversubscribe=1 OMPI_MCA_pmix=^s1,s2,cray,isolated PMIX_MCA_mca_base_component_show_load_errors=1 OMPI_COMMAND=printenv OMPI_MCA_orte_precondition_transports=292330298efddf25-9f33019ee5ce121d GJS_DEBUG_TOPICS=JS ERROR;JS LOG LESSOPEN=| /usr/bin/lesspipe %s CONDA_PROMPT_MODIFIER=(base) USER=pesun SSH_AGENT_PID=2333 XDG_SESSION_TYPE=x11 SHLVL=1 LD_LIBRARY_PATH=/home/pesun/opt/openmpi/lib:/usr/local/cuda-11.7/lib64 HOME=/home/pesun CONDA_SHLVL=1 OLDPWD=/home/pesun/.emopt/build DESKTOP_SESSION=ubuntu MODULEPATH_modshare=/etc/environment-modules/modules:1:/usr/share/modules/$MODULE_VERSION/modulefiles:1:/usr/share/modules/modulefiles:1:/usr/share/modules/versions:1 GNOME_SHELL_SESSION_MODE=ubuntu GTK_MODULES=gail:atk-bridge MODULES_CMD=/usr/lib/x86_64-linux-gnu/modulecmd.tcl MANAGERPID=2113 ENV=/usr/share/modules/init/profile.sh DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus COLORTERM=truecolor _CE_M= LOGNAME=pesun JOURNAL_STREAM=8:59561 _=./configure XDG_SESSION_CLASS=user USERNAME=pesun TERM=xterm-256color COLUMNS=193 GNOME_DESKTOP_SESSION_ID=this-is-deprecated _CE_CONDA= WINDOWPATH=2 PATH=/home/pesun/opt/openmpi/bin:/home/pesun/anaconda3/bin:/home/pesun/anaconda3/condabin:/home/pesun/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/sbin:/usr/games:/usr/local/games:/snap/bin:/bin:/usr/bin:/usr/local/cuda-11.7/bin SESSION_MANAGER=local/pesun-lt:@/tmp/.ICE-unix/2371,unix/pesun-lt:/tmp/.ICE-unix/2371 INVOCATION_ID=69b50ac7d3174bc4809e341dcc2ce7b3 XDG_MENU_PREFIX=gnome- GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/cca09c68_5015_4ae3_92ac_2f21a3c06d65 XDG_RUNTIME_DIR=/run/user/1000 DISPLAY=:1 LANG=en_US.UTF-8 XDG_CURRENT_DESKTOP=ubuntu:GNOME XMODIFIERS=@im=ibus XDG_SESSION_DESKTOP=ubuntu XAUTHORITY=/run/user/1000/gdm/Xauthority LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: GNOME_TERMINAL_SERVICE=:1.107 SSH_AUTH_SOCK=/run/user/1000/keyring/ssh CONDA_PYTHON_EXE=/home/pesun/anaconda3/bin/python SHELL=/bin/bash QT_ACCESSIBILITY=1 GDMSESSION=ubuntu LESSCLOSE=/usr/bin/lesspipe %s %s CONDA_DEFAULT_ENV=base GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1 GJS_DEBUG_OUTPUT=stderr BASH_ENV=/usr/share/modules/init/bash QT_IM_MODULE=ibus PWD=/home/pesun/.emopt/build/petsc-3.12.1 LOADEDMODULES= XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg CONDA_EXE=/home/pesun/anaconda3/bin/conda XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop OMP_NUM_THREADS=1 LINES=27 CONDA_PREFIX=/home/pesun/anaconda3 MANPATH=: VTE_VERSION=6003 MODULEPATH=/etc/environment-modules/modules:/usr/share/modules/versions:/usr/share/modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles MODULESHOME=/usr/share/modules IPATH_NO_BACKTRACE=1 HFI_NO_BACKTRACE=1 OMPI_MCA_orte_local_daemon_uri=2453012480.0;tcp://192.168.0.150,172.17.0.1,192.168.0.144:55171 OMPI_MCA_orte_hnp_uri=2453012480.0;tcp://192.168.0.150,172.17.0.1,192.168.0.144:55171 OMPI_MCA_mpi_oversubscribe=0 OMPI_MCA_orte_app_num=0 OMPI_UNIVERSE_SIZE=8 OMPI_MCA_orte_num_nodes=1 OMPI_MCA_shmem_RUNTIME_QUERY_hint=mmap OMPI_MCA_orte_bound_at_launch=1 OMPI_MCA_ess=^singleton OMPI_MCA_orte_ess_num_procs=1 OMPI_COMM_WORLD_SIZE=1 OMPI_COMM_WORLD_LOCAL_SIZE=1 OMPI_MCA_orte_tmpdir_base=/tmp OMPI_MCA_orte_top_session_dir=/tmp/ompi.pesun-lt.1000 OMPI_MCA_orte_jobfam_session_dir=/tmp/ompi.pesun-lt.1000/pid.46529 OMPI_NUM_APP_CTX=1 OMPI_FIRST_RANKS=0 OMPI_APP_CTX_NUM_PROCS=1 OMPI_MCA_initial_wdir=/home/pesun/.emopt/build/petsc-3.12.1 OMPI_MCA_orte_launch=1 PMIX_NAMESPACE=2453012481 PMIX_RANK=0 PMIX_SERVER_URI3=2453012480.0;tcp4://127.0.0.1:39377 PMIX_SERVER_URI2=2453012480.0;tcp4://127.0.0.1:39377 PMIX_SERVER_URI21=2453012480.0;tcp4://127.0.0.1:39377 PMIX_SECURITY_MODE=native PMIX_PTL_MODULE=tcp,usock PMIX_BFROP_BUFFER_TYPE=PMIX_BFROP_BUFFER_NON_DESC PMIX_GDS_MODULE=ds21,ds12,hash PMIX_SERVER_TMPDIR=/tmp/ompi.pesun-lt.1000/pid.46529 PMIX_SYSTEM_TMPDIR=/tmp PMIX_DSTORE_21_BASE_PATH=/tmp/ompi.pesun-lt.1000/pid.46529/pmix_dstor_ds21_46529 PMIX_DSTORE_ESH_BASE_PATH=/tmp/ompi.pesun-lt.1000/pid.46529/pmix_dstor_ds12_46529 PMIX_HOSTNAME=pesun-lt PMIX_VERSION=3.1.5 OMPI_MCA_ess_base_jobid=2453012481 OMPI_MCA_ess_base_vpid=0 OMPI_COMM_WORLD_RANK=0 OMPI_COMM_WORLD_LOCAL_RANK=0 OMPI_COMM_WORLD_NODE_RANK=0 OMPI_MCA_orte_ess_node_rank=0 PMIX_ID=2453012481.0 OMPI_FILE_LOCATION=/tmp/ompi.pesun-lt.1000/pid.46529/0/0 Defined "HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE" to "OMP" Defined make macro "MPIEXEC" to "mpiexec --oversubscribe" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { MPI_Init(0,0); MPI_Finalize(); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.MPI/conftest to see if it can be run Executing: mpiexec --oversubscribe -n 1 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Executing: mpiexec --oversubscribe -n 1 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest Checking for functions [MPI_Type_get_envelope MPI_Type_dup MPI_Init_thread MPI_Iallreduce MPI_Ibarrier MPI_Finalized MPI_Exscan MPI_Reduce_scatter MPI_Reduce_scatter_block] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPI_Type_get_envelope(); static void _check_MPI_Type_get_envelope() { MPI_Type_get_envelope(); } char MPI_Type_dup(); static void _check_MPI_Type_dup() { MPI_Type_dup(); } char MPI_Init_thread(); static void _check_MPI_Init_thread() { MPI_Init_thread(); } char MPI_Iallreduce(); static void _check_MPI_Iallreduce() { MPI_Iallreduce(); } char MPI_Ibarrier(); static void _check_MPI_Ibarrier() { MPI_Ibarrier(); } char MPI_Finalized(); static void _check_MPI_Finalized() { MPI_Finalized(); } char MPI_Exscan(); static void _check_MPI_Exscan() { MPI_Exscan(); } char MPI_Reduce_scatter(); static void _check_MPI_Reduce_scatter() { MPI_Reduce_scatter(); } char MPI_Reduce_scatter_block(); static void _check_MPI_Reduce_scatter_block() { MPI_Reduce_scatter_block(); } int main() { _check_MPI_Type_get_envelope(); _check_MPI_Type_dup(); _check_MPI_Init_thread(); _check_MPI_Iallreduce(); _check_MPI_Ibarrier(); _check_MPI_Finalized(); _check_MPI_Exscan(); _check_MPI_Reduce_scatter(); _check_MPI_Reduce_scatter_block();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_MPI_TYPE_GET_ENVELOPE" to "1" Defined "HAVE_MPI_TYPE_DUP" to "1" Defined "HAVE_MPI_INIT_THREAD" to "1" Defined "HAVE_MPI_IALLREDUCE" to "1" Defined "HAVE_MPI_IBARRIER" to "1" Defined "HAVE_MPI_FINALIZED" to "1" Defined "HAVE_MPI_EXSCAN" to "1" Defined "HAVE_MPI_REDUCE_SCATTER" to "1" Defined "HAVE_MPI_REDUCE_SCATTER_BLOCK" to "1" Checking for functions [MPIX_Iallreduce] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Iallreduce(); static void _check_MPIX_Iallreduce() { MPIX_Iallreduce(); } int main() { _check_MPIX_Iallreduce();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `MPIX_Iallreduce' collect2: error: ld returned 1 exit status Checking for functions [MPIX_Ibarrier] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char MPIX_Ibarrier(); static void _check_MPIX_Ibarrier() { MPIX_Ibarrier(); } int main() { _check_MPIX_Ibarrier();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `MPIX_Ibarrier' collect2: error: ld returned 1 exit status Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:5: warning: unused variable ���combiner��� [-Wunused-variable] 6 | int combiner = MPI_COMBINER_DUP;; | ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_DUP;; return 0; } Defined "HAVE_MPI_COMBINER_DUP" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:5: warning: unused variable ���combiner��� [-Wunused-variable] 6 | int combiner = MPI_COMBINER_CONTIGUOUS;; | ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_CONTIGUOUS;; return 0; } Defined "HAVE_MPI_COMBINER_CONTIGUOUS" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c:6:5: warning: unused variable ���combiner��� [-Wunused-variable] 6 | int combiner = MPI_COMBINER_NAMED;; | ^~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int combiner = MPI_COMBINER_NAMED;; return 0; } Defined "HAVE_MPI_COMBINER_NAMED" to "1" ================================================================================ TEST checkVersion from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.MPI(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "mpi.h" version=MPI_VERSION Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI /tmp/petsc-xk72m0wq/config.packages.MPI/conftest.c For mpi need 2 <= 3 <= ================================================================================ TEST checkSharedLibrary from config.packages.MPI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.MPI(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.MPI 7.161326 ================================================================================ TEST alternateConfigureLibrary from config.packages.yaml(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.yaml(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.yaml 0.001071 ================================================================================ TEST configureLibrary from config.packages.valgrind(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:854) TESTING: configureLibrary from config.packages.valgrind(config/BuildSystem/config/package.py:854) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional valgrind Not checking for library in Compiler specific search VALGRIND: [] because no functions given to check for ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] No functions to check for in library [] [] Checking for headers Compiler specific search VALGRIND: ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~compilation terminated.: Not checking for library in Package specific search directory VALGRIND: [] because no functions given to check for ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] No functions to check for in library [] [] Checking for headers Package specific search directory VALGRIND: ['/usr/local/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['valgrind/valgrind.h'] in ['/usr/local/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/usr/local/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/usr/local/include -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Possible ERROR while running preprocessor: exit code 1 stdout: # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.headers/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.headers/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.headers/conftest.c" 2 stderr: /tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. : Preprocess stderr after filtering:/tmp/petsc-xk72m0wq/config.headers/conftest.c:3:10: fatal error: valgrind/valgrind.h: No such file or directory 3 | #include | ^~~~~~~~~~~~~~~~~~~~~compilation terminated.: VALGRIND: DirPath not found.. skipping: /usr/local/lib64 VALGRIND: SearchDir DirPath not found.. skipping: /opt/local Executing: uname -s stdout: Linux =============================================================================== It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure =============================================================================== child config.packages.valgrind 0.039090 ================================================================================ TEST alternateConfigureLibrary from config.packages.ssl(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ssl(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ssl 0.001155 ================================================================================ TEST alternateConfigureLibrary from config.packages.sprng(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.sprng(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.sprng 0.001013 Not a clone of PETSc or no Fortran compiler or fortran-bindings disabled, don't need Sowing child config.packages.sowing 0.000452 ================================================================================ TEST alternateConfigureLibrary from config.packages.revolve(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.revolve(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.revolve 0.001076 ================================================================================ TEST alternateConfigureLibrary from config.packages.radau5(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.radau5(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.radau5 0.000961 ================================================================================ TEST alternateConfigureLibrary from config.packages.pami(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.pami(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.pami 0.000526 ================================================================================ TEST alternateConfigureLibrary from config.packages.opengles(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.opengles(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.opengles 0.000448 ================================================================================ TEST alternateConfigureLibrary from config.packages.opencl(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.opencl(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.opencl 0.000450 ================================================================================ TEST alternateConfigureLibrary from config.packages.muparser(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.muparser(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.muparser 0.000574 Defined "PYTHON_EXE" to ""/home/pesun/anaconda3/bin/python"" Executing: /home/pesun/anaconda3/bin/python -c "import Cython" Executing: /home/pesun/anaconda3/bin/python -c "import numpy" child config.packages.python 0.082286 ================================================================================ TEST alternateConfigureLibrary from config.packages.petsc4py(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/petsc4py.py:97) TESTING: alternateConfigureLibrary from config.packages.petsc4py(config/BuildSystem/config/packages/petsc4py.py:97) Defined make rule "petsc4py-build" with dependencies "" and code [] Defined make rule "petsc4py-install" with dependencies "" and code [] child config.packages.petsc4py 0.000695 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpi4py(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/mpi4py.py:74) TESTING: alternateConfigureLibrary from config.packages.mpi4py(config/BuildSystem/config/packages/mpi4py.py:74) Defined make rule "mpi4py-build" with dependencies "" and code [] Defined make rule "mpi4py-install" with dependencies "" and code [] child config.packages.mpi4py 0.000356 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpe(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.mpe(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.mpe 0.000228 ================================================================================ TEST alternateConfigureLibrary from config.packages.memkind(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.memkind(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.memkind 0.000201 ================================================================================ TEST alternateConfigureLibrary from config.packages.libmesh(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/libmesh.py:76) TESTING: alternateConfigureLibrary from config.packages.libmesh(config/BuildSystem/config/packages/libmesh.py:76) Defined make rule "libmesh-build" with dependencies "" and code [] Defined make rule "libmesh-install" with dependencies "" and code [] child config.packages.libmesh 0.000374 ================================================================================ TEST alternateConfigureLibrary from config.packages.moose(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.moose(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.moose 0.000233 ================================================================================ TEST alternateConfigureLibrary from config.packages.libjpeg(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.libjpeg(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.libjpeg 0.000230 ================================================================================ TEST alternateConfigureLibrary from config.packages.libceed(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.libceed(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.libceed 0.000238 Not a clone of PETSc, don't need Lgrind child config.packages.lgrind 0.000082 ================================================================================ TEST alternateConfigureLibrary from config.packages.slepc(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/slepc.py:88) TESTING: alternateConfigureLibrary from config.packages.slepc(config/BuildSystem/config/packages/slepc.py:88) Defined make rule "slepc-build" with dependencies "" and code [] Defined make rule "slepc-install" with dependencies "" and code [] child config.packages.slepc 0.000366 ================================================================================ TEST alternateConfigureLibrary from config.packages.gmp(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.gmp(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.gmp 0.000234 ================================================================================ TEST alternateConfigureLibrary from config.packages.mpfr(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.mpfr(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.mpfr 0.000234 ================================================================================ TEST alternateConfigureLibrary from config.packages.giflib(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.giflib 0.000207 ================================================================================ TEST alternateConfigureLibrary from config.packages.cuda(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.cuda(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.cuda 0.000182 ================================================================================ TEST alternateConfigureLibrary from config.packages.ctetgen(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ctetgen(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ctetgen 0.000208 ================================================================================ TEST alternateConfigureLibrary from config.packages.concurrencykit(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.concurrencykit(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.concurrencykit 0.000211 ================================================================================ TEST locateC2html from config.packages.c2html(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/c2html.py:33) TESTING: locateC2html from config.packages.c2html(config/BuildSystem/config/packages/c2html.py:33) Looking for default C2html executable Checking for program /home/pesun/opt/openmpi/bin/c2html...not found Checking for program /home/pesun/anaconda3/bin/c2html...not found Checking for program /home/pesun/anaconda3/condabin/c2html...not found Checking for program /home/pesun/.local/bin/c2html...not found Checking for program /usr/local/sbin/c2html...not found Checking for program /usr/local/bin/c2html...not found Checking for program /usr/sbin/c2html...not found Checking for program /sbin/c2html...not found Checking for program /usr/games/c2html...not found Checking for program /usr/local/games/c2html...not found Checking for program /snap/bin/c2html...not found Checking for program /bin/c2html...not found Checking for program /usr/bin/c2html...not found Checking for program /usr/local/cuda-11.7/bin/c2html...not found Checking for program /home/pesun/.emopt/build/petsc-3.12.1/lib/petsc/bin/win32fe/c2html...not found child config.packages.c2html 0.000302 ================================================================================ TEST alternateConfigureLibrary from config.packages.boost(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.boost(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.boost 0.000216 ================================================================================ TEST alternateConfigureLibrary from config.packages.silo(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.silo(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.silo 0.000236 ================================================================================ TEST alternateConfigureLibrary from config.packages.Random123(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Random123(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Random123 0.000217 ================================================================================ TEST alternateConfigureLibrary from config.packages.PARTY(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.PARTY(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.PARTY 0.000215 ================================================================================ TEST alternateConfigureLibrary from config.packages.Matlab(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Matlab(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Matlab 0.000179 ================================================================================ TEST alternateConfigureLibrary from config.packages.MatlabEngine(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.MatlabEngine(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.MatlabEngine 0.000187 ================================================================================ TEST alternateConfigureLibrary from config.packages.Mathematica(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Mathematica(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Mathematica 0.000188 child config.packages.cxxlibs 0.000008 ================================================================================ TEST alternateConfigureLibrary from config.packages.opengl(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.opengl(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.opengl 0.000190 ================================================================================ TEST alternateConfigureLibrary from config.packages.glut(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.glut 0.000190 ================================================================================ TEST checkDependencies from config.packages.X(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.X(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.X(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:854) TESTING: configureLibrary from config.packages.X(config/BuildSystem/config/package.py:854) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional X Checking for library in Compiler specific search X: [] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [XSetWMName] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char XSetWMName(); static void _check_XSetWMName() { XSetWMName(); } int main() { _check_XSetWMName();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl Possible ERROR while running linker: exit code 1 stderr: /bin/ld: /tmp/petsc-xk72m0wq/config.libraries/conftest.o: in function `main': conftest.c:(.text.startup+0xb): undefined reference to `XSetWMName' collect2: error: ld returned 1 exit status Checking for library in Compiler specific search X: ['libX11.a'] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [XSetWMName] in library ['libX11.a'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char XSetWMName(); static void _check_XSetWMName() { XSetWMName(); } int main() { _check_XSetWMName();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lX11 -lquadmath -lstdc++ -ldl Defined "HAVE_LIBX11" to "1" No functions to check for in library ['libX11.a'] [] Checking for headers Compiler specific search X: ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['X11/Xlib.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['X11/Xlib.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.X(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.X(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.X(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.X(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.X 0.105397 ================================================================================ TEST alternateConfigureLibrary from config.packages.GLVis(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.GLVis(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.GLVis 0.000764 ================================================================================ TEST alternateConfigureLibrary from config.packages.CoDiPack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.CoDiPack(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.CoDiPack 0.000427 ================================================================================ TEST alternateConfigureLibrary from config.packages.adblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.adblaslapack(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.adblaslapack 0.000435 ================================================================================ TEST alternateConfigureLibrary from config.packages.ADOLC(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ADOLC(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ADOLC 0.000437 ================================================================================ TEST locateCMake from config.packages.cmake(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/cmake.py:39) TESTING: locateCMake from config.packages.cmake(config/BuildSystem/config/packages/cmake.py:39) Looking for default CMake executable Checking for program /home/pesun/opt/openmpi/bin/cmake...not found Checking for program /home/pesun/anaconda3/bin/cmake...not found Checking for program /home/pesun/anaconda3/condabin/cmake...not found Checking for program /home/pesun/.local/bin/cmake...not found Checking for program /usr/local/sbin/cmake...not found Checking for program /usr/local/bin/cmake...not found Checking for program /usr/sbin/cmake...not found Checking for program /sbin/cmake...not found Checking for program /usr/games/cmake...not found Checking for program /usr/local/games/cmake...not found Checking for program /snap/bin/cmake...not found Checking for program /bin/cmake...not found Checking for program /usr/bin/cmake...not found Checking for program /usr/local/cuda-11.7/bin/cmake...not found Checking for program /home/pesun/.emopt/build/petsc-3.12.1/lib/petsc/bin/win32fe/cmake...not found Looking for default CTest executable Checking for program /home/pesun/opt/openmpi/bin/ctest...not found Checking for program /home/pesun/anaconda3/bin/ctest...not found Checking for program /home/pesun/anaconda3/condabin/ctest...not found Checking for program /home/pesun/.local/bin/ctest...not found Checking for program /usr/local/sbin/ctest...not found Checking for program /usr/local/bin/ctest...not found Checking for program /usr/sbin/ctest...not found Checking for program /sbin/ctest...not found Checking for program /usr/games/ctest...not found Checking for program /usr/local/games/ctest...not found Checking for program /snap/bin/ctest...not found Checking for program /bin/ctest...not found Checking for program /usr/bin/ctest...not found Checking for program /usr/local/cuda-11.7/bin/ctest...not found Checking for program /home/pesun/.emopt/build/petsc-3.12.1/lib/petsc/bin/win32fe/ctest...not found cmake not found child config.packages.cmake 0.000926 ================================================================================ TEST alternateConfigureLibrary from config.packages.googletest(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.googletest(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.googletest 0.000679 ================================================================================ TEST alternateConfigureLibrary from config.packages.unittestcpp(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.unittestcpp(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.unittestcpp 0.000920 ================================================================================ TEST alternateConfigureLibrary from config.packages.eigen(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.eigen(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.eigen 0.000844 ================================================================================ TEST alternateConfigureLibrary from config.packages.szlib(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.szlib(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.szlib 0.000566 ================================================================================ TEST alternateConfigureLibrary from config.packages.zlib(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.zlib(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.zlib 0.000638 child config.packages.mathlib 0.000026 ================================================================================ TEST alternateConfigureLibrary from config.packages.tetgen(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.tetgen(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.tetgen 0.000638 ================================================================================ TEST alternateConfigureLibrary from config.packages.tchem(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.tchem(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.tchem 0.000515 ================================================================================ TEST alternateConfigureLibrary from config.packages.saws(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.saws(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.saws 0.000510 ================================================================================ TEST alternateConfigureLibrary from config.packages.libpng(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.libpng(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.libpng 0.000517 ================================================================================ TEST alternateConfigureLibrary from config.packages.combblas(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.combblas(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.combblas 0.000510 ================================================================================ TEST alternateConfigureLibrary from config.packages.Triangle(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Triangle(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Triangle 0.000511 ================================================================================ TEST alternateConfigureLibrary from config.packages.metis(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.metis(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.metis 0.000510 ================================================================================ TEST alternateConfigureLibrary from config.packages.pragmatic(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.pragmatic(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.pragmatic 0.000357 ================================================================================ TEST alternateConfigureLibrary from config.packages.parmetis(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.parmetis(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.parmetis 0.000360 ================================================================================ TEST alternateConfigureLibrary from config.packages.Chaco(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Chaco(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Chaco 0.000381 ================================================================================ TEST alternateConfigureLibrary from config.packages.hdf5(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.hdf5(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.hdf5 0.000363 ================================================================================ TEST alternateConfigureLibrary from config.packages.med(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.med(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.med 0.000368 ================================================================================ TEST alternateConfigureLibrary from config.packages.cgns(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.cgns(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.cgns 0.000319 ================================================================================ TEST alternateConfigureLibrary from config.packages.ascem-io(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ascem-io(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ascem-io 0.000371 ================================================================================ TEST alternateConfigureLibrary from config.packages.pflotran(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.pflotran(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.pflotran 0.000380 ================================================================================ TEST alternateConfigureLibrary from config.packages.alquimia(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.alquimia(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.alquimia 0.000363 ================================================================================ TEST alternateConfigureLibrary from config.packages.SAMRAI(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.SAMRAI(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.SAMRAI 0.000344 ================================================================================ TEST alternateConfigureLibrary from config.packages.ADIOS2(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ADIOS2(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ADIOS2 0.000239 child config.packages.flibs 0.000006 ================================================================================ TEST alternateConfigureLibrary from config.packages.pnetcdf(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.pnetcdf(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.pnetcdf 0.000244 ================================================================================ TEST alternateConfigureLibrary from config.packages.netcdf(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.netcdf(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.netcdf 0.000237 ================================================================================ TEST alternateConfigureLibrary from config.packages.exodusii(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.exodusii(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.exodusii 0.000253 ================================================================================ TEST alternateConfigureLibrary from config.packages.hwloc(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.hwloc(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.hwloc 0.000242 ================================================================================ TEST checkDependencies from config.packages.pthread(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.pthread(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.pthread(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/pthread.py:20) TESTING: configureLibrary from config.packages.pthread(config/BuildSystem/config/packages/pthread.py:20) Checks for pthread_barrier_t, cpu_set_t, and sys/sysctl.h ================================================================================== Checking for a functional pthread Checking for library in Compiler specific search PTHREAD: [] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [pthread_create] in library [] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char pthread_create(); static void _check_pthread_create() { pthread_create(); } int main() { _check_pthread_create();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -lquadmath -lstdc++ -ldl No functions to check for in library [] [] Checking for headers Compiler specific search PTHREAD: ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['pthread.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['pthread.h'] in ['/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.packages.pthread Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c:6:20: warning: unused variable ���a��� [-Wunused-variable] 6 | pthread_barrier_t *a; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { pthread_barrier_t *a; ; return 0; } Defined "HAVE_PTHREAD_BARRIER_T" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c:6:12: warning: unused variable ���a��� [-Wunused-variable] 6 | cpu_set_t *a; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { cpu_set_t *a; ; return 0; } Defined "HAVE_SCHED_CPU_SET_T" to "1" Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c Possible ERROR while running preprocessor: stdout: # 1 "/tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c" # 1 "" # 1 "" # 31 "" # 1 "/usr/include/stdc-predef.h" 1 3 4 # 32 "" 2 # 1 "/tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c" # 1 "/tmp/petsc-xk72m0wq/config.packages.pthread/confdefs.h" 1 # 2 "/tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c" 2 # 1 "/tmp/petsc-xk72m0wq/config.packages.pthread/conffix.h" 1 # 3 "/tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c" 2 # 1 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 1 3 4 # 23 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 3 4 # 1 "/usr/include/features.h" 1 3 4 # 461 "/usr/include/features.h" 3 4 # 1 "/usr/include/x86_64-linux-gnu/sys/cdefs.h" 1 3 4 # 452 "/usr/include/x86_64-linux-gnu/sys/cdefs.h" 3 4 # 1 "/usr/include/x86_64-linux-gnu/bits/wordsize.h" 1 3 4 # 453 "/usr/include/x86_64-linux-gnu/sys/cdefs.h" 2 3 4 # 1 "/usr/include/x86_64-linux-gnu/bits/long-double.h" 1 3 4 # 454 "/usr/include/x86_64-linux-gnu/sys/cdefs.h" 2 3 4 # 462 "/usr/include/features.h" 2 3 4 # 485 "/usr/include/features.h" 3 4 # 1 "/usr/include/x86_64-linux-gnu/gnu/stubs.h" 1 3 4 # 10 "/usr/include/x86_64-linux-gnu/gnu/stubs.h" 3 4 # 1 "/usr/include/x86_64-linux-gnu/gnu/stubs-64.h" 1 3 4 # 11 "/usr/include/x86_64-linux-gnu/gnu/stubs.h" 2 3 4 # 486 "/usr/include/features.h" 2 3 4 # 24 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 2 3 4 # 1 "/usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h" 1 3 4 # 209 "/usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h" 3 4 # 209 "/usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h" 3 4 typedef long unsigned int size_t; # 26 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 2 3 4 # 45 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 3 4 # 1 "/usr/include/linux/sysctl.h" 1 3 4 # 26 "/usr/include/linux/sysctl.h" 3 4 # 1 "/usr/include/linux/const.h" 1 3 4 # 27 "/usr/include/linux/sysctl.h" 2 3 4 # 1 "/usr/include/linux/types.h" 1 3 4 # 28 "/usr/include/linux/sysctl.h" 2 3 4 struct __sysctl_args { int *name; int nlen; void *oldval; size_t *oldlenp; void *newval; size_t newlen; unsigned long __unused[4]; }; enum { CTL_KERN=1, CTL_VM=2, CTL_NET=3, CTL_PROC=4, CTL_FS=5, CTL_DEBUG=6, CTL_DEV=7, CTL_BUS=8, CTL_ABI=9, CTL_CPU=10, CTL_ARLAN=254, CTL_S390DBF=5677, CTL_SUNRPC=7249, CTL_PM=9899, CTL_FRV=9898, }; enum { CTL_BUS_ISA=1 }; enum { INOTIFY_MAX_USER_INSTANCES=1, INOTIFY_MAX_USER_WATCHES=2, INOTIFY_MAX_QUEUED_EVENTS=3 }; enum { KERN_OSTYPE=1, KERN_OSRELEASE=2, KERN_OSREV=3, KERN_VERSION=4, KERN_SECUREMASK=5, KERN_PROF=6, KERN_NODENAME=7, KERN_DOMAINNAME=8, KERN_PANIC=15, KERN_REALROOTDEV=16, KERN_SPARC_REBOOT=21, KERN_CTLALTDEL=22, KERN_PRINTK=23, KERN_NAMETRANS=24, KERN_PPC_HTABRECLAIM=25, KERN_PPC_ZEROPAGED=26, KERN_PPC_POWERSAVE_NAP=27, KERN_MODPROBE=28, KERN_SG_BIG_BUFF=29, KERN_ACCT=30, KERN_PPC_L2CR=31, KERN_RTSIGNR=32, KERN_RTSIGMAX=33, KERN_SHMMAX=34, KERN_MSGMAX=35, KERN_MSGMNB=36, KERN_MSGPOOL=37, KERN_SYSRQ=38, KERN_MAX_THREADS=39, KERN_RANDOM=40, KERN_SHMALL=41, KERN_MSGMNI=42, KERN_SEM=43, KERN_SPARC_STOP_A=44, KERN_SHMMNI=45, KERN_OVERFLOWUID=46, KERN_OVERFLOWGID=47, KERN_SHMPATH=48, KERN_HOTPLUG=49, KERN_IEEE_EMULATION_WARNINGS=50, KERN_S390_USER_DEBUG_LOGGING=51, KERN_CORE_USES_PID=52, KERN_TAINTED=53, KERN_CADPID=54, KERN_PIDMAX=55, KERN_CORE_PATTERN=56, KERN_PANIC_ON_OOPS=57, KERN_HPPA_PWRSW=58, KERN_HPPA_UNALIGNED=59, KERN_PRINTK_RATELIMIT=60, KERN_PRINTK_RATELIMIT_BURST=61, KERN_PTY=62, KERN_NGROUPS_MAX=63, KERN_SPARC_SCONS_PWROFF=64, KERN_HZ_TIMER=65, KERN_UNKNOWN_NMI_PANIC=66, KERN_BOOTLOADER_TYPE=67, KERN_RANDOMIZE=68, KERN_SETUID_DUMPABLE=69, KERN_SPIN_RETRY=70, KERN_ACPI_VIDEO_FLAGS=71, KERN_IA64_UNALIGNED=72, KERN_COMPAT_LOG=73, KERN_MAX_LOCK_DEPTH=74, KERN_NMI_WATCHDOG=75, KERN_PANIC_ON_NMI=76, KERN_PANIC_ON_WARN=77, KERN_PANIC_PRINT=78, }; enum { VM_UNUSED1=1, VM_UNUSED2=2, VM_UNUSED3=3, VM_UNUSED4=4, VM_OVERCOMMIT_MEMORY=5, VM_UNUSED5=6, VM_UNUSED7=7, VM_UNUSED8=8, VM_UNUSED9=9, VM_PAGE_CLUSTER=10, VM_DIRTY_BACKGROUND=11, VM_DIRTY_RATIO=12, VM_DIRTY_WB_CS=13, VM_DIRTY_EXPIRE_CS=14, VM_NR_PDFLUSH_THREADS=15, VM_OVERCOMMIT_RATIO=16, VM_PAGEBUF=17, VM_HUGETLB_PAGES=18, VM_SWAPPINESS=19, VM_LOWMEM_RESERVE_RATIO=20, VM_MIN_FREE_KBYTES=21, VM_MAX_MAP_COUNT=22, VM_LAPTOP_MODE=23, VM_BLOCK_DUMP=24, VM_HUGETLB_GROUP=25, VM_VFS_CACHE_PRESSURE=26, VM_LEGACY_VA_LAYOUT=27, VM_SWAP_TOKEN_TIMEOUT=28, VM_DROP_PAGECACHE=29, VM_PERCPU_PAGELIST_FRACTION=30, VM_ZONE_RECLAIM_MODE=31, VM_MIN_UNMAPPED=32, VM_PANIC_ON_OOM=33, VM_VDSO_ENABLED=34, VM_MIN_SLAB=35, }; enum { NET_CORE=1, NET_ETHER=2, NET_802=3, NET_UNIX=4, NET_IPV4=5, NET_IPX=6, NET_ATALK=7, NET_NETROM=8, NET_AX25=9, NET_BRIDGE=10, NET_ROSE=11, NET_IPV6=12, NET_X25=13, NET_TR=14, NET_DECNET=15, NET_ECONET=16, NET_SCTP=17, NET_LLC=18, NET_NETFILTER=19, NET_DCCP=20, NET_IRDA=412, }; enum { RANDOM_POOLSIZE=1, RANDOM_ENTROPY_COUNT=2, RANDOM_READ_THRESH=3, RANDOM_WRITE_THRESH=4, RANDOM_BOOT_ID=5, RANDOM_UUID=6 }; enum { PTY_MAX=1, PTY_NR=2 }; enum { BUS_ISA_MEM_BASE=1, BUS_ISA_PORT_BASE=2, BUS_ISA_PORT_SHIFT=3 }; enum { NET_CORE_WMEM_MAX=1, NET_CORE_RMEM_MAX=2, NET_CORE_WMEM_DEFAULT=3, NET_CORE_RMEM_DEFAULT=4, NET_CORE_MAX_BACKLOG=6, NET_CORE_FASTROUTE=7, NET_CORE_MSG_COST=8, NET_CORE_MSG_BURST=9, NET_CORE_OPTMEM_MAX=10, NET_CORE_HOT_LIST_LENGTH=11, NET_CORE_DIVERT_VERSION=12, NET_CORE_NO_CONG_THRESH=13, NET_CORE_NO_CONG=14, NET_CORE_LO_CONG=15, NET_CORE_MOD_CONG=16, NET_CORE_DEV_WEIGHT=17, NET_CORE_SOMAXCONN=18, NET_CORE_BUDGET=19, NET_CORE_AEVENT_ETIME=20, NET_CORE_AEVENT_RSEQTH=21, NET_CORE_WARNINGS=22, }; enum { NET_UNIX_DESTROY_DELAY=1, NET_UNIX_DELETE_DELAY=2, NET_UNIX_MAX_DGRAM_QLEN=3, }; enum { NET_NF_CONNTRACK_MAX=1, NET_NF_CONNTRACK_TCP_TIMEOUT_SYN_SENT=2, NET_NF_CONNTRACK_TCP_TIMEOUT_SYN_RECV=3, NET_NF_CONNTRACK_TCP_TIMEOUT_ESTABLISHED=4, NET_NF_CONNTRACK_TCP_TIMEOUT_FIN_WAIT=5, NET_NF_CONNTRACK_TCP_TIMEOUT_CLOSE_WAIT=6, NET_NF_CONNTRACK_TCP_TIMEOUT_LAST_ACK=7, NET_NF_CONNTRACK_TCP_TIMEOUT_TIME_WAIT=8, NET_NF_CONNTRACK_TCP_TIMEOUT_CLOSE=9, NET_NF_CONNTRACK_UDP_TIMEOUT=10, NET_NF_CONNTRACK_UDP_TIMEOUT_STREAM=11, NET_NF_CONNTRACK_ICMP_TIMEOUT=12, NET_NF_CONNTRACK_GENERIC_TIMEOUT=13, NET_NF_CONNTRACK_BUCKETS=14, NET_NF_CONNTRACK_LOG_INVALID=15, NET_NF_CONNTRACK_TCP_TIMEOUT_MAX_RETRANS=16, NET_NF_CONNTRACK_TCP_LOOSE=17, NET_NF_CONNTRACK_TCP_BE_LIBERAL=18, NET_NF_CONNTRACK_TCP_MAX_RETRANS=19, NET_NF_CONNTRACK_SCTP_TIMEOUT_CLOSED=20, NET_NF_CONNTRACK_SCTP_TIMEOUT_COOKIE_WAIT=21, NET_NF_CONNTRACK_SCTP_TIMEOUT_COOKIE_ECHOED=22, NET_NF_CONNTRACK_SCTP_TIMEOUT_ESTABLISHED=23, NET_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_SENT=24, NET_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_RECD=25, NET_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_ACK_SENT=26, NET_NF_CONNTRACK_COUNT=27, NET_NF_CONNTRACK_ICMPV6_TIMEOUT=28, NET_NF_CONNTRACK_FRAG6_TIMEOUT=29, NET_NF_CONNTRACK_FRAG6_LOW_THRESH=30, NET_NF_CONNTRACK_FRAG6_HIGH_THRESH=31, NET_NF_CONNTRACK_CHECKSUM=32, }; enum { NET_IPV4_FORWARD=8, NET_IPV4_DYNADDR=9, NET_IPV4_CONF=16, NET_IPV4_NEIGH=17, NET_IPV4_ROUTE=18, NET_IPV4_FIB_HASH=19, NET_IPV4_NETFILTER=20, NET_IPV4_TCP_TIMESTAMPS=33, NET_IPV4_TCP_WINDOW_SCALING=34, NET_IPV4_TCP_SACK=35, NET_IPV4_TCP_RETRANS_COLLAPSE=36, NET_IPV4_DEFAULT_TTL=37, NET_IPV4_AUTOCONFIG=38, NET_IPV4_NO_PMTU_DISC=39, NET_IPV4_TCP_SYN_RETRIES=40, NET_IPV4_IPFRAG_HIGH_THRESH=41, NET_IPV4_IPFRAG_LOW_THRESH=42, NET_IPV4_IPFRAG_TIME=43, NET_IPV4_TCP_MAX_KA_PROBES=44, NET_IPV4_TCP_KEEPALIVE_TIME=45, NET_IPV4_TCP_KEEPALIVE_PROBES=46, NET_IPV4_TCP_RETRIES1=47, NET_IPV4_TCP_RETRIES2=48, NET_IPV4_TCP_FIN_TIMEOUT=49, NET_IPV4_IP_MASQ_DEBUG=50, NET_TCP_SYNCOOKIES=51, NET_TCP_STDURG=52, NET_TCP_RFC1337=53, NET_TCP_SYN_TAILDROP=54, NET_TCP_MAX_SYN_BACKLOG=55, NET_IPV4_LOCAL_PORT_RANGE=56, NET_IPV4_ICMP_ECHO_IGNORE_ALL=57, NET_IPV4_ICMP_ECHO_IGNORE_BROADCASTS=58, NET_IPV4_ICMP_SOURCEQUENCH_RATE=59, NET_IPV4_ICMP_DESTUNREACH_RATE=60, NET_IPV4_ICMP_TIMEEXCEED_RATE=61, NET_IPV4_ICMP_PARAMPROB_RATE=62, NET_IPV4_ICMP_ECHOREPLY_RATE=63, NET_IPV4_ICMP_IGNORE_BOGUS_ERROR_RESPONSES=64, NET_IPV4_IGMP_MAX_MEMBERSHIPS=65, NET_TCP_TW_RECYCLE=66, NET_IPV4_ALWAYS_DEFRAG=67, NET_IPV4_TCP_KEEPALIVE_INTVL=68, NET_IPV4_INET_PEER_THRESHOLD=69, NET_IPV4_INET_PEER_MINTTL=70, NET_IPV4_INET_PEER_MAXTTL=71, NET_IPV4_INET_PEER_GC_MINTIME=72, NET_IPV4_INET_PEER_GC_MAXTIME=73, NET_TCP_ORPHAN_RETRIES=74, NET_TCP_ABORT_ON_OVERFLOW=75, NET_TCP_SYNACK_RETRIES=76, NET_TCP_MAX_ORPHANS=77, NET_TCP_MAX_TW_BUCKETS=78, NET_TCP_FACK=79, NET_TCP_REORDERING=80, NET_TCP_ECN=81, NET_TCP_DSACK=82, NET_TCP_MEM=83, NET_TCP_WMEM=84, NET_TCP_RMEM=85, NET_TCP_APP_WIN=86, NET_TCP_ADV_WIN_SCALE=87, NET_IPV4_NONLOCAL_BIND=88, NET_IPV4_ICMP_RATELIMIT=89, NET_IPV4_ICMP_RATEMASK=90, NET_TCP_TW_REUSE=91, NET_TCP_FRTO=92, NET_TCP_LOW_LATENCY=93, NET_IPV4_IPFRAG_SECRET_INTERVAL=94, NET_IPV4_IGMP_MAX_MSF=96, NET_TCP_NO_METRICS_SAVE=97, NET_TCP_DEFAULT_WIN_SCALE=105, NET_TCP_MODERATE_RCVBUF=106, NET_TCP_TSO_WIN_DIVISOR=107, NET_TCP_BIC_BETA=108, NET_IPV4_ICMP_ERRORS_USE_INBOUND_IFADDR=109, NET_TCP_CONG_CONTROL=110, NET_TCP_ABC=111, NET_IPV4_IPFRAG_MAX_DIST=112, NET_TCP_MTU_PROBING=113, NET_TCP_BASE_MSS=114, NET_IPV4_TCP_WORKAROUND_SIGNED_WINDOWS=115, NET_TCP_DMA_COPYBREAK=116, NET_TCP_SLOW_START_AFTER_IDLE=117, NET_CIPSOV4_CACHE_ENABLE=118, NET_CIPSOV4_CACHE_BUCKET_SIZE=119, NET_CIPSOV4_RBM_OPTFMT=120, NET_CIPSOV4_RBM_STRICTVALID=121, NET_TCP_AVAIL_CONG_CONTROL=122, NET_TCP_ALLOWED_CONG_CONTROL=123, NET_TCP_MAX_SSTHRESH=124, NET_TCP_FRTO_RESPONSE=125, }; enum { NET_IPV4_ROUTE_FLUSH=1, NET_IPV4_ROUTE_MIN_DELAY=2, NET_IPV4_ROUTE_MAX_DELAY=3, NET_IPV4_ROUTE_GC_THRESH=4, NET_IPV4_ROUTE_MAX_SIZE=5, NET_IPV4_ROUTE_GC_MIN_INTERVAL=6, NET_IPV4_ROUTE_GC_TIMEOUT=7, NET_IPV4_ROUTE_GC_INTERVAL=8, NET_IPV4_ROUTE_REDIRECT_LOAD=9, NET_IPV4_ROUTE_REDIRECT_NUMBER=10, NET_IPV4_ROUTE_REDIRECT_SILENCE=11, NET_IPV4_ROUTE_ERROR_COST=12, NET_IPV4_ROUTE_ERROR_BURST=13, NET_IPV4_ROUTE_GC_ELASTICITY=14, NET_IPV4_ROUTE_MTU_EXPIRES=15, NET_IPV4_ROUTE_MIN_PMTU=16, NET_IPV4_ROUTE_MIN_ADVMSS=17, NET_IPV4_ROUTE_SECRET_INTERVAL=18, NET_IPV4_ROUTE_GC_MIN_INTERVAL_MS=19, }; enum { NET_PROTO_CONF_ALL=-2, NET_PROTO_CONF_DEFAULT=-3 }; enum { NET_IPV4_CONF_FORWARDING=1, NET_IPV4_CONF_MC_FORWARDING=2, NET_IPV4_CONF_PROXY_ARP=3, NET_IPV4_CONF_ACCEPT_REDIRECTS=4, NET_IPV4_CONF_SECURE_REDIRECTS=5, NET_IPV4_CONF_SEND_REDIRECTS=6, NET_IPV4_CONF_SHARED_MEDIA=7, NET_IPV4_CONF_RP_FILTER=8, NET_IPV4_CONF_ACCEPT_SOURCE_ROUTE=9, NET_IPV4_CONF_BOOTP_RELAY=10, NET_IPV4_CONF_LOG_MARTIANS=11, NET_IPV4_CONF_TAG=12, NET_IPV4_CONF_ARPFILTER=13, NET_IPV4_CONF_MEDIUM_ID=14, NET_IPV4_CONF_NOXFRM=15, NET_IPV4_CONF_NOPOLICY=16, NET_IPV4_CONF_FORCE_IGMP_VERSION=17, NET_IPV4_CONF_ARP_ANNOUNCE=18, NET_IPV4_CONF_ARP_IGNORE=19, NET_IPV4_CONF_PROMOTE_SECONDARIES=20, NET_IPV4_CONF_ARP_ACCEPT=21, NET_IPV4_CONF_ARP_NOTIFY=22, }; enum { NET_IPV4_NF_CONNTRACK_MAX=1, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_SYN_SENT=2, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_SYN_RECV=3, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_ESTABLISHED=4, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_FIN_WAIT=5, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_CLOSE_WAIT=6, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_LAST_ACK=7, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_TIME_WAIT=8, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_CLOSE=9, NET_IPV4_NF_CONNTRACK_UDP_TIMEOUT=10, NET_IPV4_NF_CONNTRACK_UDP_TIMEOUT_STREAM=11, NET_IPV4_NF_CONNTRACK_ICMP_TIMEOUT=12, NET_IPV4_NF_CONNTRACK_GENERIC_TIMEOUT=13, NET_IPV4_NF_CONNTRACK_BUCKETS=14, NET_IPV4_NF_CONNTRACK_LOG_INVALID=15, NET_IPV4_NF_CONNTRACK_TCP_TIMEOUT_MAX_RETRANS=16, NET_IPV4_NF_CONNTRACK_TCP_LOOSE=17, NET_IPV4_NF_CONNTRACK_TCP_BE_LIBERAL=18, NET_IPV4_NF_CONNTRACK_TCP_MAX_RETRANS=19, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_CLOSED=20, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_COOKIE_WAIT=21, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_COOKIE_ECHOED=22, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_ESTABLISHED=23, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_SENT=24, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_RECD=25, NET_IPV4_NF_CONNTRACK_SCTP_TIMEOUT_SHUTDOWN_ACK_SENT=26, NET_IPV4_NF_CONNTRACK_COUNT=27, NET_IPV4_NF_CONNTRACK_CHECKSUM=28, }; enum { NET_IPV6_CONF=16, NET_IPV6_NEIGH=17, NET_IPV6_ROUTE=18, NET_IPV6_ICMP=19, NET_IPV6_BINDV6ONLY=20, NET_IPV6_IP6FRAG_HIGH_THRESH=21, NET_IPV6_IP6FRAG_LOW_THRESH=22, NET_IPV6_IP6FRAG_TIME=23, NET_IPV6_IP6FRAG_SECRET_INTERVAL=24, NET_IPV6_MLD_MAX_MSF=25, }; enum { NET_IPV6_ROUTE_FLUSH=1, NET_IPV6_ROUTE_GC_THRESH=2, NET_IPV6_ROUTE_MAX_SIZE=3, NET_IPV6_ROUTE_GC_MIN_INTERVAL=4, NET_IPV6_ROUTE_GC_TIMEOUT=5, NET_IPV6_ROUTE_GC_INTERVAL=6, NET_IPV6_ROUTE_GC_ELASTICITY=7, NET_IPV6_ROUTE_MTU_EXPIRES=8, NET_IPV6_ROUTE_MIN_ADVMSS=9, NET_IPV6_ROUTE_GC_MIN_INTERVAL_MS=10 }; enum { NET_IPV6_FORWARDING=1, NET_IPV6_HOP_LIMIT=2, NET_IPV6_MTU=3, NET_IPV6_ACCEPT_RA=4, NET_IPV6_ACCEPT_REDIRECTS=5, NET_IPV6_AUTOCONF=6, NET_IPV6_DAD_TRANSMITS=7, NET_IPV6_RTR_SOLICITS=8, NET_IPV6_RTR_SOLICIT_INTERVAL=9, NET_IPV6_RTR_SOLICIT_DELAY=10, NET_IPV6_USE_TEMPADDR=11, NET_IPV6_TEMP_VALID_LFT=12, NET_IPV6_TEMP_PREFERED_LFT=13, NET_IPV6_REGEN_MAX_RETRY=14, NET_IPV6_MAX_DESYNC_FACTOR=15, NET_IPV6_MAX_ADDRESSES=16, NET_IPV6_FORCE_MLD_VERSION=17, NET_IPV6_ACCEPT_RA_DEFRTR=18, NET_IPV6_ACCEPT_RA_PINFO=19, NET_IPV6_ACCEPT_RA_RTR_PREF=20, NET_IPV6_RTR_PROBE_INTERVAL=21, NET_IPV6_ACCEPT_RA_RT_INFO_MAX_PLEN=22, NET_IPV6_PROXY_NDP=23, NET_IPV6_ACCEPT_SOURCE_ROUTE=25, NET_IPV6_ACCEPT_RA_FROM_LOCAL=26, NET_IPV6_ACCEPT_RA_RT_INFO_MIN_PLEN=27, __NET_IPV6_MAX }; enum { NET_IPV6_ICMP_RATELIMIT = 1, NET_IPV6_ICMP_ECHO_IGNORE_ALL = 2 }; enum { NET_NEIGH_MCAST_SOLICIT=1, NET_NEIGH_UCAST_SOLICIT=2, NET_NEIGH_APP_SOLICIT=3, NET_NEIGH_RETRANS_TIME=4, NET_NEIGH_REACHABLE_TIME=5, NET_NEIGH_DELAY_PROBE_TIME=6, NET_NEIGH_GC_STALE_TIME=7, NET_NEIGH_UNRES_QLEN=8, NET_NEIGH_PROXY_QLEN=9, NET_NEIGH_ANYCAST_DELAY=10, NET_NEIGH_PROXY_DELAY=11, NET_NEIGH_LOCKTIME=12, NET_NEIGH_GC_INTERVAL=13, NET_NEIGH_GC_THRESH1=14, NET_NEIGH_GC_THRESH2=15, NET_NEIGH_GC_THRESH3=16, NET_NEIGH_RETRANS_TIME_MS=17, NET_NEIGH_REACHABLE_TIME_MS=18, }; enum { NET_DCCP_DEFAULT=1, }; enum { NET_IPX_PPROP_BROADCASTING=1, NET_IPX_FORWARDING=2 }; enum { NET_LLC2=1, NET_LLC_STATION=2, }; enum { NET_LLC2_TIMEOUT=1, }; enum { NET_LLC_STATION_ACK_TIMEOUT=1, }; enum { NET_LLC2_ACK_TIMEOUT=1, NET_LLC2_P_TIMEOUT=2, NET_LLC2_REJ_TIMEOUT=3, NET_LLC2_BUSY_TIMEOUT=4, }; enum { NET_ATALK_AARP_EXPIRY_TIME=1, NET_ATALK_AARP_TICK_TIME=2, NET_ATALK_AARP_RETRANSMIT_LIMIT=3, NET_ATALK_AARP_RESOLVE_TIME=4 }; enum { NET_NETROM_DEFAULT_PATH_QUALITY=1, NET_NETROM_OBSOLESCENCE_COUNT_INITIALISER=2, NET_NETROM_NETWORK_TTL_INITIALISER=3, NET_NETROM_TRANSPORT_TIMEOUT=4, NET_NETROM_TRANSPORT_MAXIMUM_TRIES=5, NET_NETROM_TRANSPORT_ACKNOWLEDGE_DELAY=6, NET_NETROM_TRANSPORT_BUSY_DELAY=7, NET_NETROM_TRANSPORT_REQUESTED_WINDOW_SIZE=8, NET_NETROM_TRANSPORT_NO_ACTIVITY_TIMEOUT=9, NET_NETROM_ROUTING_CONTROL=10, NET_NETROM_LINK_FAILS_COUNT=11, NET_NETROM_RESET=12 }; enum { NET_AX25_IP_DEFAULT_MODE=1, NET_AX25_DEFAULT_MODE=2, NET_AX25_BACKOFF_TYPE=3, NET_AX25_CONNECT_MODE=4, NET_AX25_STANDARD_WINDOW=5, NET_AX25_EXTENDED_WINDOW=6, NET_AX25_T1_TIMEOUT=7, NET_AX25_T2_TIMEOUT=8, NET_AX25_T3_TIMEOUT=9, NET_AX25_IDLE_TIMEOUT=10, NET_AX25_N2=11, NET_AX25_PACLEN=12, NET_AX25_PROTOCOL=13, NET_AX25_DAMA_SLAVE_TIMEOUT=14 }; enum { NET_ROSE_RESTART_REQUEST_TIMEOUT=1, NET_ROSE_CALL_REQUEST_TIMEOUT=2, NET_ROSE_RESET_REQUEST_TIMEOUT=3, NET_ROSE_CLEAR_REQUEST_TIMEOUT=4, NET_ROSE_ACK_HOLD_BACK_TIMEOUT=5, NET_ROSE_ROUTING_CONTROL=6, NET_ROSE_LINK_FAIL_TIMEOUT=7, NET_ROSE_MAX_VCS=8, NET_ROSE_WINDOW_SIZE=9, NET_ROSE_NO_ACTIVITY_TIMEOUT=10 }; enum { NET_X25_RESTART_REQUEST_TIMEOUT=1, NET_X25_CALL_REQUEST_TIMEOUT=2, NET_X25_RESET_REQUEST_TIMEOUT=3, NET_X25_CLEAR_REQUEST_TIMEOUT=4, NET_X25_ACK_HOLD_BACK_TIMEOUT=5, NET_X25_FORWARD=6 }; enum { NET_TR_RIF_TIMEOUT=1 }; enum { NET_DECNET_NODE_TYPE = 1, NET_DECNET_NODE_ADDRESS = 2, NET_DECNET_NODE_NAME = 3, NET_DECNET_DEFAULT_DEVICE = 4, NET_DECNET_TIME_WAIT = 5, NET_DECNET_DN_COUNT = 6, NET_DECNET_DI_COUNT = 7, NET_DECNET_DR_COUNT = 8, NET_DECNET_DST_GC_INTERVAL = 9, NET_DECNET_CONF = 10, NET_DECNET_NO_FC_MAX_CWND = 11, NET_DECNET_MEM = 12, NET_DECNET_RMEM = 13, NET_DECNET_WMEM = 14, NET_DECNET_DEBUG_LEVEL = 255 }; enum { NET_DECNET_CONF_LOOPBACK = -2, NET_DECNET_CONF_DDCMP = -3, NET_DECNET_CONF_PPP = -4, NET_DECNET_CONF_X25 = -5, NET_DECNET_CONF_GRE = -6, NET_DECNET_CONF_ETHER = -7 }; enum { NET_DECNET_CONF_DEV_PRIORITY = 1, NET_DECNET_CONF_DEV_T1 = 2, NET_DECNET_CONF_DEV_T2 = 3, NET_DECNET_CONF_DEV_T3 = 4, NET_DECNET_CONF_DEV_FORWARDING = 5, NET_DECNET_CONF_DEV_BLKSIZE = 6, NET_DECNET_CONF_DEV_STATE = 7 }; enum { NET_SCTP_RTO_INITIAL = 1, NET_SCTP_RTO_MIN = 2, NET_SCTP_RTO_MAX = 3, NET_SCTP_RTO_ALPHA = 4, NET_SCTP_RTO_BETA = 5, NET_SCTP_VALID_COOKIE_LIFE = 6, NET_SCTP_ASSOCIATION_MAX_RETRANS = 7, NET_SCTP_PATH_MAX_RETRANS = 8, NET_SCTP_MAX_INIT_RETRANSMITS = 9, NET_SCTP_HB_INTERVAL = 10, NET_SCTP_PRESERVE_ENABLE = 11, NET_SCTP_MAX_BURST = 12, NET_SCTP_ADDIP_ENABLE = 13, NET_SCTP_PRSCTP_ENABLE = 14, NET_SCTP_SNDBUF_POLICY = 15, NET_SCTP_SACK_TIMEOUT = 16, NET_SCTP_RCVBUF_POLICY = 17, }; enum { NET_BRIDGE_NF_CALL_ARPTABLES = 1, NET_BRIDGE_NF_CALL_IPTABLES = 2, NET_BRIDGE_NF_CALL_IP6TABLES = 3, NET_BRIDGE_NF_FILTER_VLAN_TAGGED = 4, NET_BRIDGE_NF_FILTER_PPPOE_TAGGED = 5, }; enum { FS_NRINODE=1, FS_STATINODE=2, FS_MAXINODE=3, FS_NRDQUOT=4, FS_MAXDQUOT=5, FS_NRFILE=6, FS_MAXFILE=7, FS_DENTRY=8, FS_NRSUPER=9, FS_MAXSUPER=10, FS_OVERFLOWUID=11, FS_OVERFLOWGID=12, FS_LEASES=13, FS_DIR_NOTIFY=14, FS_LEASE_TIME=15, FS_DQSTATS=16, FS_XFS=17, FS_AIO_NR=18, FS_AIO_MAX_NR=19, FS_INOTIFY=20, FS_OCFS2=988, }; enum { FS_DQ_LOOKUPS = 1, FS_DQ_DROPS = 2, FS_DQ_READS = 3, FS_DQ_WRITES = 4, FS_DQ_CACHE_HITS = 5, FS_DQ_ALLOCATED = 6, FS_DQ_FREE = 7, FS_DQ_SYNCS = 8, FS_DQ_WARNINGS = 9, }; enum { DEV_CDROM=1, DEV_HWMON=2, DEV_PARPORT=3, DEV_RAID=4, DEV_MAC_HID=5, DEV_SCSI=6, DEV_IPMI=7, }; enum { DEV_CDROM_INFO=1, DEV_CDROM_AUTOCLOSE=2, DEV_CDROM_AUTOEJECT=3, DEV_CDROM_DEBUG=4, DEV_CDROM_LOCK=5, DEV_CDROM_CHECK_MEDIA=6 }; enum { DEV_PARPORT_DEFAULT=-3 }; enum { DEV_RAID_SPEED_LIMIT_MIN=1, DEV_RAID_SPEED_LIMIT_MAX=2 }; enum { DEV_PARPORT_DEFAULT_TIMESLICE=1, DEV_PARPORT_DEFAULT_SPINTIME=2 }; enum { DEV_PARPORT_SPINTIME=1, DEV_PARPORT_BASE_ADDR=2, DEV_PARPORT_IRQ=3, DEV_PARPORT_DMA=4, DEV_PARPORT_MODES=5, DEV_PARPORT_DEVICES=6, DEV_PARPORT_AUTOPROBE=16 }; enum { DEV_PARPORT_DEVICES_ACTIVE=-3, }; enum { DEV_PARPORT_DEVICE_TIMESLICE=1, }; enum { DEV_MAC_HID_KEYBOARD_SENDS_LINUX_KEYCODES=1, DEV_MAC_HID_KEYBOARD_LOCK_KEYCODES=2, DEV_MAC_HID_MOUSE_BUTTON_EMULATION=3, DEV_MAC_HID_MOUSE_BUTTON2_KEYCODE=4, DEV_MAC_HID_MOUSE_BUTTON3_KEYCODE=5, DEV_MAC_HID_ADB_MOUSE_SENDS_KEYCODES=6 }; enum { DEV_SCSI_LOGGING_LEVEL=1, }; enum { DEV_IPMI_POWEROFF_POWERCYCLE=1, }; enum { ABI_DEFHANDLER_COFF=1, ABI_DEFHANDLER_ELF=2, ABI_DEFHANDLER_LCALL7=3, ABI_DEFHANDLER_LIBCSO=4, ABI_TRACE=5, ABI_FAKE_UTSNAME=6, }; # 46 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 2 3 4 # 65 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 3 4 # 1 "/usr/include/x86_64-linux-gnu/bits/sysctl.h" 1 3 4 # 66 "/usr/include/x86_64-linux-gnu/sys/sysctl.h" 2 3 4 extern int sysctl (int *__name, int __nlen, void *__oldval, size_t *__oldlenp, void *__newval, size_t __newlen) __attribute__ ((__nothrow__ , __leaf__)) __attribute__ ((__deprecated__)); # 3 "/tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c" 2 stderr: In file included from /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c:3: /usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include Preprocess stderr before filtering:In file included from /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c:3: /usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~ : Preprocess stderr after filtering:In file included from /tmp/petsc-xk72m0wq/config.packages.pthread/conftest.c:3:/usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~: ================================================================================ TEST checkVersion from config.packages.pthread(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.pthread(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.pthread(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.pthread(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.pthread 0.153987 ================================================================================ TEST alternateConfigureLibrary from config.packages.PTScotch(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.PTScotch(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.PTScotch 0.001132 ================================================================================ TEST alternateConfigureLibrary from config.packages.Zoltan(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Zoltan(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Zoltan 0.000663 ================================================================================ TEST alternateConfigureLibrary from config.packages.ADIOS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ADIOS(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ADIOS 0.000646 ================================================================================ TEST alternateConfigureLibrary from config.packages.openmp(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.openmp(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.openmp 0.000567 ================================================================================ TEST alternateConfigureLibrary from config.packages.viennacl(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.viennacl(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.viennacl 0.000655 ================================================================================ TEST alternateConfigureLibrary from config.packages.ColPack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ColPack(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ColPack 0.000638 ================================================================================ TEST alternateConfigureLibrary from config.packages.openblas(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.openblas(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.openblas 0.000670 ================================================================================ TEST checkDependencies from config.packages.fblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.fblaslapack(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.fblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/fblaslapack.py:18) TESTING: configureLibrary from config.packages.fblaslapack(config/BuildSystem/config/packages/fblaslapack.py:18) ================================================================================== Checking for a functional fblaslapack Looking for FBLASLAPACK at git.fblaslapack, hg.fblaslapack or a directory starting with ['fblaslapack'] Found a copy of FBLASLAPACK in git.fblaslapack Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'fetch'] Executing: ['git', 'rev-parse', 'origin/barry/2019-08-22/fix-syntax-for-nag'] stdout: d28880efc974e971e6e71be8cf519a3d8de2492c Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing pkg.gitcommit Removing tmpmakefile Executing: ['git', 'checkout', '-f', 'd28880efc974e971e6e71be8cf519a3d8de2492c'] Executing: mpif90 -qversion Executing: mpif90 -V Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -O0 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Successful compile: Source: program main end Executing: mpif90 -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 -mfp16-format=ieee /tmp/petsc-xk72m0wq/config.setCompilers/conftest.F90 Possible ERROR while running compiler: exit code 1 stderr: gfortran: error: unrecognized command line option ���-mfp16-format=ieee��� Source: program main end Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gfortran: error: unrecognized command line option ���-mfp16-format=ieee��� PETSc Error: No output file produced Executing: mpif90 -V Makefile /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.conf.fblaslapack has correct checksum Commit file /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.gitcommit.fblaslapack has correct checksum Do not need to rebuild FBLASLAPACK Not checking for library in Download FBLASLAPACK: [] because no functions given to check for ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names No functions to check for in library [] [] No functions to check for in library [] [] Checking for headers Download FBLASLAPACK: ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.fblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.fblaslapack(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.fblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.fblaslapack(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.fblaslapack 1.168164 ================================================================================ TEST alternateConfigureLibrary from config.packages.f2cblaslapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.f2cblaslapack(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.f2cblaslapack 0.001174 ================================================================================ TEST checkDependencies from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.BlasLapack(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/BlasLapack.py:447) TESTING: configureLibrary from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:447) ================================================================================ Checking for BLAS and LAPACK in fblaslapack ================================================================================ TEST checkLib from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/BlasLapack.py:120) TESTING: checkLib from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:120) Checking for BLAS and LAPACK symbols Checking for Fortran name mangling underscore on BLAS/LAPACK Checking for functions [sdot_] in library ['/home/pesun/.emopt/lib/libfblas.a'] ['libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char sdot_(); static void _check_sdot_() { sdot_(); } int main() { _check_sdot_();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Defined "HAVE_LIBFBLAS" to "1" Checking for functions [sgetrs_] in library ['/home/pesun/.emopt/lib/libflapack.a'] ['/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char sgetrs_(); static void _check_sgetrs_() { sgetrs_(); } int main() { _check_sgetrs_();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Defined "HAVE_LIBFLAPACK" to "1" Found Fortran mangling on BLAS/LAPACK which is underscore Defined "BLASLAPACK_UNDERSCORE" to "1" ================================================================================ TEST checklsame from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/BlasLapack.py:609) TESTING: checklsame from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:609) Do the BLAS/LAPACK libraries have a valid lsame() function with correct binding. Checking for functions [lsame_] in library ['/home/pesun/.emopt/lib/libflapack.a', '/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char lsame_(); static void _check_lsame_() { lsame_(); } int main() { _check_lsame_();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Defined "HAVE_LIBFLAPACK" to "1" Defined "HAVE_LIBFBLAS" to "1" Defined "HAVE_LIBM" to "1" Defined "HAVE_LIBSTDC__" to "1" Defined "HAVE_LIBDL" to "1" Defined "HAVE_LIBMPI_USEMPIF08" to "1" Defined "HAVE_LIBMPI_USEMPI_IGNORE_TKR" to "1" Defined "HAVE_LIBMPI_MPIFH" to "1" Defined "HAVE_LIBMPI" to "1" Defined "HAVE_LIBGFORTRAN" to "1" Defined "HAVE_LIBM" to "1" Defined "HAVE_LIBGFORTRAN" to "1" Defined "HAVE_LIBM" to "1" Defined "HAVE_LIBGCC_S" to "1" Defined "HAVE_LIBQUADMATH" to "1" Defined "HAVE_LIBPTHREAD" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" char *dgeev_(void); char* testroutine(void){return dgeev_(); }Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" char *dgeev_(void); char* testroutine(void){return dgeev_(); }Executing: mpicc -o /tmp/petsc-xk72m0wq/config.setCompilers/libconftest.so -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lflapack -lfblas -lflapack -lfblas -lm -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl ================================================================================ TEST checkRuntimeIssues from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/BlasLapack.py:668) TESTING: checkRuntimeIssues from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:668) Determines if BLAS/LAPACK routines use 32 or 64 bit integers 32 bit blas indices based on the BLAS/LAPACK library being used Checking if sdot() returns a float or a double All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.packages.BlasLapack Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { FILE *output = fopen("runtimetestoutput","w"); extern float sdot_(const int*,const float*,const int *,const float*,const int*); float x1[1] = {3.0}; int one1 = 1; long long int ione1 = 1; float sdotresult = 0; int blasint64 = 0; if (!blasint64) { sdotresult = sdot_(&one1,x1,&one1,x1,&one1); } else { sdotresult = sdot_((const int*)&ione1,x1,(const int*)&ione1,x1,(const int*)&ione1); } fprintf(output, "--known-sdot-returns-double=%d",sdotresult != 9); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest Executing: /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest Checking for sdot() return double: result 0 Checking if snrm() returns a float or a double Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include #include #include #include int main() { FILE *output = fopen("runtimetestoutput","w"); extern float snrm2_(const int*,const float*,const int*); float x2[1] = {3.0}; int one2 = 1; long long int ione2 = 1; float normresult = 0; int blasint64 = 0; if (!blasint64) { normresult = snrm2_(&one2,x2,&one2); } else { normresult = snrm2_((const int*)&ione2,x2,(const int*)&ione2); } fprintf(output, "--known-snrm2-returns-double=%d",normresult != 3); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Testing executable /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest to see if it can be run Executing: /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest Executing: /tmp/petsc-xk72m0wq/config.packages.BlasLapack/conftest Checking for snrm2() return double: result 0 ================================================================================ TEST checkVersion from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.BlasLapack(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.BlasLapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.BlasLapack(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.BlasLapack 0.423031 ================================================================================ TEST alternateConfigureLibrary from config.packages.sundials(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.sundials(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.sundials 0.000260 ================================================================================ TEST alternateConfigureLibrary from config.packages.spai(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.spai(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.spai 0.000263 ================================================================================ TEST alternateConfigureLibrary from config.packages.pARMS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.pARMS(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.pARMS 0.000248 ================================================================================ TEST alternateConfigureLibrary from config.packages.p4est(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.p4est(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.p4est 0.000209 ================================================================================ TEST checkDependencies from config.packages.mkl_sparse_optimize(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.mkl_sparse_optimize(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.mkl_sparse_optimize(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/mkl_sparse_optimize.py:48) TESTING: configureLibrary from config.packages.mkl_sparse_optimize(config/BuildSystem/config/packages/mkl_sparse_optimize.py:48) ================================================================================ TEST checkVersion from config.packages.mkl_sparse_optimize(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.mkl_sparse_optimize(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.mkl_sparse_optimize(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.mkl_sparse_optimize(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.mkl_sparse_optimize 0.000307 ================================================================================ TEST checkDependencies from config.packages.mkl_sparse(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.mkl_sparse(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.mkl_sparse(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/mkl_sparse.py:21) TESTING: configureLibrary from config.packages.mkl_sparse(config/BuildSystem/config/packages/mkl_sparse.py:21) ================================================================================ TEST checkVersion from config.packages.mkl_sparse(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.mkl_sparse(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.mkl_sparse(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.mkl_sparse(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.mkl_sparse 0.000266 ================================================================================ TEST alternateConfigureLibrary from config.packages.mkl_cpardiso(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.mkl_cpardiso(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.mkl_cpardiso 0.000204 ================================================================================ TEST alternateConfigureLibrary from config.packages.hpddm(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/hpddm.py:114) TESTING: alternateConfigureLibrary from config.packages.hpddm(config/BuildSystem/config/packages/hpddm.py:114) Defined make rule "hpddm-build" with dependencies "" and code [] Defined make rule "hpddm-install" with dependencies "" and code [] child config.packages.hpddm 0.000414 ================================================================================ TEST alternateConfigureLibrary from config.packages.fftw(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.fftw 0.000224 ================================================================================ TEST alternateConfigureLibrary from config.packages.elemental(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.elemental(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.elemental 0.000263 ================================================================================ TEST alternateConfigureLibrary from config.packages.ml(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.ml(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.ml 0.000233 ================================================================================ TEST alternateConfigureLibrary from config.packages.mkl_pardiso(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.mkl_pardiso(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.mkl_pardiso 0.000202 ================================================================================ TEST alternateConfigureLibrary from config.packages.SuperLU_DIST(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.SuperLU_DIST(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.SuperLU_DIST 0.000211 ================================================================================ TEST alternateConfigureLibrary from config.packages.SuperLU(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.SuperLU(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.SuperLU 0.000214 ================================================================================ TEST alternateConfigureLibrary from config.packages.SuiteSparse(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.SuiteSparse(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.SuiteSparse 0.000246 ================================================================================ TEST alternateConfigureLibrary from config.packages.PaStiX(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.PaStiX(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.PaStiX 0.000231 ================================================================================ TEST checkDependencies from config.packages.scalapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.scalapack(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.scalapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:854) TESTING: configureLibrary from config.packages.scalapack(config/BuildSystem/config/package.py:854) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional scalapack Looking for SCALAPACK at git.scalapack, hg.scalapack or a directory starting with ['petsc-pkg-scalapack', 'scalapack'] Found a copy of SCALAPACK in git.scalapack Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', 'v2.0.2-p2^{commit}'] Executing: ['git', 'rev-parse', 'v2.0.2-p2'] stdout: bf5290f5d002fe43a6fc59f83730ff5141860380 Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing SLmake.inc Removing pkg.gitcommit Executing: ['git', 'checkout', '-f', 'bf5290f5d002fe43a6fc59f83730ff5141860380'] Executing: mpif90 -V Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -O0 /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.setCompilers/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -mfp16-format=ieee /tmp/petsc-xk72m0wq/config.setCompilers/conftest.c Possible ERROR while running compiler: exit code 1 stderr: gcc: error: unrecognized command line option ���-mfp16-format=ieee��� Source: #include "confdefs.h" #include "conffix.h" int main() { ; return 0; } Rejecting compiler flag -mfp16-format=ieee due to nonzero status from link Rejecting compiler flag -mfp16-format=ieee due to gcc: error: unrecognized command line option ���-mfp16-format=ieee��� PETSc Error: No output file produced Makefile /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.conf.scalapack has correct checksum Commit file /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.gitcommit.scalapack has correct checksum Do not need to rebuild SCALAPACK Checking for library in Download SCALAPACK: ['/home/pesun/.emopt/lib/libscalapack.a'] Contents: ['lib', 'share', 'build', 'include'] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [pssytrd_] in library ['/home/pesun/.emopt/lib/libscalapack.a'] ['/home/pesun/.emopt/lib/libflapack.a', '/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char pssytrd_(); static void _check_pssytrd_() { pssytrd_(); } int main() { _check_pssytrd_();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lscalapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Defined "HAVE_LIBSCALAPACK" to "1" No functions to check for in library ['/home/pesun/.emopt/lib/libscalapack.a'] ['/home/pesun/.emopt/lib/libflapack.a', '/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Checking for headers Download SCALAPACK: ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.scalapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.scalapack(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version ================================================================================ TEST checkSharedLibrary from config.packages.scalapack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.scalapack(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.scalapack 0.184951 ================================================================================ TEST alternateConfigureLibrary from config.packages.strumpack(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.strumpack(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.strumpack 0.000282 ================================================================================ TEST checkDependencies from config.packages.MUMPS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:829) TESTING: checkDependencies from config.packages.MUMPS(config/BuildSystem/config/package.py:829) ================================================================================ TEST configureLibrary from config.packages.MUMPS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:854) TESTING: configureLibrary from config.packages.MUMPS(config/BuildSystem/config/package.py:854) Find an installation and check if it can work with PETSc ================================================================================== Checking for a functional MUMPS Looking for MUMPS at git.mumps, hg.mumps or a directory starting with ['petsc-pkg-mumps', 'MUMPS'] Found a copy of MUMPS in git.mumps Executing: ['git', 'rev-parse', '--git-dir'] stdout: .git Executing: ['git', 'cat-file', '-e', 'v5.2.1-p2^{commit}'] Executing: ['git', 'rev-parse', 'v5.2.1-p2'] stdout: d1a5c931b762d0da8183dea55b69f7fd59e00a48 Executing: ['git', '-c', 'user.name=petsc-configure', '-c', 'user.email=petsc@configure', 'stash'] stdout: No local changes to save Executing: ['git', 'clean', '-f', '-d', '-x'] stdout: Removing Makefile.inc Removing pkg.gitcommit Executing: ['git', 'checkout', '-f', 'd1a5c931b762d0da8183dea55b69f7fd59e00a48'] Executing: mpif90 -V Makefile /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.conf.mumps has correct checksum Commit file /home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/lib/petsc/conf/pkg.gitcommit.mumps has correct checksum Do not need to rebuild MUMPS Checking for library in Download MUMPS: ['/home/pesun/.emopt/lib/libcmumps.a', 'libdmumps.a', 'libsmumps.a', 'libzmumps.a', 'libmumps_common.a', 'libpord.a'] Contents: ['lib', 'share', 'build', 'include'] ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names ================================================================================ TEST check from config.libraries(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/libraries.py:157) TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157) Checks that the library "libName" contains "funcs", and if it does defines HAVE_LIB"libName" - libDir may be a list of directories - libName may be a list of library names Checking for functions [dmumps_c] in library ['/home/pesun/.emopt/lib/libcmumps.a', 'libdmumps.a', 'libsmumps.a', 'libzmumps.a', 'libmumps_common.a', 'libpord.a'] ['/home/pesun/.emopt/lib/libscalapack.a', '/home/pesun/.emopt/lib/libflapack.a', '/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ char dmumps_c(); static void _check_dmumps_c() { dmumps_c(); } int main() { _check_dmumps_c();; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/config.libraries/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.o -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lscalapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lfblas -lm -lstdc++ -ldl -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -Wl,-rpath,/home/pesun/opt/openmpi/lib -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl Defined "HAVE_LIBCMUMPS" to "1" Defined "HAVE_LIBDMUMPS" to "1" Defined "HAVE_LIBSMUMPS" to "1" Defined "HAVE_LIBZMUMPS" to "1" Defined "HAVE_LIBMUMPS_COMMON" to "1" Defined "HAVE_LIBPORD" to "1" No functions to check for in library ['/home/pesun/.emopt/lib/libcmumps.a', 'libdmumps.a', 'libsmumps.a', 'libzmumps.a', 'libmumps_common.a', 'libpord.a'] ['/home/pesun/.emopt/lib/libscalapack.a', '/home/pesun/.emopt/lib/libflapack.a', '/home/pesun/.emopt/lib/libfblas.a', 'libm.a', '-lstdc++', '-ldl', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-L/home/pesun/opt/openmpi/lib', '-lmpi_usempif08', '-lmpi_usempi_ignore_tkr', '-lmpi_mpifh', '-lmpi', '-lgfortran', '-lm', '-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9', '-L/usr/lib/gcc/x86_64-linux-gnu/9', '-Wl,-rpath,/usr/lib/x86_64-linux-gnu', '-L/usr/lib/x86_64-linux-gnu', '-Wl,-rpath,/lib/x86_64-linux-gnu', '-L/lib/x86_64-linux-gnu', '-Wl,-rpath,/home/pesun/opt/openmpi/lib', '-lgfortran', '-lm', '-lgcc_s', '-lquadmath', '-lpthread'] Checking for headers Download MUMPS: ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkInclude from config.headers(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/headers.py:86) TESTING: checkInclude from config.headers(config/BuildSystem/config/headers.py:86) Checks if a particular include file can be found along particular include paths Checking for header files ['dmumps_c.h'] in ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Checking include with compiler flags var CPPFLAGS ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] Preprocessing source: #include "confdefs.h" #include "conffix.h" #include Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.headers -I/home/pesun/.emopt/include -I/home/pesun/opt/openmpi/include -I/home/pesun/opt/openmpi/lib /tmp/petsc-xk72m0wq/config.headers/conftest.c Preprocess stderr before filtering:: Preprocess stderr after filtering:: Found header files ['dmumps_c.h'] in ['/home/pesun/.emopt/include', '/home/pesun/opt/openmpi/include', '/home/pesun/opt/openmpi/lib'] ================================================================================ TEST checkVersion from config.packages.MUMPS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:974) TESTING: checkVersion from config.packages.MUMPS(config/BuildSystem/config/package.py:974) Uses self.version, self.minversion, self.maxversion, self.versionname, and self.versioninclude to determine if package has required version All intermediate test results are stored in /tmp/petsc-xk72m0wq/config.packages.MUMPS Preprocessing source: #include "confdefs.h" #include "conffix.h" #include "dmumps_c.h" version=MUMPS_VERSION Executing: mpicc -E -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.packages.MUMPS -I/home/pesun/.emopt/include /tmp/petsc-xk72m0wq/config.packages.MUMPS/conftest.c For mumps need <= 5.2.1 <= ================================================================================ TEST checkSharedLibrary from config.packages.MUMPS(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:908) TESTING: checkSharedLibrary from config.packages.MUMPS(config/BuildSystem/config/package.py:908) By default we don't care about checking if the library is shared child config.packages.MUMPS 0.166011 ================================================================================ TEST alternateConfigureLibrary from config.packages.MOAB(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.MOAB(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.MOAB 0.000435 ================================================================================ TEST alternateConfigureLibrary from config.packages.hypre(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.hypre(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.hypre 0.000355 ================================================================================ TEST alternateConfigureLibrary from config.packages.Trilinos(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Trilinos(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Trilinos 0.000361 ================================================================================ TEST alternateConfigureLibrary from config.packages.xSDKTrilinos(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.xSDKTrilinos(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.xSDKTrilinos 0.000363 ================================================================================ TEST alternateConfigureLibrary from config.packages.mstk(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.mstk(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.mstk 0.000357 ================================================================================ TEST alternateConfigureLibrary from config.packages.amanzi(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.amanzi(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.amanzi 0.000358 ================================================================================ TEST alternateConfigureLibrary from config.packages.MFEM(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/packages/MFEM.py:146) TESTING: alternateConfigureLibrary from config.packages.MFEM(config/BuildSystem/config/packages/MFEM.py:146) Defined make rule "mfem-build" with dependencies "" and code [] Defined make rule "mfem-install" with dependencies "" and code [] child config.packages.MFEM 0.000667 ================================================================================ TEST alternateConfigureLibrary from config.packages.Chombo(/home/pesun/.emopt/build/petsc-3.12.1/config/BuildSystem/config/package.py:912) TESTING: alternateConfigureLibrary from config.packages.Chombo(config/BuildSystem/config/package.py:912) Called if --with-packagename=0; does nothing by default child config.packages.Chombo 0.000409 ================================================================================ TEST configureRTLDDefault from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:675) TESTING: configureRTLDDefault from PETSc.Configure(config/PETSc/Configure.py:675) All intermediate test results are stored in /tmp/petsc-xk72m0wq/PETSc.Configure Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:4:15: error: ���RTLD_DEFAULT��� undeclared here (not in a function) 4 | void *ptr = RTLD_DEFAULT; | ^~~~~~~~~~~~ Source: #include "confdefs.h" #include "conffix.h" #include void *ptr = RTLD_DEFAULT; int main() { ; return 0; } ================================================================================ TEST configurePrefetch from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:500) TESTING: configurePrefetch from PETSc.Configure(config/PETSc/Configure.py:500) Sees if there are any prefetch functions supported Executing: uname -s stdout: Linux Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { void *v = 0;_mm_prefetch((const char*)v,_MM_HINT_NTA); ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_XMMINTRIN_H" to "1" Defined "Prefetch(a,b,c)" to "_mm_prefetch((const char*)(a),(c))" Defined "PREFETCH_HINT_NTA" to "_MM_HINT_NTA" Defined "PREFETCH_HINT_T0" to "_MM_HINT_T0" Defined "PREFETCH_HINT_T1" to "_MM_HINT_T1" Defined "PREFETCH_HINT_T2" to "_MM_HINT_T2" ================================================================================ TEST configureUnused from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:561) TESTING: configureUnused from PETSc.Configure(config/PETSc/Configure.py:561) Sees if __attribute((unused)) is supported Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:7:5: warning: unused variable ���j��� [-Wunused-variable] 7 | int j = myfunc(&i); | ^ Source: #include "confdefs.h" #include "conffix.h" __attribute((unused)) static int myfunc(__attribute((unused)) void *name){ return 1;} int main() { int i = 0; int j = myfunc(&i); typedef void* atype; __attribute((unused)) atype a; ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "UNUSED" to "__attribute((unused))" ================================================================================ TEST configureDeprecated from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:579) TESTING: configureDeprecated from PETSc.Configure(config/PETSc/Configure.py:579) Check if __attribute((deprecated)) is supported Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:3:38: warning: ���myfunc��� defined but not used [-Wunused-function] 3 | __attribute((deprecated)) static int myfunc(void) { return 1;} | ^~~~~~ Source: #include "confdefs.h" #include "conffix.h" __attribute((deprecated)) static int myfunc(void) { return 1;} int main() { ; return 0; } Defined "DEPRECATED_FUNCTION(why)" to "__attribute((deprecated))" Defined "DEPRECATED_TYPEDEF(why)" to "__attribute((deprecated))" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" enum E {oldval __attribute((deprecated)), newval }; int main() { ; return 0; } Defined "DEPRECATED_ENUM(why)" to "__attribute((deprecated))" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define TEST _Pragma("GCC warning "Testing _Pragma"") value int main() { ; return 0; } Defined "DEPRECATED_MACRO(why)" to "_Pragma(why)" ================================================================================ TEST configureIsatty from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:573) TESTING: configureIsatty from PETSc.Configure(config/PETSc/Configure.py:573) Check if the Unix C function isatty() works correctly Actually just assumes it does not work correctly on batch systems Defined "USE_ISATTY" to "1" ================================================================================ TEST configureExpect from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:628) TESTING: configureExpect from PETSc.Configure(config/PETSc/Configure.py:628) Sees if the __builtin_expect directive is supported Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { if (__builtin_expect(0,1)) return 1;; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_BUILTIN_EXPECT" to "1" ================================================================================ TEST configureAlign from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:612) TESTING: configureAlign from PETSc.Configure(config/PETSc/Configure.py:612) Check if __attribute(aligned) is supported Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" struct mystruct {int myint;} __attribute((aligned(16))); char assert_aligned[(sizeof(struct mystruct)==16)*2-1]; int main() { ; return 0; } Defined "ATTRIBUTEALIGNED(size)" to "__attribute((aligned(size)))" Defined "HAVE_ATTRIBUTEALIGNED" to "1" ================================================================================ TEST configureFunctionName from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:635) TESTING: configureFunctionName from PETSc.Configure(config/PETSc/Configure.py:635) Sees if the compiler supports __func__ or a variant. Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { if (__func__[0] != 'm') return 1;; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { if (__func__[0] != 'm') return 1;; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "FUNCTION_NAME_C" to "__func__" Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { if (__func__[0] != 'm') return 1;; return 0; } Executing: mpicxx -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.cc Successful compile: Source: #include "confdefs.h" #include "conffix.h" int main() { if (__func__[0] != 'm') return 1;; return 0; } Executing: mpicxx -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "FUNCTION_NAME_CXX" to "__func__" ================================================================================ TEST configureIntptrt from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:653) TESTING: configureIntptrt from PETSc.Configure(config/PETSc/Configure.py:653) Determine what to use for uintptr_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:6:18: warning: unused variable ���i��� [-Wunused-variable] 6 | int x; uintptr_t i = (uintptr_t)&x;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { int x; uintptr_t i = (uintptr_t)&x;; return 0; } Defined "UINTPTR_T" to "uintptr_t" ================================================================================ TEST configureSolaris from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:680) TESTING: configureSolaris from PETSc.Configure(config/PETSc/Configure.py:680) Solaris specific stuff ================================================================================ TEST configureLinux from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:693) TESTING: configureLinux from PETSc.Configure(config/PETSc/Configure.py:693) Linux specific stuff Defined "HAVE_DOUBLE_ALIGN_MALLOC" to "1" ================================================================================ TEST configureWin32 from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:699) TESTING: configureWin32 from PETSc.Configure(config/PETSc/Configure.py:699) Win32 non-cygwin specific stuff Checking for functions [GetComputerName] in library ['Kernel32.lib'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetComputerName() { GetComputerName(NULL,NULL);; } int main() { _check_GetComputerName();; return 0; } Compile failed inside link Checking for functions [GetComputerName] in library ['kernel32'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetComputerName() { GetComputerName(NULL,NULL);; } int main() { _check_GetComputerName();; return 0; } Compile failed inside link Checking for functions [GetUserName] in library ['Advapi32.lib'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetUserName() { GetUserName(NULL,NULL);; } int main() { _check_GetUserName();; return 0; } Compile failed inside link Checking for functions [GetUserName] in library ['advapi32'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetUserName() { GetUserName(NULL,NULL);; } int main() { _check_GetUserName();; return 0; } Compile failed inside link Checking for functions [GetDC] in library ['User32.lib'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetDC() { GetDC(0);; } int main() { _check_GetDC();; return 0; } Compile failed inside link Checking for functions [GetDC] in library ['user32'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_GetDC() { GetDC(0);; } int main() { _check_GetDC();; return 0; } Compile failed inside link Checking for functions [CreateCompatibleDC] in library ['Gdi32.lib'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_CreateCompatibleDC() { CreateCompatibleDC(0);; } int main() { _check_CreateCompatibleDC();; return 0; } Compile failed inside link Checking for functions [CreateCompatibleDC] in library ['gdi32'] [] Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.libraries/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.libraries/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/config.libraries/conftest.c:4:10: fatal error: Windows.h: No such file or directory 4 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" /* Override any gcc2 internal prototype to avoid an error. */ #include static void _check_CreateCompatibleDC() { CreateCompatibleDC(0);; } int main() { _check_CreateCompatibleDC();; return 0; } Compile failed inside link Checking for type: int32_t Executing: mpicc -c -o /tmp/petsc-xk72m0wq/config.types/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/config.types/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/config.types/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/config.types/conftest.c:11:9: warning: unused variable ���a��� [-Wunused-variable] 11 | int32_t a;; | ^ Source: #include "confdefs.h" #include "conffix.h" #include #include #include int main() { int32_t a;; return 0; } int32_t found Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:6:7: warning: unused variable ���u��� [-Wunused-variable] 6 | uid_t u; | ^ Source: #include "confdefs.h" #include "conffix.h" #include int main() { uid_t u; ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:8:5: warning: unused variable ���a��� [-Wunused-variable] 8 | int a=R_OK; | ^ Source: #include "confdefs.h" #include "conffix.h" #if defined(PETSC_HAVE_UNISTD_H) #include #endif int main() { int a=R_OK; ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { int a=0; if (S_ISDIR(a)){} ; return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:3:10: fatal error: Windows.h: No such file or directory 3 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include int main() { LARGE_INTEGER a; DWORD b=a.u.HighPart; ; return 0; } Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: exit code 1 stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:3:10: fatal error: Windows.h: No such file or directory 3 | #include | ^~~~~~~~~~~ compilation terminated. Source: #include "confdefs.h" #include "conffix.h" #include #include int main() { int flags = O_BINARY;; return 0; } Defined "REPLACE_DIR_SEPARATOR" to "'\\'" Defined "DIR_SEPARATOR" to "'/'" Defined "DIR" to ""/home/pesun/.emopt"" Defined make macro "wPETSC_DIR" to "/home/pesun/.emopt" Defined "ARCH" to """" ================================================================================ TEST configureCygwinBrokenPipe from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:771) TESTING: configureCygwinBrokenPipe from PETSc.Configure(config/PETSc/Configure.py:771) Cygwin version <= 1.7.18 had issues with pipes and long commands invoked from gnu-make http://cygwin.com/ml/cygwin/2013-05/msg00340.html Executing: uname -s stdout: Linux ================================================================================ TEST configureDefaultArch from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:787) TESTING: configureDefaultArch from PETSc.Configure(config/PETSc/Configure.py:787) ================================================================================ TEST configureScript from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:804) TESTING: configureScript from PETSc.Configure(config/PETSc/Configure.py:804) Output a script in the conf directory which will reproduce the configuration ================================================================================ TEST configureInstall from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:843) TESTING: configureInstall from PETSc.Configure(config/PETSc/Configure.py:843) Setup the directories for installation Defined make rule "print_mesg_after_build" with dependencies "" and code ['-@echo "Now to install the libraries do:"', '-@echo "make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} install"', '-@echo "========================================="'] ================================================================================ TEST configureGCOV from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:855) TESTING: configureGCOV from PETSc.Configure(config/PETSc/Configure.py:855) ================================================================================ TEST configureAtoll from PETSc.Configure(/home/pesun/.emopt/build/petsc-3.12.1/config/PETSc/Configure.py:556) TESTING: configureAtoll from PETSc.Configure(config/PETSc/Configure.py:556) Checks if atoll exists Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Possible ERROR while running compiler: stderr: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c: In function ���main���: /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c:7:6: warning: unused variable ���v��� [-Wunused-variable] 7 | long v = atoll("25"); | ^ Source: #include "confdefs.h" #include "conffix.h" #define _POSIX_C_SOURCE 200112L #include int main() { long v = atoll("25"); return 0; } Executing: mpicc -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -lquadmath -lstdc++ -ldl Defined "HAVE_ATOLL" to "1" Executing: mpicc -show stdout: gcc -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi Defined "MPICC_SHOW" to ""gcc -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi"" Defined make macro "CC_FLAGS" to " -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 " Defined "HAVE_CXX" to "1" Defined make macro "CXX_FLAGS" to " -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC " Defined make macro "CXX_LINKER" to "mpicxx" Defined make macro "CXX_LINKER_FLAGS" to " -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3" Defined make macro "CPP_FLAGS" to "" Defined make macro "PCC" to "mpicc" Defined make macro "PCC_FLAGS" to " -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 " Defined make macro "CC_SUFFIX" to "o" Defined make macro "PCC_LINKER" to "mpicc" Defined make macro "PCC_LINKER_FLAGS" to " -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3" Defined make macro "CC_LINKER_SUFFIX" to "" Defined "HAVE_FORTRAN" to "1" Defined make macro "FPP_FLAGS" to "" Defined make macro "FC_FLAGS" to " -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 " Defined make macro "FC_SUFFIX" to "o" Defined make macro "FC_LINKER" to "mpif90" Defined make macro "FC_LINKER_FLAGS" to " -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 " Defined make macro "FC_MODULE_FLAG" to "-I" Defined make macro "FC_MODULE_OUTPUT_FLAG" to "-J" Defined make macro "CUDAC_FLAGS" to " -Xcompiler -fPIC -I/home/pesun/opt/openmpi/include -Wno-deprecated-gpu-targets" Defined make macro "SL_LINKER" to "mpicc" Defined make macro "SL_LINKER_FLAGS" to "${PCC_LINKER_FLAGS}" Defined make macro "SL_LINKER_SUFFIX" to "so" Defined "SLSUFFIX" to ""so"" Defined make macro "SL_LINKER_LIBS" to "${PETSC_EXTERNAL_LIB_BASIC}" Defined make macro "PETSC_LANGUAGE" to "CONLY" Defined make macro "PETSC_SCALAR" to "complex" Defined make macro "PETSC_PRECISION" to "single" Executing: CC -VV Defined "USE_SOCKET_VIEWER" to "1" Executing: mpicc -c -o /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.o -I/tmp/petsc-xk72m0wq/config.compilers -I/tmp/petsc-xk72m0wq/config.utilities.closure -I/tmp/petsc-xk72m0wq/config.compilersFortran -I/tmp/petsc-xk72m0wq/config.headers -I/tmp/petsc-xk72m0wq/config.utilities.cacheDetails -I/tmp/petsc-xk72m0wq/config.functions -I/tmp/petsc-xk72m0wq/config.utilities.featureTestMacros -I/tmp/petsc-xk72m0wq/config.utilities.missing -I/tmp/petsc-xk72m0wq/PETSc.options.scalarTypes -I/tmp/petsc-xk72m0wq/config.packages.MPI -I/tmp/petsc-xk72m0wq/config.packages.pthread -I/tmp/petsc-xk72m0wq/config.setCompilers -I/tmp/petsc-xk72m0wq/config.packages.BlasLapack -I/tmp/petsc-xk72m0wq/config.libraries -I/tmp/petsc-xk72m0wq/config.types -I/tmp/petsc-xk72m0wq/PETSc.Configure -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 /tmp/petsc-xk72m0wq/PETSc.Configure/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #include int main() { setsockopt(0,SOL_SOCKET,SO_REUSEADDR,0,0); return 0; } Defined "HAVE_SO_REUSEADDR" to "1" Defined "HAVE_MUMPS" to "1" Defined make macro "MUMPS_LIB" to "-Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" Defined make macro "MUMPS_INCLUDE" to "-I/home/pesun/.emopt/include" Defined "HAVE_SCALAPACK" to "1" Defined make macro "SCALAPACK_LIB" to "-Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lscalapack" Defined make macro "SCALAPACK_INCLUDE" to "" Defined make macro "BLASLAPACK_LIB" to "-Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -lfblas" Defined make macro "BLASLAPACK_INCLUDE" to "" Defined "HAVE_FBLASLAPACK" to "1" Defined make macro "FBLASLAPACK_LIB" to "" Defined make macro "FBLASLAPACK_INCLUDE" to "" Defined "HAVE_PTHREAD" to "1" Defined make macro "PTHREAD_LIB" to "" Defined make macro "PTHREAD_INCLUDE" to "" Defined "HAVE_MATHLIB" to "1" Defined make macro "MATHLIB_LIB" to "-lm" Defined make macro "MATHLIB_INCLUDE" to "" Defined "HAVE_X" to "1" Defined make macro "X_LIB" to "-lX11" Defined make macro "X_INCLUDE" to "" Defined make macro "MPI_LIB" to "" Defined make macro "MPI_INCLUDE" to "" Defined make macro "PETSC_EXTERNAL_LIB_BASIC" to "-Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lflapack -lfblas -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl" Defined make macro "PETSC_CC_INCLUDES" to "-I/home/pesun/.emopt/build/petsc-3.12.1/include -I/home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/include -I/home/pesun/.emopt/include" Defined make macro "PETSC_CC_INCLUDES_INSTALL" to "-I/home/pesun/.emopt/include" Defined make macro "PETSC_FC_INCLUDES" to "-I/home/pesun/.emopt/build/petsc-3.12.1/include -I/home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/include -I/home/pesun/.emopt/include" Defined make macro "PETSC_FC_INCLUDES_INSTALL" to "-I/home/pesun/.emopt/include" Defined "LIB_DIR" to ""/home/pesun/.emopt/lib"" Defined make macro "LIBNAME" to "${INSTALL_LIB_DIR}/libpetsc.${AR_LIB_SUFFIX}" Defined make macro "SHLIBS" to "libpetsc" Defined make macro "PETSC_LIB_BASIC" to "-lpetsc" Defined make macro "PETSC_KSP_LIB_BASIC" to "-lpetsc" Defined make macro "PETSC_TS_LIB_BASIC" to "-lpetsc" Defined make macro "PETSC_TAO_LIB_BASIC" to "-lpetsc" Defined make macro "PETSC_WITH_EXTERNAL_LIB" to "-L${PETSC_DIR}/${PETSC_ARCH}/lib -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lflapack -lfblas -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl" Defined "USE_SINGLE_LIBRARY" to "1" Defined make macro "PETSC_SYS_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_VEC_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_MAT_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_DM_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_KSP_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_SNES_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_TS_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_TAO_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_CHARACTERISTIC_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_LIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "PETSC_CONTRIB" to "${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB}" Defined make macro "CONFIGURE_OPTIONS" to "--with-scalar-type=complex --with-mpi=1 --COPTFLAGS=-O3 --FOPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with-debugging=0 --prefix=/home/pesun/.emopt/ --download-scalapack --download-mumps --download-fblaslapack=1 --with-precision=single" ================================================================================ child PETSc.Configure 1.034791 child sum 25.761110 child total 25.771430 **** arch-linux-c-opt/lib/petsc/conf/petscvariables **** FAST_AR_FLAGS = Scq AR_FLAGS = cr C_VERSION = gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 MPICC_SHOW = Unavailable Cxx_VERSION = g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 MPICXX_SHOW = g++ -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi FC_VERSION = GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 MPIFC_SHOW = gfortran -I/home/pesun/opt/openmpi/include -pthread -I/home/pesun/opt/openmpi/lib -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi CUDA_VERSION = nvcc: NVIDIA (R) Cuda compiler driver C_DEPFLAGS = -MMD -MP CXX_DEPFLAGS = -MMD -MP CUDA_DEPFLAGS = -MMD -MP FC_DEFINE_FLAG = -D FC_DEPFLAGS = -MMD -MP wPETSC_DIR = /home/pesun/.emopt CC_FLAGS = -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 CXX_FLAGS = -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC CXX_LINKER = mpicxx CXX_LINKER_FLAGS = -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 CPP_FLAGS = PCC = mpicc PCC_FLAGS = -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 CC_SUFFIX = o PCC_LINKER = mpicc PCC_LINKER_FLAGS = -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 CC_LINKER_SUFFIX = FPP_FLAGS = FC_FLAGS = -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 FC_SUFFIX = o FC_LINKER = mpif90 FC_LINKER_FLAGS = -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 FC_MODULE_FLAG = -I FC_MODULE_OUTPUT_FLAG = -J CUDAC_FLAGS = -Xcompiler -fPIC -I/home/pesun/opt/openmpi/include -Wno-deprecated-gpu-targets SL_LINKER = mpicc SL_LINKER_FLAGS = ${PCC_LINKER_FLAGS} SL_LINKER_SUFFIX = so SL_LINKER_LIBS = ${PETSC_EXTERNAL_LIB_BASIC} PETSC_LANGUAGE = CONLY PETSC_SCALAR = complex PETSC_PRECISION = single MUMPS_LIB = -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord MUMPS_INCLUDE = -I/home/pesun/.emopt/include SCALAPACK_LIB = -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lscalapack SCALAPACK_INCLUDE = BLASLAPACK_LIB = -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -lfblas BLASLAPACK_INCLUDE = FBLASLAPACK_LIB = FBLASLAPACK_INCLUDE = PTHREAD_LIB = PTHREAD_INCLUDE = MATHLIB_LIB = -lm MATHLIB_INCLUDE = X_LIB = -lX11 X_INCLUDE = MPI_LIB = MPI_INCLUDE = PETSC_EXTERNAL_LIB_BASIC = -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lflapack -lfblas -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl PETSC_CC_INCLUDES = -I/home/pesun/.emopt/build/petsc-3.12.1/include -I/home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/include -I/home/pesun/.emopt/include PETSC_CC_INCLUDES_INSTALL = -I/home/pesun/.emopt/include PETSC_FC_INCLUDES = -I/home/pesun/.emopt/build/petsc-3.12.1/include -I/home/pesun/.emopt/build/petsc-3.12.1/arch-linux-c-opt/include -I/home/pesun/.emopt/include PETSC_FC_INCLUDES_INSTALL = -I/home/pesun/.emopt/include LIBNAME = ${INSTALL_LIB_DIR}/libpetsc.${AR_LIB_SUFFIX} SHLIBS = libpetsc PETSC_LIB_BASIC = -lpetsc PETSC_KSP_LIB_BASIC = -lpetsc PETSC_TS_LIB_BASIC = -lpetsc PETSC_TAO_LIB_BASIC = -lpetsc PETSC_WITH_EXTERNAL_LIB = -L${PETSC_DIR}/${PETSC_ARCH}/lib -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -Wl,-rpath,/home/pesun/opt/openmpi/lib -L/home/pesun/opt/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lflapack -lfblas -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl PETSC_SYS_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_VEC_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_MAT_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_DM_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_KSP_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_SNES_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_TS_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_TAO_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_CHARACTERISTIC_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_LIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} PETSC_CONTRIB = ${C_SH_LIB_PATH} ${PETSC_WITH_EXTERNAL_LIB} CONFIGURE_OPTIONS = --with-scalar-type=complex --with-mpi=1 --COPTFLAGS=-O3 --FOPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with-debugging=0 --prefix=/home/pesun/.emopt/ --download-scalapack --download-mumps --download-fblaslapack=1 --with-precision=single MKDIR = /bin/mkdir -p SHELL = /bin/sh SED = /bin/sed SEDINPLACE = /bin/sed -i MV = /bin/mv CP = /bin/cp GREP = /bin/grep RM = /bin/rm -f DIFF = /bin/diff -w PYTHON = /home/pesun/anaconda3/bin/python M4 = /bin/m4 CC = mpicc CPP = mpicc -E CUDAC = nvcc CUDAPP = nvcc -E CXX = mpicxx CXXPP = mpicxx -E FC = mpif90 AR = /bin/ar RANLIB = /bin/ranlib AR_LIB_SUFFIX = a LD_SHARED = mpicc DYNAMICLINKER = mpicc CC_LINKER_SLFLAG = -Wl,-rpath, FC_LINKER_SLFLAG = -Wl,-rpath, GIT = git PREFIXDIR = /home/pesun/.emopt PETSC_SCALAR_SIZE = 32 PETSC_INDEX_SIZE = 32 MAKE = /bin/make OMAKE_PRINTDIR = /bin/make --print-directory OMAKE = /bin/make --no-print-directory MAKE_PAR_OUT_FLG = --output-sync=recurse MAKE_NP = 13 MAKE_TEST_NP = 8 MAKE_LOAD = 24.0 NPMAX = 16 SONAME_FUNCTION = $(1).so.$(2) SL_LINKER_FUNCTION = -shared -Wl,-soname,$(call SONAME_FUNCTION,$(notdir $(1)),$(2)) BUILDSHAREDLIB = yes GDB = /bin/gdb DSYMUTIL = true MPIEXEC = mpiexec --oversubscribe **** arch-linux-c-opt/lib/petsc/conf/petscrules **** print_mesg_after_build: -@echo "Now to install the libraries do:" -@echo "make PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} install" -@echo "=========================================" libc: ${LIBNAME}(${OBJSC}) libcxx: ${LIBNAME}(${OBJSCXX}) libcu: ${LIBNAME}(${OBJSCU}) libf: ${OBJSF} -${AR} ${AR_FLAGS} ${LIBNAME} ${OBJSF} shared_arch: shared_linux mfem-build: mfem-install: hpddm-build: hpddm-install: slepc-build: slepc-install: libmesh-build: libmesh-install: mpi4py-build: mpi4py-install: petsc4py-build: petsc4py-install: **** arch-linux-c-opt/include/petscconf.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define IS_COLORING_MAX USHRT_MAX #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_ARCH "" #define PETSC_ATTRIBUTEALIGNED(size) __attribute((aligned(size))) #define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated)) #define PETSC_DEPRECATED_FUNCTION(why) __attribute((deprecated)) #define PETSC_DEPRECATED_MACRO(why) _Pragma(why) #define PETSC_DEPRECATED_TYPEDEF(why) __attribute((deprecated)) #define PETSC_DIR "/home/pesun/.emopt" #define PETSC_DIR_SEPARATOR '/' #define PETSC_FUNCTION_NAME_C __func__ #define PETSC_FUNCTION_NAME_CXX __func__ #define PETSC_HAVE_ATOLL 1 #define PETSC_HAVE_ATTRIBUTEALIGNED 1 #define PETSC_HAVE_BUILTIN_EXPECT 1 #define PETSC_HAVE_CXX 1 #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1 #define PETSC_HAVE_FBLASLAPACK 1 #define PETSC_HAVE_FORTRAN 1 #define PETSC_HAVE_MUMPS 1 #define PETSC_HAVE_PTHREAD 1 #define PETSC_HAVE_SCALAPACK 1 #define PETSC_HAVE_SO_REUSEADDR 1 #define PETSC_HAVE_X 1 #define PETSC_HAVE_XMMINTRIN_H 1 #define PETSC_LIB_DIR "/home/pesun/.emopt/lib" #define PETSC_MPICC_SHOW "gcc -I/home/pesun/opt/openmpi/include -pthread -Wl,-rpath -Wl,/home/pesun/opt/openmpi/lib -Wl,--enable-new-dtags -L/home/pesun/opt/openmpi/lib -lmpi" #define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA #define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0 #define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1 #define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2 #define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c)) #define PETSC_REPLACE_DIR_SEPARATOR '\\' #define PETSC_SLSUFFIX "so" #define PETSC_UINTPTR_T uintptr_t #define PETSC_UNUSED __attribute((unused)) #define PETSC_USE_ISATTY 1 #define PETSC_USE_SINGLE_LIBRARY 1 #define PETSC_USE_SOCKET_VIEWER 1 #define PETSC_CLANGUAGE_C 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_CXX_INLINE inline #define PETSC_CXX_RESTRICT __restrict #define PETSC_C_INLINE inline #define PETSC_C_RESTRICT __restrict #define PETSC_FORTRAN_CHARLEN_T size_t #define PETSC_HAVE_C99 1 #define PETSC_HAVE_CXX_DIALECT_CXX11 1 #define PETSC_HAVE_CXX_DIALECT_CXX14 1 #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_IMMINTRIN_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_HAVE_REAL___FLOAT128 1 #define PETSC_USE_COMPLEX 1 #define PETSC_USE_REAL_SINGLE 1 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_HAVE_STRUCT_SIGACTION 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG 8 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE_MMAP 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_SIGNAL_CAST #define PETSC_FORTRAN_TYPE_INITIALIZE = -2 #define PETSC_HAVE_FORTRAN_FLUSH 1 #define PETSC_HAVE_FORTRAN_TYPE_STAR 1 #define PETSC_USING_F2003 1 #define PETSC_USING_F90 1 #define PETSC_USING_F90FREEFORM 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_USE_SHARED_LIBRARIES 1 #define PETSC_USE_DEBUGGER "gdb" #define PETSC_BLASLAPACK_UNDERSCORE 1 #define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE OMP #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPI_COMBINER_NAMED 1 #define PETSC_HAVE_MPI_C_DOUBLE_COMPLEX 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1 #define PETSC_HAVE_MPI_IALLREDUCE 1 #define PETSC_HAVE_MPI_IBARRIER 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_INT64_T 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1 #define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1 #define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_OMPI_MAJOR_VERSION 4 #define PETSC_HAVE_OMPI_MINOR_VERSION 0 #define PETSC_HAVE_OMPI_RELEASE_VERSION 3 #define PETSC_HAVE_PTHREAD_BARRIER_T 1 #define PETSC_HAVE_SCHED_CPU_SET_T 1 #define PETSC_Alignx(a,b) #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_USE_AVX512_KERNELS 1 #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_CTABLE 1 #define PETSC_USE_INFO 1 #define PETSC_USE_LOG 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_MEMALIGN 16 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC__GNU_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_PYTHON_EXE "/home/pesun/anaconda3/bin/python" #endif **** arch-linux-c-opt/include/petscfix.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #if defined(__cplusplus) extern "C" { } #else #endif #endif **** arch-linux-c-opt/include/petscpkg_version.h **** #if !defined(INCLUDED_UNKNOWN) #define INCLUDED_UNKNOWN #define PETSC_PKG_MPI_VERSION_MAJOR 3 #define PETSC_PKG_MPI_VERSION_MINOR 0 #define PETSC_PKG_MPI_VERSION_SUBMINOR 0 #define PETSC_PKG_MPI_VERSION_ PETSC_PKG_MPI_VERSION_EQ #define PETSC_PKG_MPI_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ ((PETSC_PKG_MPI_VERSION_MAJOR == (MAJOR)) && \ (PETSC_PKG_MPI_VERSION_MINOR == (MINOR)) && \ (PETSC_PKG_MPI_VERSION_SUBMINOR == (SUBMINOR))) #define PETSC_PKG_MPI_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ (PETSC_PKG_MPI_VERSION_MAJOR < (MAJOR) || \ (PETSC_PKG_MPI_VERSION_MAJOR == (MAJOR) && \ (PETSC_PKG_MPI_VERSION_MINOR < (MINOR) || \ (PETSC_PKG_MPI_VERSION_MINOR == (MINOR) && \ (PETSC_PKG_MPI_VERSION_SUBMINOR < (SUBMINOR)))))) #define PETSC_PKG_MPI_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ (PETSC_PKG_MPI_VERSION_LT(MAJOR,MINOR,SUBMINOR) || \ PETSC_PKG_MPI_VERSION_EQ(MAJOR,MINOR,SUBMINOR)) #define PETSC_PKG_MPI_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ ( 0 == PETSC_PKG_MPI_VERSION_LE(MAJOR,MINOR,SUBMINOR)) #define PETSC_PKG_MPI_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ ( 0 == PETSC_PKG_MPI_VERSION_LT(MAJOR,MINOR,SUBMINOR)) #define PETSC_PKG_MUMPS_VERSION_MAJOR 5 #define PETSC_PKG_MUMPS_VERSION_MINOR 2 #define PETSC_PKG_MUMPS_VERSION_SUBMINOR 1 #define PETSC_PKG_MUMPS_VERSION_ PETSC_PKG_MUMPS_VERSION_EQ #define PETSC_PKG_MUMPS_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \ ((PETSC_PKG_MUMPS_VERSION_MAJOR == (MAJOR)) && \ (PETSC_PKG_MUMPS_VERSION_MINOR == (MINOR)) && \ (PETSC_PKG_MUMPS_VERSION_SUBMINOR == (SUBMINOR))) #define PETSC_PKG_MUMPS_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ (PETSC_PKG_MUMPS_VERSION_MAJOR < (MAJOR) || \ (PETSC_PKG_MUMPS_VERSION_MAJOR == (MAJOR) && \ (PETSC_PKG_MUMPS_VERSION_MINOR < (MINOR) || \ (PETSC_PKG_MUMPS_VERSION_MINOR == (MINOR) && \ (PETSC_PKG_MUMPS_VERSION_SUBMINOR < (SUBMINOR)))))) #define PETSC_PKG_MUMPS_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ (PETSC_PKG_MUMPS_VERSION_LT(MAJOR,MINOR,SUBMINOR) || \ PETSC_PKG_MUMPS_VERSION_EQ(MAJOR,MINOR,SUBMINOR)) #define PETSC_PKG_MUMPS_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ ( 0 == PETSC_PKG_MUMPS_VERSION_LE(MAJOR,MINOR,SUBMINOR)) #define PETSC_PKG_MUMPS_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ ( 0 == PETSC_PKG_MUMPS_VERSION_LT(MAJOR,MINOR,SUBMINOR)) #endif Attempting to save configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash Saved configure hash file: arch-linux-c-opt/lib/petsc/conf/configure-hash Configure Actions These are the actions performed by configure on the filesystem ----------------------------------------------------------------- PETSc: Build : Set default architecture to arch-linux-c-opt in lib/petsc/conf/petscvariables File creation : Created arch-linux-c-opt/lib/petsc/conf/reconfigure-arch-linux-c-opt.py for automatic reconfiguration Framework: RDict update : Substitutions were stored in RDict with parent None File creation : Created makefile configure header arch-linux-c-opt/lib/petsc/conf/petscvariables File creation : Created makefile configure header arch-linux-c-opt/lib/petsc/conf/petscrules File creation : Created configure header arch-linux-c-opt/include/petscconf.h File creation : Created C specific configure header arch-linux-c-opt/include/petscfix.h File creation : Created configure pkg header arch-linux-c-opt/include/petscpkg_version.h Compilers: C Compiler: mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 CUDA Compiler: nvcc -Xcompiler -fPIC -I/home/pesun/opt/openmpi/include -Wno-deprecated-gpu-targets Version: nvcc: NVIDIA (R) Cuda compiler driver C++ Compiler: mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Fortran Compiler: mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 Linkers: Shared linker: mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Dynamic linker: mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Libraries linked against: -lquadmath -lstdc++ -ldl make: Version: 4.2 /bin/make BlasLapack: Library: -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lflapack -lfblas uses 4 byte integers MPI: Version: 3 Mpiexec: mpiexec --oversubscribe OMPI_VERSION: 4.0.3 fblaslapack: pthread: X: Library: -lX11 MUMPS: Version: 5.2.1 Includes: -I/home/pesun/.emopt/include Library: -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord scalapack: Library: -Wl,-rpath,/home/pesun/.emopt/lib -L/home/pesun/.emopt/lib -lscalapack Language used to compile PETSc: C PETSc: PETSC_ARCH: arch-linux-c-opt PETSC_DIR: /home/pesun/.emopt/build/petsc-3.12.1 Scalar type: complex Precision: single Support for __float128 Integer size: 4.0 bytes shared libraries: enabled Memory alignment from malloc(): 16 bytes xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/home/pesun/.emopt/build/petsc-3.12.1 PETSC_ARCH=arch-linux-c-opt all xxx=========================================================================xxx ================================================================================ Finishing configure run at Mon, 10 Oct 2022 16:50:08 -0700 ================================================================================