February 2017 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] install petsc on windows 10 with mpi
by Satish Balay 06 Feb '17

06 Feb '17

Them Intel-MPI was not removed. You can resend configure.log to confirm.. Satish On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > I removed the INTEL-MPI from the environmental variables and I still have the same problem. When I configure it looks like it accepts the mpi_include and mpi_lib but when I want to build , it says the configure was with mpi but in build it appears to compile is using a non-mpich. > > Mohammad > > ________________________________ > From: Satish Balay <balay(a)mcs.anl.gov> > Sent: Monday, February 6, 2017 6:13:04 PM > To: Mohammad S Dodaran > Cc: petsc-dev > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > 1. configure.log is a cygwin simlink - so native mail app is unable to > attach correctly. The actual file is in > PETSC_DIR/PETSC_ARCH/lib/petsc/conf > > 2. Suggest doing the build without fftw and hdf5 packages [once the > basic build succeeds - you can look at adding these pacakges.] > > 3. remove INTEL-MPI from your env - before running configure. [you > might be able to use intel-mpi instead of ms-mpi - but we don't have > any experience with it] > > Satish > > On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > > > now I'm trying to configure petsc 3.7 > > i used the format you showd in your previous email for the directories of fftw and hdf5 as below > > > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > > > the result is the following > > > > TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.scientificpython(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.fiat(config/BuildSystem/config/package.py:742) TESTING: configureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:679) ******************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > > ------------------------------------------------------------------------------- > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw did not work > > ******************************************************************************* > > > > i also attached the configure.log > > > > > > ________________________________ > > From: Satish Balay <balay(a)mcs.anl.gov> > > Sent: Monday, February 6, 2017 4:28:09 PM > > To: Mohammad S Dodaran > > Cc: Matthew Knepley; petsc-dev > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > >>>> > > > > Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 > > <<<< > > > > > 'PETSC_ARCH=' > > > > Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default.. > > > > > --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" > > > > I don't think I've built these packages with MS compilers > > before. Somehow they are not picked up anyway. For one - the format > > here should be the following [but I don't know if that will make > > configure check for them]: > > > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > > > > PETSC_DIR=/home/petsc-3.6.4 > > > > Also - please use latest petsc-3.7 release. > > > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > > now appears to be compiling using a non-MPICH mpi.h" > > > > Hm - configure is picking up Intel-MPI from your 'INCLUDE' env > > variable - but not 'make' - not sure whats hapenning - but I think its > > best to start a clean build with petsc-3.7 [unless you need 3.6 for a > > specific need] > > > > Satish > > > > On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > > > > > hello > > > > > > > > > i configured petsc and i was trying to make then this error appeared > > > > > > > > > Using mpiexec: mpiexec > > > ========================================== > > > Building PETSc using GNU Make with 4 build threads > > > ========================================== > > > make[2]: Entering directory '/home/petsc-3.6.4' > > > /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 > > > Use "/usr/bin/make V=1" to see the verbose compile lines. > > > CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o > > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o > > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o > > > CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o > > > verboseinfo.c > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > > now appears to be compiling using a non-MPICH mpi.h" > > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 > > > make[2]: *** Waiting for unfinished jobs.... > > > verboseinfof.c > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > > now appears to be compiling using a non-MPICH mpi.h" > > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 > > > zverboseinfof.c > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > > now appears to be compiling using a non-MPICH mpi.h" > > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 > > > zsys.c > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > > now appears to be compiling using a non-MPICH mpi.h" > > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 > > > make[2]: Leaving directory '/home/petsc-3.6.4' > > > make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 > > > make[1]: Leaving directory '/home/petsc-3.6.4' > > > **************************ERROR************************************* > > > Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log > > > Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov > > > ******************************************************************** > > > make: *** [makefile:30: all] Error 1 > > > > > > i have also attached the configure.log and make.log > > > > > > regards > > > Mohammad > > > > > > > > > > > > ________________________________ > > > From: Matthew Knepley <knepley(a)gmail.com> > > > Sent: Monday, February 6, 2017 8:07:41 AM > > > To: Mohammad S Dodaran > > > Cc: petsc-dev > > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > > > On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: > > > > > > Satish, > > > > > > Thanks for your quick response. as you see I can ls to the directory: > > > > > > ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ > > > > > > Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. > > > You cannot give a path to configure with spaces. > > > > > > You can remove the spaces using the cygpath command that Satish showed. Please use that command. > > > Remove the spaces from this path and give the spaceless path to configure. > > > > > > Thanks, > > > > > > Matt > > > > > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ > > > > > > > > > > > > but I do not know why still it has the same problem. and my configure file looks strange. > > > > > > Best, > > > > > > Mohammad > > > > > > ________________________________ > > > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > > > Sent: Sunday, February 5, 2017 10:58:35 PM > > > To: Mohammad S Dodaran > > > Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> > > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > > > Try to figureout path without spaces. > > > > > > cygpath -u `cygpath -s -m PATH` > > > > > > Make sure you can do "ls" on this path. > > > > > > And use it with petsc configure. > > > > > > balay@ps4 ~ > > > $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` > > > /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > > > > > balay@ps4 ~ > > > $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 > > > > > > balay@ps4 ~ > > > $ > > > > > > For ex: - I use: > > > > > > >>>>>>>> > > > $ cat config/examples/arch-mswin-intel.py > > > #!/usr/bin/python > > > if __name__ == '__main__': > > > import sys > > > import os > > > sys.path.insert(0, os.path.abspath('config')) > > > import configure > > > configure_options = [ > > > '--download-fblaslapack=1', > > > '--with-cc=win32fe icl', > > > '--with-cxx=win32fe icl', > > > '--with-fc=win32fe ifort', > > > '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', > > > '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', > > > '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', > > > '--with-shared-libraries=0', > > > 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', > > > ] > > > configure.petsc_configure(configure_options) > > > > > > <<<<<<<<<<< > > > > > > if you still have issues - send us configure.log for the failure. > > > > > > Satish > > > > > > On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > > > > > > > Dear Petsc developers, > > > > > > > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > > > > > > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > > > > > > > > > > But it gives error which says: > > > > > > > > *************************************************************** > > > > ERROR in COMMAND LINE ARGUMENT to ./configure > > > > ------------------------------------------------------------------------------- > > > > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > > > > > > > > > > How should I solve it? > > > > > > > > Mohammad > > > > > > > > > > > > > > > > > > > -- > > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > > -- Norbert Wiener > > > > > > > > >

1 0

Re: [petsc-dev] install petsc on windows 10 with mpi
by Mohammad S Dodaran 06 Feb '17

06 Feb '17

I removed the INTEL-MPI from the environmental variables and I still have the same problem. When I configure it looks like it accepts the mpi_include and mpi_lib but when I want to build , it says the configure was with mpi but in build it appears to compile is using a non-mpich. Mohammad ________________________________ From: Satish Balay <balay(a)mcs.anl.gov> Sent: Monday, February 6, 2017 6:13:04 PM To: Mohammad S Dodaran Cc: petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi 1. configure.log is a cygwin simlink - so native mail app is unable to attach correctly. The actual file is in PETSC_DIR/PETSC_ARCH/lib/petsc/conf 2. Suggest doing the build without fftw and hdf5 packages [once the basic build succeeds - you can look at adding these pacakges.] 3. remove INTEL-MPI from your env - before running configure. [you might be able to use intel-mpi instead of ms-mpi - but we don't have any experience with it] Satish On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > now I'm trying to configure petsc 3.7 > i used the format you showd in your previous email for the directories of fftw and hdf5 as below > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > the result is the following > > TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.scientificpython(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.fiat(config/BuildSystem/config/package.py:742) TESTING: configureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:679) ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw did not work > ******************************************************************************* > > i also attached the configure.log > > > ________________________________ > From: Satish Balay <balay(a)mcs.anl.gov> > Sent: Monday, February 6, 2017 4:28:09 PM > To: Mohammad S Dodaran > Cc: Matthew Knepley; petsc-dev > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > >>>> > > Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 > <<<< > > > 'PETSC_ARCH=' > > Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default.. > > > --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" > > I don't think I've built these packages with MS compilers > before. Somehow they are not picked up anyway. For one - the format > here should be the following [but I don't know if that will make > configure check for them]: > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > > PETSC_DIR=/home/petsc-3.6.4 > > Also - please use latest petsc-3.7 release. > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > Hm - configure is picking up Intel-MPI from your 'INCLUDE' env > variable - but not 'make' - not sure whats hapenning - but I think its > best to start a clean build with petsc-3.7 [unless you need 3.6 for a > specific need] > > Satish > > On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > > > hello > > > > > > i configured petsc and i was trying to make then this error appeared > > > > > > Using mpiexec: mpiexec > > ========================================== > > Building PETSc using GNU Make with 4 build threads > > ========================================== > > make[2]: Entering directory '/home/petsc-3.6.4' > > /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 > > Use "/usr/bin/make V=1" to see the verbose compile lines. > > CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o > > CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o > > verboseinfo.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 > > make[2]: *** Waiting for unfinished jobs.... > > verboseinfof.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 > > zverboseinfof.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 > > zsys.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 > > make[2]: Leaving directory '/home/petsc-3.6.4' > > make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 > > make[1]: Leaving directory '/home/petsc-3.6.4' > > **************************ERROR************************************* > > Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log > > Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov > > ******************************************************************** > > make: *** [makefile:30: all] Error 1 > > > > i have also attached the configure.log and make.log > > > > regards > > Mohammad > > > > > > > > ________________________________ > > From: Matthew Knepley <knepley(a)gmail.com> > > Sent: Monday, February 6, 2017 8:07:41 AM > > To: Mohammad S Dodaran > > Cc: petsc-dev > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: > > > > Satish, > > > > Thanks for your quick response. as you see I can ls to the directory: > > > > ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ > > > > Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. > > You cannot give a path to configure with spaces. > > > > You can remove the spaces using the cygpath command that Satish showed. Please use that command. > > Remove the spaces from this path and give the spaceless path to configure. > > > > Thanks, > > > > Matt > > > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ > > > > > > > > but I do not know why still it has the same problem. and my configure file looks strange. > > > > Best, > > > > Mohammad > > > > ________________________________ > > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > > Sent: Sunday, February 5, 2017 10:58:35 PM > > To: Mohammad S Dodaran > > Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > Try to figureout path without spaces. > > > > cygpath -u `cygpath -s -m PATH` > > > > Make sure you can do "ls" on this path. > > > > And use it with petsc configure. > > > > balay@ps4 ~ > > $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` > > /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > > > balay@ps4 ~ > > $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 > > > > balay@ps4 ~ > > $ > > > > For ex: - I use: > > > > >>>>>>>> > > $ cat config/examples/arch-mswin-intel.py > > #!/usr/bin/python > > if __name__ == '__main__': > > import sys > > import os > > sys.path.insert(0, os.path.abspath('config')) > > import configure > > configure_options = [ > > '--download-fblaslapack=1', > > '--with-cc=win32fe icl', > > '--with-cxx=win32fe icl', > > '--with-fc=win32fe ifort', > > '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', > > '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', > > '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', > > '--with-shared-libraries=0', > > 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', > > ] > > configure.petsc_configure(configure_options) > > > > <<<<<<<<<<< > > > > if you still have issues - send us configure.log for the failure. > > > > Satish > > > > On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > > > > > Dear Petsc developers, > > > > > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > > > > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > > > > > > > But it gives error which says: > > > > > > *************************************************************** > > > ERROR in COMMAND LINE ARGUMENT to ./configure > > > ------------------------------------------------------------------------------- > > > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > > > > > > > How should I solve it? > > > > > > Mohammad > > > > > > > > > > > > > -- > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > -- Norbert Wiener > > > >

1 0

Re: [petsc-dev] plex test examples give different partitionings than output file even with simple partitioner? WTF
by Barry Smith 06 Feb '17

06 Feb '17

There appear to be several examples with "the wrong partitioning" in the output files? I think you need to list in the args: the partitioning you want otherwise it depends on what you currently have installed; which is worthless for regression tests. See attached: all the different iteration counts are due to partitioning. Barry > On Feb 6, 2017, at 7:20 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Mon, Feb 6, 2017 at 6:30 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Matt, > > How come? I check and it is using the simple partitioner and no random number generator is called. How come when I run it it gives a different partitioning than in the output file? The vectors also have different partitionings. Are the output files out of date? > > In my branch, ex15 has not had its partitioning replaced. It is still using ParMetis. > > I can do it. > > Matt > > ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) arch-double > $ petscmpiexec -n 2 ./ex15 -verbose -globaltonatural_sf_view > joe > ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) arch-double > $ paste output/ex15_0.out joe | more > PetscSF Object: 2 MPI processes PetscSF Object: 2 MPI processes > type not yet set type not yet set > [0] Number of roots=6, leaves=6, remote ranks=1 [0] Number of roots=4, leaves=4, remote ranks=2 > [0] 0 <- (1,0) [0] 0 <- (0,0) > [0] 1 <- (1,1) [0] 1 <- (0,1) > [0] 2 <- (1,2) [0] 2 <- (1,0) > [0] 3 <- (1,3) [0] 3 <- (1,1) > [0] 4 <- (1,4) [1] Number of roots=14, leaves=14, remote ranks=2 > [0] 5 <- (1,5) [1] 0 <- (1,2) > [1] Number of roots=12, leaves=12, remote ranks=2 [1] 1 <- (1,3) > [1] 0 <- (1,6) [1] 2 <- (0,2) > [1] 1 <- (1,7) [1] 3 <- (0,3) > [1] 2 <- (1,8) [1] 4 <- (1,4) > [1] 3 <- (1,9) [1] 5 <- (1,5) > [1] 4 <- (0,0) [1] 6 <- (1,6) > [1] 5 <- (0,1) [1] 7 <- (1,7) > [1] 6 <- (1,10) [1] 8 <- (1,8) > [1] 7 <- (1,11) [1] 9 <- (1,9) > [1] 8 <- (0,2) [1] 10 <- (1,10) > [1] 9 <- (0,3) [1] 11 <- (1,11) > [1] 10 <- (0,4) [1] 12 <- (1,12) > [1] 11 <- (0,5) [1] 13 <- (1,13) > ==== original V in global ordering. size==18 block size=2 ==== original V in global ordering. size==18 block size=2 > Vec Object: V 2 MPI processes Vec Object: V 2 MPI processes > type: mpi type: mpi > Process [0] Process [0] > > > > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener

1 0

Re: [petsc-dev] plex test examples give different partitionings than output file even with simple partitioner? WTF
by Matthew Knepley 06 Feb '17

06 Feb '17

On Mon, Feb 6, 2017 at 6:30 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Matt, > > How come? I check and it is using the simple partitioner and no random > number generator is called. How come when I run it it gives a different > partitioning than in the output file? The vectors also have different > partitionings. Are the output files out of date? > In my branch, ex15 has not had its partitioning replaced. It is still using ParMetis. I can do it. Matt > ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) > arch-double > $ petscmpiexec -n 2 ./ex15 -verbose -globaltonatural_sf_view > joe > ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) > arch-double > $ paste output/ex15_0.out joe | more > PetscSF Object: 2 MPI processes PetscSF Object: 2 MPI processes > type not yet set type not yet set > [0] Number of roots=6, leaves=6, remote ranks=1 [0] Number of > roots=4, leaves=4, remote ranks=2 > [0] 0 <- (1,0) [0] 0 <- (0,0) > [0] 1 <- (1,1) [0] 1 <- (0,1) > [0] 2 <- (1,2) [0] 2 <- (1,0) > [0] 3 <- (1,3) [0] 3 <- (1,1) > [0] 4 <- (1,4) [1] Number of roots=14, leaves=14, remote ranks=2 > [0] 5 <- (1,5) [1] 0 <- (1,2) > [1] Number of roots=12, leaves=12, remote ranks=2 [1] 1 <- (1,3) > [1] 0 <- (1,6) [1] 2 <- (0,2) > [1] 1 <- (1,7) [1] 3 <- (0,3) > [1] 2 <- (1,8) [1] 4 <- (1,4) > [1] 3 <- (1,9) [1] 5 <- (1,5) > [1] 4 <- (0,0) [1] 6 <- (1,6) > [1] 5 <- (0,1) [1] 7 <- (1,7) > [1] 6 <- (1,10) [1] 8 <- (1,8) > [1] 7 <- (1,11) [1] 9 <- (1,9) > [1] 8 <- (0,2) [1] 10 <- (1,10) > [1] 9 <- (0,3) [1] 11 <- (1,11) > [1] 10 <- (0,4) [1] 12 <- (1,12) > [1] 11 <- (0,5) [1] 13 <- (1,13) > ==== original V in global ordering. size==18 block size=2 ==== > original V in global ordering. size==18 block size=2 > Vec Object: V 2 MPI processes Vec Object: V 2 MPI processes > type: mpi type: mpi > Process [0] Process [0] > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

1 0

plex test examples give different partitionings than output file even with simple partitioner? WTF
by Barry Smith 06 Feb '17

06 Feb '17

Matt, How come? I check and it is using the simple partitioner and no random number generator is called. How come when I run it it gives a different partitioning than in the output file? The vectors also have different partitionings. Are the output files out of date? ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) arch-double $ petscmpiexec -n 2 ./ex15 -verbose -globaltonatural_sf_view > joe ~/Src/petsc/src/dm/impls/plex/examples/tests (knepley/feature-plex-tests-new=) arch-double $ paste output/ex15_0.out joe | more PetscSF Object: 2 MPI processes PetscSF Object: 2 MPI processes type not yet set type not yet set [0] Number of roots=6, leaves=6, remote ranks=1 [0] Number of roots=4, leaves=4, remote ranks=2 [0] 0 <- (1,0) [0] 0 <- (0,0) [0] 1 <- (1,1) [0] 1 <- (0,1) [0] 2 <- (1,2) [0] 2 <- (1,0) [0] 3 <- (1,3) [0] 3 <- (1,1) [0] 4 <- (1,4) [1] Number of roots=14, leaves=14, remote ranks=2 [0] 5 <- (1,5) [1] 0 <- (1,2) [1] Number of roots=12, leaves=12, remote ranks=2 [1] 1 <- (1,3) [1] 0 <- (1,6) [1] 2 <- (0,2) [1] 1 <- (1,7) [1] 3 <- (0,3) [1] 2 <- (1,8) [1] 4 <- (1,4) [1] 3 <- (1,9) [1] 5 <- (1,5) [1] 4 <- (0,0) [1] 6 <- (1,6) [1] 5 <- (0,1) [1] 7 <- (1,7) [1] 6 <- (1,10) [1] 8 <- (1,8) [1] 7 <- (1,11) [1] 9 <- (1,9) [1] 8 <- (0,2) [1] 10 <- (1,10) [1] 9 <- (0,3) [1] 11 <- (1,11) [1] 10 <- (0,4) [1] 12 <- (1,12) [1] 11 <- (0,5) [1] 13 <- (1,13) ==== original V in global ordering. size==18 block size=2 ==== original V in global ordering. size==18 block size=2 Vec Object: V 2 MPI processes Vec Object: V 2 MPI processes type: mpi type: mpi Process [0] Process [0]

1 0

Re: [petsc-dev] install petsc on windows 10 with mpi
by Satish Balay 06 Feb '17

06 Feb '17

1. configure.log is a cygwin simlink - so native mail app is unable to attach correctly. The actual file is in PETSC_DIR/PETSC_ARCH/lib/petsc/conf 2. Suggest doing the build without fftw and hdf5 packages [once the basic build succeeds - you can look at adding these pacakges.] 3. remove INTEL-MPI from your env - before running configure. [you might be able to use intel-mpi instead of ms-mpi - but we don't have any experience with it] Satish On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > now I'm trying to configure petsc 3.7 > i used the format you showd in your previous email for the directories of fftw and hdf5 as below > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > the result is the following > > TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.scientificpython(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.fiat(config/BuildSystem/config/package.py:742) TESTING: configureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:679) ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw did not work > ******************************************************************************* > > i also attached the configure.log > > > ________________________________ > From: Satish Balay <balay(a)mcs.anl.gov> > Sent: Monday, February 6, 2017 4:28:09 PM > To: Mohammad S Dodaran > Cc: Matthew Knepley; petsc-dev > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > >>>> > > Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 > <<<< > > > 'PETSC_ARCH=' > > Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default.. > > > --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" > > I don't think I've built these packages with MS compilers > before. Somehow they are not picked up anyway. For one - the format > here should be the following [but I don't know if that will make > configure check for them]: > > --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > > > PETSC_DIR=/home/petsc-3.6.4 > > Also - please use latest petsc-3.7 release. > > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > Hm - configure is picking up Intel-MPI from your 'INCLUDE' env > variable - but not 'make' - not sure whats hapenning - but I think its > best to start a clean build with petsc-3.7 [unless you need 3.6 for a > specific need] > > Satish > > On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > > > hello > > > > > > i configured petsc and i was trying to make then this error appeared > > > > > > Using mpiexec: mpiexec > > ========================================== > > Building PETSc using GNU Make with 4 build threads > > ========================================== > > make[2]: Entering directory '/home/petsc-3.6.4' > > /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 > > Use "/usr/bin/make V=1" to see the verbose compile lines. > > CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o > > CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o > > CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o > > verboseinfo.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 > > make[2]: *** Waiting for unfinished jobs.... > > verboseinfof.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 > > zverboseinfof.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 > > zsys.c > > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > > now appears to be compiling using a non-MPICH mpi.h" > > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 > > make[2]: Leaving directory '/home/petsc-3.6.4' > > make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 > > make[1]: Leaving directory '/home/petsc-3.6.4' > > **************************ERROR************************************* > > Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log > > Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov > > ******************************************************************** > > make: *** [makefile:30: all] Error 1 > > > > i have also attached the configure.log and make.log > > > > regards > > Mohammad > > > > > > > > ________________________________ > > From: Matthew Knepley <knepley(a)gmail.com> > > Sent: Monday, February 6, 2017 8:07:41 AM > > To: Mohammad S Dodaran > > Cc: petsc-dev > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: > > > > Satish, > > > > Thanks for your quick response. as you see I can ls to the directory: > > > > ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ > > > > Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. > > You cannot give a path to configure with spaces. > > > > You can remove the spaces using the cygpath command that Satish showed. Please use that command. > > Remove the spaces from this path and give the spaceless path to configure. > > > > Thanks, > > > > Matt > > > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ > > > > > > > > but I do not know why still it has the same problem. and my configure file looks strange. > > > > Best, > > > > Mohammad > > > > ________________________________ > > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > > Sent: Sunday, February 5, 2017 10:58:35 PM > > To: Mohammad S Dodaran > > Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> > > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > > > Try to figureout path without spaces. > > > > cygpath -u `cygpath -s -m PATH` > > > > Make sure you can do "ls" on this path. > > > > And use it with petsc configure. > > > > balay@ps4 ~ > > $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` > > /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > > > balay@ps4 ~ > > $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 > > > > balay@ps4 ~ > > $ > > > > For ex: - I use: > > > > >>>>>>>> > > $ cat config/examples/arch-mswin-intel.py > > #!/usr/bin/python > > if __name__ == '__main__': > > import sys > > import os > > sys.path.insert(0, os.path.abspath('config')) > > import configure > > configure_options = [ > > '--download-fblaslapack=1', > > '--with-cc=win32fe icl', > > '--with-cxx=win32fe icl', > > '--with-fc=win32fe ifort', > > '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', > > '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', > > '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', > > '--with-shared-libraries=0', > > 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', > > ] > > configure.petsc_configure(configure_options) > > > > <<<<<<<<<<< > > > > if you still have issues - send us configure.log for the failure. > > > > Satish > > > > On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > > > > > Dear Petsc developers, > > > > > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > > > > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > > > > > > > But it gives error which says: > > > > > > *************************************************************** > > > ERROR in COMMAND LINE ARGUMENT to ./configure > > > ------------------------------------------------------------------------------- > > > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > > > > > > > How should I solve it? > > > > > > Mohammad > > > > > > > > > > > > > -- > > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > > -- Norbert Wiener > > > >

1 0

Re: [petsc-dev] install petsc on windows 10 with mpi
by Mohammad S Dodaran 06 Feb '17

06 Feb '17

now I'm trying to configure petsc 3.7 i used the format you showd in your previous email for the directories of fftw and hdf5 as below --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 the result is the following TESTING: alternateConfigureLibrary from config.packages.glut(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.giflib(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.scientificpython(config/BuildSystem/config/package.py:742) TESTING: alternateConfigureLibrary from config.packages.fiat(config/BuildSystem/config/package.py:742) TESTING: configureLibrary from config.packages.fftw(config/BuildSystem/config/package.py:679) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw did not work ******************************************************************************* i also attached the configure.log ________________________________ From: Satish Balay <balay(a)mcs.anl.gov> Sent: Monday, February 6, 2017 4:28:09 PM To: Mohammad S Dodaran Cc: Matthew Knepley; petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi >>>> Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 <<<< > 'PETSC_ARCH=' Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default.. > --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" I don't think I've built these packages with MS compilers before. Somehow they are not picked up anyway. For one - the format here should be the following [but I don't know if that will make configure check for them]: --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > PETSC_DIR=/home/petsc-3.6.4 Also - please use latest petsc-3.7 release. > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" Hm - configure is picking up Intel-MPI from your 'INCLUDE' env variable - but not 'make' - not sure whats hapenning - but I think its best to start a clean build with petsc-3.7 [unless you need 3.6 for a specific need] Satish On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > hello > > > i configured petsc and i was trying to make then this error appeared > > > Using mpiexec: mpiexec > ========================================== > Building PETSc using GNU Make with 4 build threads > ========================================== > make[2]: Entering directory '/home/petsc-3.6.4' > /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 > Use "/usr/bin/make V=1" to see the verbose compile lines. > CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o > CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o > CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o > CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o > verboseinfo.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 > make[2]: *** Waiting for unfinished jobs.... > verboseinfof.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 > zverboseinfof.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 > zsys.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 > make[2]: Leaving directory '/home/petsc-3.6.4' > make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 > make[1]: Leaving directory '/home/petsc-3.6.4' > **************************ERROR************************************* > Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log > Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov > ******************************************************************** > make: *** [makefile:30: all] Error 1 > > i have also attached the configure.log and make.log > > regards > Mohammad > > > > ________________________________ > From: Matthew Knepley <knepley(a)gmail.com> > Sent: Monday, February 6, 2017 8:07:41 AM > To: Mohammad S Dodaran > Cc: petsc-dev > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: > > Satish, > > Thanks for your quick response. as you see I can ls to the directory: > > ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ > > Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. > You cannot give a path to configure with spaces. > > You can remove the spaces using the cygpath command that Satish showed. Please use that command. > Remove the spaces from this path and give the spaceless path to configure. > > Thanks, > > Matt > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ > > > > but I do not know why still it has the same problem. and my configure file looks strange. > > Best, > > Mohammad > > ________________________________ > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > Sent: Sunday, February 5, 2017 10:58:35 PM > To: Mohammad S Dodaran > Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > Try to figureout path without spaces. > > cygpath -u `cygpath -s -m PATH` > > Make sure you can do "ls" on this path. > > And use it with petsc configure. > > balay@ps4 ~ > $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` > /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > balay@ps4 ~ > $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 > > balay@ps4 ~ > $ > > For ex: - I use: > > >>>>>>>> > $ cat config/examples/arch-mswin-intel.py > #!/usr/bin/python > if __name__ == '__main__': > import sys > import os > sys.path.insert(0, os.path.abspath('config')) > import configure > configure_options = [ > '--download-fblaslapack=1', > '--with-cc=win32fe icl', > '--with-cxx=win32fe icl', > '--with-fc=win32fe ifort', > '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', > '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', > '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', > '--with-shared-libraries=0', > 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', > ] > configure.petsc_configure(configure_options) > > <<<<<<<<<<< > > if you still have issues - send us configure.log for the failure. > > Satish > > On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > > > Dear Petsc developers, > > > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > > > > But it gives error which says: > > > > *************************************************************** > > ERROR in COMMAND LINE ARGUMENT to ./configure > > ------------------------------------------------------------------------------- > > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > > > > How should I solve it? > > > > Mohammad > > > > > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener >

1 0

Re: [petsc-dev] install petsc on windows 10 with mpi
by Satish Balay 06 Feb '17

06 Feb '17

>>>> Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc="win32fe cl" --with-fc="win32fe ifort" --with-cxx="win32fe cl" --with-mpi-include="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Include/x64]" --with-mpi-lib="[/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpi.lib,/cygdrive/c/PROGRA~2/MICROS~4/MPI/Lib/x64/msmpifec.lib]" --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" --download-fblaslapack=1 --with-c2html=0 --with-debugging=0 --with-ssl=0 --with-x=0 PETSC_ARCH= PETSC_DIR=/home/petsc-3.6.4 <<<< > 'PETSC_ARCH=' Can you rerun with a non-empty PETSC_ARCH string - or let configure choost default.. > --with-fftw-dir="[/cygdrive/c/cygwin64/home/fftw]" --with-hdf5-dir="[/cygdrive/c/cygwin64/home/hdf5]" I don't think I've built these packages with MS compilers before. Somehow they are not picked up anyway. For one - the format here should be the following [but I don't know if that will make configure check for them]: --with-fftw-dir=/cygdrive/c/cygwin64/home/fftw --with-hdf5-dir=/cygdrive/c/cygwin64/home/hdf5 > PETSC_DIR=/home/petsc-3.6.4 Also - please use latest petsc-3.7 release. > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" Hm - configure is picking up Intel-MPI from your 'INCLUDE' env variable - but not 'make' - not sure whats hapenning - but I think its best to start a clean build with petsc-3.7 [unless you need 3.6 for a specific need] Satish On Mon, 6 Feb 2017, Mohammad S Dodaran wrote: > hello > > > i configured petsc and i was trying to make then this error appeared > > > Using mpiexec: mpiexec > ========================================== > Building PETSc using GNU Make with 4 build threads > ========================================== > make[2]: Entering directory '/home/petsc-3.6.4' > /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 > Use "/usr/bin/make V=1" to see the verbose compile lines. > CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o > CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o > CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o > CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o > verboseinfo.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 > make[2]: *** Waiting for unfinished jobs.... > verboseinfof.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 > zverboseinfof.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 > zsys.c > C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but > now appears to be compiling using a non-MPICH mpi.h" > make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 > make[2]: Leaving directory '/home/petsc-3.6.4' > make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 > make[1]: Leaving directory '/home/petsc-3.6.4' > **************************ERROR************************************* > Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log > Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov > ******************************************************************** > make: *** [makefile:30: all] Error 1 > > i have also attached the configure.log and make.log > > regards > Mohammad > > > > ________________________________ > From: Matthew Knepley <knepley(a)gmail.com> > Sent: Monday, February 6, 2017 8:07:41 AM > To: Mohammad S Dodaran > Cc: petsc-dev > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: > > Satish, > > Thanks for your quick response. as you see I can ls to the directory: > > ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ > > Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. > You cannot give a path to configure with spaces. > > You can remove the spaces using the cygpath command that Satish showed. Please use that command. > Remove the spaces from this path and give the spaceless path to configure. > > Thanks, > > Matt > > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ > > > > but I do not know why still it has the same problem. and my configure file looks strange. > > Best, > > Mohammad > > ________________________________ > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > Sent: Sunday, February 5, 2017 10:58:35 PM > To: Mohammad S Dodaran > Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> > Subject: Re: [petsc-dev] install petsc on windows 10 with mpi > > Try to figureout path without spaces. > > cygpath -u `cygpath -s -m PATH` > > Make sure you can do "ls" on this path. > > And use it with petsc configure. > > balay@ps4 ~ > $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` > /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > > balay@ps4 ~ > $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include > mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 > > balay@ps4 ~ > $ > > For ex: - I use: > > >>>>>>>> > $ cat config/examples/arch-mswin-intel.py > #!/usr/bin/python > if __name__ == '__main__': > import sys > import os > sys.path.insert(0, os.path.abspath('config')) > import configure > configure_options = [ > '--download-fblaslapack=1', > '--with-cc=win32fe icl', > '--with-cxx=win32fe icl', > '--with-fc=win32fe ifort', > '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', > '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', > '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', > '--with-shared-libraries=0', > 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', > ] > configure.petsc_configure(configure_options) > > <<<<<<<<<<< > > if you still have issues - send us configure.log for the failure. > > Satish > > On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > > > Dear Petsc developers, > > > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > > > > But it gives error which says: > > > > *************************************************************** > > ERROR in COMMAND LINE ARGUMENT to ./configure > > ------------------------------------------------------------------------------- > > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > > > > How should I solve it? > > > > Mohammad > > > > > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener >

1 0

Re: [petsc-dev] install petsc on windows 10 with mpi
by Mohammad S Dodaran 06 Feb '17

06 Feb '17

hello i configured petsc and i was trying to make then this error appeared Using mpiexec: mpiexec ========================================== Building PETSc using GNU Make with 4 build threads ========================================== make[2]: Entering directory '/home/petsc-3.6.4' /usr/bin/python ./config/gmakegen.py --petsc-arch=../petsc-3.6.4 Use "/usr/bin/make V=1" to see the verbose compile lines. CC ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o CC ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o CC ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o CC ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o verboseinfo.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/verboseinfo.o] Error 2 make[2]: *** Waiting for unfinished jobs.... verboseinfof.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-auto/verboseinfof.o] Error 2 zverboseinfof.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/info/ftn-custom/zverboseinfof.o] Error 2 zsys.c C:\cygwin64\home\PETSC-~1.4\include\petscsys.h(122) : fatal error C1189: #error : "PETSc was configured with MPICH but now appears to be compiling using a non-MPICH mpi.h" make[2]: *** [gmakefile:161: ../petsc-3.6.4/obj/src/sys/ftn-custom/zsys.o] Error 2 make[2]: Leaving directory '/home/petsc-3.6.4' make[1]: *** [/home/petsc-3.6.4/lib/petsc/conf/rules:107: gnumake] Error 2 make[1]: Leaving directory '/home/petsc-3.6.4' **************************ERROR************************************* Error during compile, check ../petsc-3.6.4/lib/petsc/conf/make.log Send it and ../petsc-3.6.4/lib/petsc/conf/configure.log to petsc-maint(a)mcs.anl.gov ******************************************************************** make: *** [makefile:30: all] Error 1 i have also attached the configure.log and make.log regards Mohammad ________________________________ From: Matthew Knepley <knepley(a)gmail.com> Sent: Monday, February 6, 2017 8:07:41 AM To: Mohammad S Dodaran Cc: petsc-dev Subject: Re: [petsc-dev] install petsc on windows 10 with mpi On Sun, Feb 5, 2017 at 11:26 PM, Mohammad S Dodaran <mdodar1(a)lsu.edu<mailto:[email protected]>> wrote: Satish, Thanks for your quick response. as you see I can ls to the directory: ls /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include/ Yes, but as Satish said, there are spaces in the path above. We do not allow spaces in the path. You cannot give a path to configure with spaces. You can remove the spaces using the cygpath command that Satish showed. Please use that command. Remove the spaces from this path and give the spaceless path to configure. Thanks, Matt mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64/ x86/ but I do not know why still it has the same problem. and my configure file looks strange. Best, Mohammad ________________________________ From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> Sent: Sunday, February 5, 2017 10:58:35 PM To: Mohammad S Dodaran Cc: petsc-dev(a)mcs.anl.gov<mailto:[email protected]> Subject: Re: [petsc-dev] install petsc on windows 10 with mpi Try to figureout path without spaces. cygpath -u `cygpath -s -m PATH` Make sure you can do "ls" on this path. And use it with petsc configure. balay@ps4 ~ $ cygpath -u `cygpath -s -m /cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include` /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include balay@ps4 ~ $ ls /cygdrive/c/PROGRA~2/MICROS~2/MPI/Include mpi.f90 mpi.h mpif.h mpio.h mspms.h pmidbg.h x64 x86 balay@ps4 ~ $ For ex: - I use: >>>>>>>> $ cat config/examples/arch-mswin-intel.py #!/usr/bin/python if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--download-fblaslapack=1', '--with-cc=win32fe icl', '--with-cxx=win32fe icl', '--with-fc=win32fe ifort', '--with-mpi-include=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]', '--with-mpi-lib=[/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpifec.lib,/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64/msmpi.lib]', '--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec', '--with-shared-libraries=0', 'DATAFILESPATH=c:/cygwin64/home/petsc/datafiles', ] configure.petsc_configure(configure_options) <<<<<<<<<<< if you still have issues - send us configure.log for the failure. Satish On Sun, 5 Feb 2017, Mohammad S Dodaran wrote: > Dear Petsc developers, > > I am trying to install Petsc on windows 10 but I have a problem. I installed MS-MPI v8<http://go.microsoft.com/FWLink/p/?LinkID=389556> separately and in the configure options I use > > --with-mpi-include="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include" --with-mpi-lib="/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Lib/x64/msmpi.lib" > > > But it gives error which says: > > *************************************************************** > ERROR in COMMAND LINE ARGUMENT to ./configure > ------------------------------------------------------------------------------- > Invalid directory: [/cygdrive/c/Program\ Files\ $x86$/Microsoft\ SDKs/MPI/Include for key with-mpi-include > > > How should I solve it? > > Mohammad > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

1 0

Re: [petsc-dev] every test example runs in a new directory with new test harness
by Scott Kruger 06 Feb '17

06 Feb '17

On 2/6/17 8:42 AM, Satish Balay wrote: > I just tried it - and it doesn't appear to work.. I see. The problem is with the argument inheritance. I broke it when I enabled command-line argument override. The fix will be in the next pull request this week > > Should the keyword for 'subtest' be different than 'test:'? Jed's initial idea was to have it be truly hierarchical although the parser currently only supports one level. Details of how to do the inheritance gets confusing in practice. Scott > > Satish > > ----------------------------------------------------- > balay@asterix /home/balay/petsc (next *=) > $ git diff|cat > diff --git a/src/snes/examples/tutorials/ex12.c b/src/snes/examples/tutorials/ex12.c > index 71166bf..c097018 100644 > --- a/src/snes/examples/tutorials/ex12.c > +++ b/src/snes/examples/tutorials/ex12.c > @@ -1168,10 +1168,8 @@ int main(int argc, char **argv) > suffix: restart_0 > requires: hdf5 > args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append > - test: > - suffix: restart_1 > - requires: hdf5 > - args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -f sol.h5 -restart > + test: > + args: -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -f sol.h5 -restart > # Periodicity > test: > suffix: periodic_0 > balay@asterix /home/balay/petsc (next *=) > $ ./config/gmakegentest.py > balay@asterix /home/balay/petsc (next *=) > $ cat arch-next/tests/src/snes/examples/tutorials/runex12_restart_0.sh > #!/usr/bin/env bash > # This script was created by gmakegentest.py > > # PATH for DLLs on windows > PATH="$PATH":"/home/balay/petsc/arch-next/lib" > > mpiexec='mpiexec' > exec='../ex12' > testname='runex12_restart_0' > label='snes_tutorials-ex12_restart_0' > runfiles='' > wPETSC_DIR='/home/balay/petsc' > petsc_dir='/home/balay/petsc' > args='-run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append' > > . "${petsc_dir}/config/petsc_harness.sh" > > # The diff flags come from script arguments > diff_exe="${petsc_dir}/bin/petscdiff ${diff_flags}" > > > printf "ok ${label} # SKIP PETSC_HAVE_HDF5 requirement not met\n" > total=1; skip=1 > petsc_testend "/home/balay/petsc/arch-next/tests" > exit > > > petsc_testrun "${mpiexec} -n 1 ${exec} ${args}" ex12_restart_0.tmp ${testname}.err "${label}" '' > > petsc_testrun "${diff_exe} /home/balay/petsc/src/snes/examples/tutorials/output/ex12_restart_0.out ex12_restart_0.tmp" diff-${testname}.out diff-${testname}.out diff-${label} "" > > petsc_testend "/home/balay/petsc/arch-next/tests" > balay@asterix /home/balay/petsc (next *=) > $ > > > On Mon, 6 Feb 2017, Scott Kruger wrote: > >> >> The basic idea of running multiple commands within a single shell >> script was what I called a subtest (for lack of a better word). >> So: >> >> >> test: >> suffix: restart >> requires: hdf5 >> args: -run_type test -refinement_limit 0.0 -bc_type dirichlet >> -interpolate 1 -petscspace_order 1 >> test: >> args: -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append >> test: >> args: -f sol.h5 -restart >> >> The args in the subtest inherit from the parent test. This seems >> to be generally useful as a testing idiom in petsc tests as this >> example nicely shows. >> >> Each mpiexec would be tested separately and reported separately. >> This would give you want you want, and should work as is. >> >> >> Tobin pointed out that I broke the for loops and some of the subtest >> functionality in some of the other feature implementations. We >> have come to consensus (right, Tobin?) on the >> desired functionality and implementation. A pull request >> is planned this week. It doesn't affect this directly, but >> should have some minor improvements (like in the reporting). >> >> Scott >> >> >> On 2/6/17 7:10 AM, Matthew Knepley wrote: >>> On Mon, Feb 6, 2017 at 1:05 AM, Jed Brown <jed(a)jedbrown.org >>> <mailto:[email protected]>> wrote: >>> >>> Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> writes: >>> >>>> test: >>>> suffix: restart_0 >>>> requires: hdf5 >>>> args: -run_type test -refinement_limit 0.0 -bc_type dirichlet >>>> -interpolate 1 -petscspace_order 1 -dm_view hdf5:sol.h5 -vec_view >>>> hdf5:sol.h5::append >>>> >>>> test: >>>> suffix: restart_1 >>>> requires: hdf5 >>>> args: -run_type test -refinement_limit 0.0 -bc_type dirichlet >>>> -interpolate 1 -petscspace_order 1 -f sol.h5 -restart >>>> >>>> See a problem? >>>> >>>> Should the same run of the example view the files and then load them back >>>> in? versus trying to read in a data file from another run that may not >>>> even have been created before and even if it was, the file was definitely >>>> created in a different directory? >>> >>> So if write only is broken, do you want both to fail? I think it's >>> better to read and write separately, with comparison using h5diff, since >>> that independently tests read vs write and establishes backward >>> compatibility, which you'd really like the test system to make you deal >>> with explicitly. >>> >>> >>> I know the test is broken, but I did already mail the list about this >>> and was waiting for an answer >>> to be worked out. >>> >>> I agree with Satish that running two commands would be great. I could >>> rewrite the example to >>> both write and load it, but it would complicate it. Also, I am trying to >>> get the pattern I expect the >>> user to follow for checkpointing. >>> >>> Matt >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which >>> their experiments lead. >>> -- Norbert Wiener >> >> -- Tech-X Corporation kruger(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 974-1841 Boulder, CO 80303 Fax: (303) 448-7756

1 0