June 2018 - petsc-dev - mailman3.cels.anl.gov

Adding p4est to nightly tests
by Stefano Zampini 30 Jun '18

30 Jun '18

Satish, when you have time can you add p4est to some of the archs we tests nightly? Matt and/or Toby, is there any reason why p4est is not under the testsuite? Thanks, Stefano

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

It builds and runs but looks like PETSc does not register aijmkl matrices. --- > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package: http://www.mcs.anl.gov/petsc/documentation/installation.html#external > [0]PETSC ERROR: Unknown Mat type given: aijmkl > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown > [0]PETSC ERROR: /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/./ex19 on a named nid02516 by madams Sat Jun 30 12:48:10 2018 > [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-memcmp-ok=1 --known-sizeof-MPI_Comm=4 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --known-mpi-int64_t=1 --known-mpi-c-double-complex=1 --known-has-attribute-aligned=1 --with-cc=cc --with-cxx=CC --with-fc=ftn COPTFLAGS=" -g -O0 -hcpu=mic-knl -qopenmp-simd" CXXOPTFLAGS="-g -O0 -hcpu=mic-knl -qopenmp-simd" FOPTFLAGS=" -g -O0 -hcpu=mic-knl -qopenmp-simd" --download-metis=1 --with-hypre-dir=/global/homes/m/madams/tmp/hypre-2.14.0 --download-parmetis=1 --with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a --with-debugging=1 --with-mpiexec=srun --with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 --with-64-bit-indices=1 PETSC_ARCH=arch-cori-knl-dbg64-intel-omp --with-openmp=1 --download-p4est=0 --with-x=0 --prefix=/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp PETSC_DIR=/global/homes/m/madams/petsc_install/petsc > [0]PETSC ERROR: #1 MatSetType() line 61 in /global/u2/m/madams/petsc_install/petsc/src/mat/interface/matreg.c > [0]PETSC ERROR: #2 MatSetFromOptions() line 229 in /global/u2/m/madams/petsc_install/petsc/src/mat/utils/gcreate.c > [0]PETSC ERROR: #3 DMCreateMatrix_DA() line 793 in /global/u2/m/madams/petsc_install/petsc/src/dm/impls/da/fdda.c > [0]PETSC ERROR: #4 DMCreateMatrix() line 1262 in /global/u2/m/madams/petsc_install/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #5 SNESSetUpMatrices() line 646 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c > [0]PETSC ERROR: #6 SNESSetUp_NEWTONLS() line 296 in /global/u2/m/madams/petsc_install/petsc/src/snes/impls/ls/ls.c > [0]PETSC ERROR: #7 SNESSetUp() line 2908 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c > [0]PETSC ERROR: #8 SNESSolve() line 4300 in /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c > [0]PETSC ERROR: #9 main() line 161 in /global/homes/m/madams/petsc_install/petsc/src/snes/examples/tutorials/ex19.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -da_refine 3 > [0]PETSC ERROR: -ksp_monitor > [0]PETSC ERROR: -mat_type aijmkl > [0]PETSC ERROR: -options_left > [0]PETSC ERROR: -pc_type gamg > [0]PETSC ERROR: -snes_monitor_short > [0]PETSC ERROR: -snes_view > [0]PETSC ERROR: ----------------End of Error Message -------se On Sat, Jun 30, 2018 at 3:08 PM Mark Adams <mfadams(a)lbl.gov> wrote: > OK, that got further. > > On Sat, Jun 30, 2018 at 3:03 PM Mark Adams <mfadams(a)lbl.gov> wrote: > >> Like this? >> >> >> '--with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', >> >> >> On Sat, Jun 30, 2018 at 3:00 PM Mark Adams <mfadams(a)lbl.gov> wrote: >> >>> >>>>> Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib >>>>> --with-blaslapack-include". But not both! >>>>> >>>> >>>> Get rid of the dir option, and give the full path to the library. >>>> >>>> >>> What is the syntax for giving the full path? >>> >>

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

OK, that got further. On Sat, Jun 30, 2018 at 3:03 PM Mark Adams <mfadams(a)lbl.gov> wrote: > Like this? > > > '--with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', > > > On Sat, Jun 30, 2018 at 3:00 PM Mark Adams <mfadams(a)lbl.gov> wrote: > >> >>>> Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib >>>> --with-blaslapack-include". But not both! >>>> >>> >>> Get rid of the dir option, and give the full path to the library. >>> >>> >> What is the syntax for giving the full path? >> >

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

Like this? '--with-blaslapack-lib=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', On Sat, Jun 30, 2018 at 3:00 PM Mark Adams <mfadams(a)lbl.gov> wrote: > >>> Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib >>> --with-blaslapack-include". But not both! >>> >> >> Get rid of the dir option, and give the full path to the library. >> >> > What is the syntax for giving the full path? >

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

> > >> Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib >> --with-blaslapack-include". But not both! >> > > Get rid of the dir option, and give the full path to the library. > > What is the syntax for giving the full path?

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Re: [petsc-dev] building with MKL
by Matthew Knepley 30 Jun '18

30 Jun '18

On Sat, Jun 30, 2018 at 1:00 PM Mark Adams <mfadams(a)lbl.gov> wrote: > Stuck again. I use: > > > '--with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64', > > '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64', > > It does not find the MKL library because, apparently, it is not > libmkl_intel.a (log file attached). > > If I add: > > '--with-blaslapack-lib=libmkl_intel_thread.a', > > I get: > > Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib > --with-blaslapack-include". But not both! > Get rid of the dir option, and give the full path to the library. Matt > Mark > > On Sat, Jun 30, 2018 at 1:25 PM Mark Adams <mfadams(a)lbl.gov> wrote: > >> Found a syntax error from Intel web page and --with-blaslapack-lib to >> specify the library. Press on. >> >> On Sat, Jun 30, 2018 at 11:50 AM Mark Adams <mfadams(a)lbl.gov> wrote: >> >>> I am configuring with MKL: >>> >>> >>> '--with-blas-lapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', >>> >>> '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', >>> >>> >>> and get this error (appended). It is looking for libmkl_intel.a but this >>> is what there is: >>> >>> 08:46 cori07 maint *= ~/petsc_install/petsc/src/snes/examples/tutorials$ >>> ll >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_inte* >>> -rw-r--r-- 1 root root 22133402 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.a >>> -rwxr-xr-x 1 root root 9783841 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.so >>> -rw-r--r-- 1 root root 23254666 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.a >>> -rwxr-xr-x 1 root root 10567885 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so >>> -rw-r--r-- 1 root root 49087274 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.a >>> -rwxr-xr-x 1 root root 37230319 Oct 6 2017 >>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so >>> >>> I would guess I want to add and LDFLAGS="lmkl_intel_thread" maybe? I >>> want to use OpenMP. >>> >>> Thanks, >>> Mark >>> >>> >>> >>> Pushing language C >>> Popping language C >>> Executing: cc -o /tmp/petsc-ZL05ng/config.libraries/conftest -g -O0 >>> -hcpu=mic-knl -qopenmp-simd -fopenmp >>> /tmp/petsc-ZL05ng/config.libraries/conftest.o >>> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin >>> -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin >>> -lmkl_intel -lmkl_core -lmkl_gnu_thread -lgomp -ldl -lpthread -lstdc++ -ldl >>> Possible ERROR while running linker: exit code 256 >>> stderr: >>> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: >>> cannot find -lmkl_intel >>> Popping language C >>> Unknown name mangling in BLAS/LAPACK >>> **** Configure header /tmp/petsc-ZL05ng/confdefs.h **** >>> #if !defined(INCLUDED_UNKNOWN) >>> >>> -- 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 https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

Stuck again. I use: '--with-blaslapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64', '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64', It does not find the MKL library because, apparently, it is not libmkl_intel.a (log file attached). If I add: '--with-blaslapack-lib=libmkl_intel_thread.a', I get: Specify either "--with-blaslapack-dir" or "--with-blaslapack-lib --with-blaslapack-include". But not both! Mark On Sat, Jun 30, 2018 at 1:25 PM Mark Adams <mfadams(a)lbl.gov> wrote: > Found a syntax error from Intel web page and --with-blaslapack-lib to > specify the library. Press on. > > On Sat, Jun 30, 2018 at 11:50 AM Mark Adams <mfadams(a)lbl.gov> wrote: > >> I am configuring with MKL: >> >> >> '--with-blas-lapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', >> >> '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', >> >> >> and get this error (appended). It is looking for libmkl_intel.a but this >> is what there is: >> >> 08:46 cori07 maint *= ~/petsc_install/petsc/src/snes/examples/tutorials$ >> ll >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_inte* >> -rw-r--r-- 1 root root 22133402 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.a >> -rwxr-xr-x 1 root root 9783841 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.so >> -rw-r--r-- 1 root root 23254666 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.a >> -rwxr-xr-x 1 root root 10567885 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so >> -rw-r--r-- 1 root root 49087274 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.a >> -rwxr-xr-x 1 root root 37230319 Oct 6 2017 >> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so >> >> I would guess I want to add and LDFLAGS="lmkl_intel_thread" maybe? I >> want to use OpenMP. >> >> Thanks, >> Mark >> >> >> >> Pushing language C >> Popping language C >> Executing: cc -o /tmp/petsc-ZL05ng/config.libraries/conftest -g -O0 >> -hcpu=mic-knl -qopenmp-simd -fopenmp >> /tmp/petsc-ZL05ng/config.libraries/conftest.o >> -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin >> -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin >> -lmkl_intel -lmkl_core -lmkl_gnu_thread -lgomp -ldl -lpthread -lstdc++ -ldl >> Possible ERROR while running linker: exit code 256 >> stderr: >> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: >> cannot find -lmkl_intel >> Popping language C >> Unknown name mangling in BLAS/LAPACK >> **** Configure header /tmp/petsc-ZL05ng/confdefs.h **** >> #if !defined(INCLUDED_UNKNOWN) >> >>

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Re: [petsc-dev] building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

Found a syntax error from Intel web page and --with-blaslapack-lib to specify the library. Press on. On Sat, Jun 30, 2018 at 11:50 AM Mark Adams <mfadams(a)lbl.gov> wrote: > I am configuring with MKL: > > > '--with-blas-lapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', > > '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', > > > and get this error (appended). It is looking for libmkl_intel.a but this > is what there is: > > 08:46 cori07 maint *= ~/petsc_install/petsc/src/snes/examples/tutorials$ > ll > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_inte* > -rw-r--r-- 1 root root 22133402 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.a > -rwxr-xr-x 1 root root 9783841 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.so > -rw-r--r-- 1 root root 23254666 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.a > -rwxr-xr-x 1 root root 10567885 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so > -rw-r--r-- 1 root root 49087274 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.a > -rwxr-xr-x 1 root root 37230319 Oct 6 2017 > /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so > > I would guess I want to add and LDFLAGS="lmkl_intel_thread" maybe? I want > to use OpenMP. > > Thanks, > Mark > > > > Pushing language C > Popping language C > Executing: cc -o /tmp/petsc-ZL05ng/config.libraries/conftest -g -O0 > -hcpu=mic-knl -qopenmp-simd -fopenmp > /tmp/petsc-ZL05ng/config.libraries/conftest.o > -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin > -lmkl_intel -lmkl_core -lmkl_gnu_thread -lgomp -ldl -lpthread -lstdc++ -ldl > Possible ERROR while running linker: exit code 256 > stderr: > /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: > cannot find -lmkl_intel > Popping language C > Unknown name mangling in BLAS/LAPACK > **** Configure header /tmp/petsc-ZL05ng/confdefs.h **** > #if !defined(INCLUDED_UNKNOWN) > >

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building with MKL
by Mark Adams 30 Jun '18

30 Jun '18

I am configuring with MKL: '--with-blas-lapack-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', '--with-mkl_pardiso-dir=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin', and get this error (appended). It is looking for libmkl_intel.a but this is what there is: 08:46 cori07 maint *= ~/petsc_install/petsc/src/snes/examples/tutorials$ ll /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_inte* -rw-r--r-- 1 root root 22133402 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.a -rwxr-xr-x 1 root root 9783841 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.so -rw-r--r-- 1 root root 23254666 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.a -rwxr-xr-x 1 root root 10567885 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so -rw-r--r-- 1 root root 49087274 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.a -rwxr-xr-x 1 root root 37230319 Oct 6 2017 /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so I would guess I want to add and LDFLAGS="lmkl_intel_thread" maybe? I want to use OpenMP. Thanks, Mark Pushing language C Popping language C Executing: cc -o /tmp/petsc-ZL05ng/config.libraries/conftest -g -O0 -hcpu=mic-knl -qopenmp-simd -fopenmp /tmp/petsc-ZL05ng/config.libraries/conftest.o -Wl,-rpath,/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin -lmkl_intel -lmkl_core -lmkl_gnu_thread -lgomp -ldl -lpthread -lstdc++ -ldl Possible ERROR while running linker: exit code 256 stderr: /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lmkl_intel Popping language C Unknown name mangling in BLAS/LAPACK **** Configure header /tmp/petsc-ZL05ng/confdefs.h **** #if !defined(INCLUDED_UNKNOWN)

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Re: [petsc-dev] testing on Titan
by Mark Adams 30 Jun '18

30 Jun '18

Thanks Rich, I may take you up on your offer but I've handed it over to the apps. It seems to be working, but I would not be surprised if there are more problems. Note, here is something that I heard from ORNL about cray-petsc: *One of the OLCF consultants sent me this table about testing petsc ex1.f90 using pgi and petsc.* *It shows the combination* *pgi 17.5, cray-petsc 3.7.6.2, cudatoolkit 7.5 worked* *At least they are aware there is a problem.* On Fri, Jun 29, 2018 at 8:30 PM Richard Tran Mills <rtmills(a)anl.gov> wrote: > Hi Mark, > > I've got an OLCF account but don't have access to Titan. Would it be > helpful for me to apply to get on whatever allocation you are using so I > can poke around at this stuff? (If so, send me a message off list with > details of what I should apply for.) > > Hopefully I could get on there faster than it took them to enable me on > Summit. I had volunteered to help with issues on Summit some time ago, but > it took so long for them to enable my account on there that I didn't matter > by then. > > --Richard > > On Fri, Jun 29, 2018 at 7:12 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > >> Thanks all, I knew this but its been a while since I've run on this file >> setup. >> >> On Fri, Jun 29, 2018 at 9:15 AM Seung-Hoe Ku <sku(a)pppl.gov> wrote: >> >>> Try copying files to scratch file system. >>> Home is not available when executive batch job. Probably interactive >>> she'll too. >>> >>> On Fri, Jun 29, 2018 at 7:47 AM Mark Adams <mfadams(a)lbl.gov> wrote: >>> >>>> I can not even run a job here. This is from an interactive shell: >>>> >>>> 64-pgi ex19-batch1:~/petsc/src/snes/examples/tutorials> make >>>> PETSC_DIR=/autofs/nccs-svm1_home1/adams/petsc PETSC_ARCH=arch-titan-dbg6 >>>> cc -o ex19.o -c -fast -mp >>>> -I/autofs/nccs-svm1_home1/adams/petsc/include >>>> -I/autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/include >>>> -I/ccs/proj/env003/petscv3.9-dbg64-pgi/include `pwd`/ex19.c >>>> cc -fast -mp -o ex19 ex19.o >>>> -L/autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib >>>> -Wl,-rpath,/ccs/proj/env003/petscv3.9-dbg64-pgi/lib >>>> -L/ccs/proj/env003/petscv3.9-dbg64-pgi/lib -lpetsc -lHYPRE -lflapack >>>> -lfblas -lparmetis -lmetis -lstdc++ -ldl >>>> /autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib/libpetsc.a(dlimpl.o): >>>> In function `PetscDLOpen': >>>> /autofs/nccs-svm1_home1/adams/petsc/src/sys/dll/dlimpl.c:54: warning: >>>> Using 'dlopen' in statically linked applications requires at runtime the >>>> shared libraries from the glibc version used for linking >>>> /autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib/libpetsc.a(send.o): >>>> In function `PetscOpenSocket': >>>> /autofs/nccs-svm1_home1/adams/petsc/src/sys/classes/viewer/impls/socket/send.c:106: >>>> warning: Using 'gethostbyname' in statically linked applications requires >>>> at runtime the shared libraries from the glibc version used for linking >>>> adams@titan-batch1:~/petsc/src/snes/examples/tutorials> aprun -n 1 >>>> ./ex19 >>>> [NID 02258] 2018-06-29 07:45:09 Exec ./ex19 failed: chdir >>>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such >>>> file or directory >>>> adams@titan-batch1:~/petsc/src/snes/examples/tutorials> >>>> >>>> Seung-Hoe runs here, maybe he can give me advice on what is wrong here. >>>> >>>> >>>> On Thu, Jun 28, 2018 at 7:53 PM Smith, Barry F. <bsmith(a)mcs.anl.gov> >>>> wrote: >>>> >>>>> >>>>> 1) We need to get this PGI compiler into our regular testing. It >>>>> doesn't like some Fortran code the other compilers are ok with >>>>> >>>>> 2) Mark, likely you just need to submit the examples manually to >>>>> run them. cd src/snes/examples/tutorials; make ex19 then use the batch >>>>> system to submit the example >>>>> >>>>> Barry >>>>> >>>>> >>>>> > On Jun 28, 2018, at 5:35 PM, Mark Adams <mfadams(a)lbl.gov> wrote: >>>>> > >>>>> > I am trying to run on Titan and I am having problems running the >>>>> tests. I get this output. It says it can not find a directory, but I do an >>>>> ls in after the error and you can see that it is there. >>>>> > >>>>> > I've attached the logs. >>>>> > >>>>> > Any ideas? >>>>> > Thanks, >>>>> > Mark >>>>> > >>>>> > adams@titan-login6:~/petsc> make >>>>> PETSC_DIR=/ccs/proj/env003/petscv3.9-opt64-pgi PETSC_ARCH="" test >>>>> > Running test examples to verify correct installation >>>>> > Using PETSC_DIR=/ccs/proj/env003/petscv3.9-opt64-pgi and PETSC_ARCH= >>>>> > *******************Error detected during compile or >>>>> link!******************* >>>>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > /ccs/home/adams/petsc/src/snes/examples/tutorials ex19 >>>>> > >>>>> ********************************************************************************* >>>>> > cc -o ex19.o -c -fast -mp >>>>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include >>>>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include >>>>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include `pwd`/ex19.c >>>>> > cc -fast -mp -o ex19 ex19.o >>>>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib >>>>> -Wl,-rpath,/ccs/proj/env003/petscv3.9-opt64-pgi/lib >>>>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib -lpetsc -lHYPRE -lflapack >>>>> -lfblas -lparmetis -lmetis -lstdc++ -ldl >>>>> > /ccs/proj/env003/petscv3.9-opt64-pgi/lib/libpetsc.a(dlimpl.o): In >>>>> function `PetscDLOpen': >>>>> > /autofs/nccs-svm1_home1/adams/petsc/src/sys/dll/dlimpl.c:53: >>>>> warning: Using 'dlopen' in statically linked applications requires at >>>>> runtime the shared libraries from the glibc version used for linking >>>>> > /ccs/proj/env003/petscv3.9-opt64-pgi/lib/libpetsc.a(send.o): In >>>>> function `PetscOpenSocket': >>>>> > >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/sys/classes/viewer/impls/socket/send.c:101: >>>>> warning: Using 'gethostbyname' in statically linked applications requires >>>>> at runtime the shared libraries from the glibc version used for linking >>>>> > /bin/rm -f ex19.o >>>>> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 >>>>> MPI process >>>>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > [NID 18525] 2018-06-28 18:25:39 Exec ./ex19 failed: chdir >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such >>>>> file or directory >>>>> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 >>>>> MPI processes >>>>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > [NID 18525] 2018-06-28 18:25:46 Exec ./ex19 failed: chdir >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such >>>>> file or directory >>>>> > 1,5c1 >>>>> > < lid velocity = 0.0016, prandtl # = 1., grashof # = 1. >>>>> > < 0 SNES Function norm 0.0406612 >>>>> > < 1 SNES Function norm 4.12227e-06 >>>>> > < 2 SNES Function norm 6.098e-11 >>>>> > < Number of SNES iterations = 2 >>>>> > --- >>>>> > > [NID 18525] 2018-06-28 18:25:55 Exec ./ex19 failed: chdir >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such >>>>> file or directory >>>>> > /ccs/home/adams/petsc/src/snes/examples/tutorials >>>>> > Possible problem with ex19_hypre, diffs above >>>>> > ========================================= >>>>> > *******************Error detected during compile or >>>>> link!******************* >>>>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > /ccs/home/adams/petsc/src/snes/examples/tutorials ex5f >>>>> > ********************************************************* >>>>> > ftn -c -fast -mp -I/ccs/proj/env003/petscv3.9-opt64-pgi/include >>>>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include >>>>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include -o ex5f.o ex5f.F90 >>>>> > PGF90-S-0155-Could not resolve generic procedure dmdacreate2d >>>>> (ex5f.F90: 120) >>>>> > PGF90-S-0450-Argument number 2 to snesgetiterationnumber: kind >>>>> mismatch (ex5f.F90: 180) >>>>> > 0 inform, 0 warnings, 2 severes, 0 fatal for main >>>>> > PGF90-S-0155-Could not resolve generic procedure matsetvalueslocal >>>>> (ex5f.F90: 464) >>>>> > PGF90-S-0155-Could not resolve generic procedure matsetvalueslocal >>>>> (ex5f.F90: 477) >>>>> > 0 inform, 0 warnings, 2 severes, 0 fatal for formjacobianlocal >>>>> > gmake[3]: [ex5f.o] Error 2 (ignored) >>>>> > ftn -fast -mp -o ex5f ex5f.o >>>>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib >>>>> -Wl,-rpath,/ccs/proj/env003/petscv3.9-opt64-pgi/lib >>>>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib -lpetsc -lHYPRE -lflapack >>>>> -lfblas -lparmetis -lmetis -lstdc++ -ldl >>>>> > /usr/bin/ld: cannot find ex5f.o: No such file or directory >>>>> > /usr/bin/sha1sum: ex5f: No such file or directory >>>>> > gmake[3]: [ex5f] Error 2 (ignored) >>>>> > /bin/rm -f ex5f.o >>>>> > Completed test examples >>>>> > adams@titan-login6:~/petsc> ll >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials >>>>> > total 1864 >>>>> > -rw-rw-r-- 1 adams adams 11134 May 3 14:26 ex1.c >>>>> > drwxr-xr-x 3 adams adams 4096 May 3 14:26 ex10d >>>>> > -rw-rw-r-- 1 adams adams 92615 May 3 14:26 ex12.c >>>>> > -rw-r--r-- 1 adams adams 19324 Jun 21 17:59 ex13.c >>>>> > -rw-rw-r-- 1 adams adams 20550 May 3 14:26 ex14.c >>>>> > >>>>> > <make.log><configure.log> >>>>> >>>>> -- >>> Sent from Iphone >>> >> >

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