May 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Strange issue with testsuite
by Scott Kruger 12 May '21

12 May '21

It's something like this: cd arch-debug-uni/tests/sys/tests/runex54_1_options_file-ex54options_1a_wrong/ cat *.tmp # Does anything look fishy? cat diff*.sh # see how diff test with filter is being setup by harness ./diff*.sh # run the diff test Hopefully you can see what's the problem is in more detail. These error catching tests are tricker to debug than the normal tests. Scott On 2021-05-12 16:48, Stefano Zampini did write: > I'm currently trying to build PETSc on a NEC-SX. Apart from other issues, > I'm facing the following issue with the testsuite. > > [zampins@stork petsc]$ make test s='sys*ex54*1a*' V=1 > Using MAKEFLAGS: -- V=1 s=sys*ex54*1a* > arch-debug-uni/tests/sys/tests/runex54_1_options_file-ex54options_1a_wrong.sh > -v > ok sys_tests-ex54_1_options_file-ex54options_1a_wrong # > /home/zampins/src/petsc/lib/petsc/bin/petsc-mpiexec.uni -n 1 ../ex54 > -options_left 0 -options_view -options_file ex54options_1a_wrong 2>&1 | > cat > ex54_1_options_file-ex54options_1a_wrong.tmp > not ok diff-sys_tests-ex54_1_options_file-ex54options_1a_wrong # Error > code: 1 > # 1a2 > # > [0]PETSC ERROR: > /home/zampins/src/petsc/arch-debug-uni/tests/sys/tests/runex54_1_options_file-ex54options_1a_wrong/../ex54 > on a arch-debug-uni named stork by zampins Wed May 12 16:45:46 2021 > > However, if I run the test directly, I think it produces the proper output > to be filtered. How can I debug this? > > [zampins@stork tests]$ ./ex54 -options_left 0 -options_view -options_file > ex54options_1a_wrong > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Invalid argument > [0]PETSC ERROR: Unknown first token in options file ex54options_1a_wrong > line 1: ! > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.15.0-298-g2115278b7a > GIT Date: 2021-05-12 14:01:17 +0300 > [0]PETSC ERROR: ./ex54 on a arch-debug-uni named stork by zampins Wed May > 12 16:46:21 2021 > [0]PETSC ERROR: Configure options --FC_LINKER_FLAGS="-Wl,-z -Wl,muldefs" > --download-sowing-configure-arguments="CC=ncc CXX=nc++" > --with-blaslapack-lib="[/opt/nec/ve/nlc/2.3.0/lib/liblapack.a,/opt/nec/ve/nlc/2.3.0/lib/libblas_sequential.a]" > --with-cc=ncc --with-cxx=nc++ --with-debugging=1 --with-fc=nfort > --with-mpi=0 --with-shared-ld=nld --with-shared-libraries=1 > PETSC_ARCH=arch-debug-uni > [0]PETSC ERROR: #1 PetscOptionsInsertFilePetsc() at > /home/zampins/src/petsc/src/sys/objects/options.c:537 > [0]PETSC ERROR: #2 PetscOptionsInsertFile() at > /home/zampins/src/petsc/src/sys/objects/options.c:645 > [0]PETSC ERROR: #3 PetscOptionsInsertArgs() at > /home/zampins/src/petsc/src/sys/objects/options.c:684 > [0]PETSC ERROR: #4 PetscOptionsInsert() at > /home/zampins/src/petsc/src/sys/objects/options.c:907 > [0]PETSC ERROR: #5 PetscInitialize() at > /home/zampins/src/petsc/src/sys/objects/pinit.c:1024 > > -- > Stefano -- Scott Kruger Tech-X Corporation kruger(a)txcorp.com 5621 Arapahoe Ave, Suite A Phone: (720) 466-3196 Boulder, CO 80303 Fax: (303) 448-7756

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Re: [petsc-dev] Error of petsc-3.15 with python-3.10
by Lawrence Mitchell 12 May '21

12 May '21

> On 12 May 2021, at 13:17, Matthew Knepley <knepley(a)gmail.com> wrote: > > We need makefile parsing, which is currently in distutils. Casual Googling does not find it in > any other packages. Where has Python moved it? I am assuming they have not just dropped > it on the floor. It's been moved into sysconfig from Python 3.10 (https://github.com/python/cpython/commit/90d02e5e63e2cb8f66a2c0dd2ea8d7d4f4…) sysconfig._parse_makefile Lawrence

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Strange issue with testsuite
by Stefano Zampini 12 May '21

12 May '21

I'm currently trying to build PETSc on a NEC-SX. Apart from other issues, I'm facing the following issue with the testsuite. [zampins@stork petsc]$ make test s='sys*ex54*1a*' V=1 Using MAKEFLAGS: -- V=1 s=sys*ex54*1a* arch-debug-uni/tests/sys/tests/runex54_1_options_file-ex54options_1a_wrong.sh -v ok sys_tests-ex54_1_options_file-ex54options_1a_wrong # /home/zampins/src/petsc/lib/petsc/bin/petsc-mpiexec.uni -n 1 ../ex54 -options_left 0 -options_view -options_file ex54options_1a_wrong 2>&1 | cat > ex54_1_options_file-ex54options_1a_wrong.tmp not ok diff-sys_tests-ex54_1_options_file-ex54options_1a_wrong # Error code: 1 # 1a2 # > [0]PETSC ERROR: /home/zampins/src/petsc/arch-debug-uni/tests/sys/tests/runex54_1_options_file-ex54options_1a_wrong/../ex54 on a arch-debug-uni named stork by zampins Wed May 12 16:45:46 2021 However, if I run the test directly, I think it produces the proper output to be filtered. How can I debug this? [zampins@stork tests]$ ./ex54 -options_left 0 -options_view -options_file ex54options_1a_wrong [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid argument [0]PETSC ERROR: Unknown first token in options file ex54options_1a_wrong line 1: ! [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.15.0-298-g2115278b7a GIT Date: 2021-05-12 14:01:17 +0300 [0]PETSC ERROR: ./ex54 on a arch-debug-uni named stork by zampins Wed May 12 16:46:21 2021 [0]PETSC ERROR: Configure options --FC_LINKER_FLAGS="-Wl,-z -Wl,muldefs" --download-sowing-configure-arguments="CC=ncc CXX=nc++" --with-blaslapack-lib="[/opt/nec/ve/nlc/2.3.0/lib/liblapack.a,/opt/nec/ve/nlc/2.3.0/lib/libblas_sequential.a]" --with-cc=ncc --with-cxx=nc++ --with-debugging=1 --with-fc=nfort --with-mpi=0 --with-shared-ld=nld --with-shared-libraries=1 PETSC_ARCH=arch-debug-uni [0]PETSC ERROR: #1 PetscOptionsInsertFilePetsc() at /home/zampins/src/petsc/src/sys/objects/options.c:537 [0]PETSC ERROR: #2 PetscOptionsInsertFile() at /home/zampins/src/petsc/src/sys/objects/options.c:645 [0]PETSC ERROR: #3 PetscOptionsInsertArgs() at /home/zampins/src/petsc/src/sys/objects/options.c:684 [0]PETSC ERROR: #4 PetscOptionsInsert() at /home/zampins/src/petsc/src/sys/objects/options.c:907 [0]PETSC ERROR: #5 PetscInitialize() at /home/zampins/src/petsc/src/sys/objects/pinit.c:1024 -- Stefano

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Re: [petsc-dev] Error of petsc-3.15 with python-3.10
by Matthew Knepley 12 May '21

12 May '21

On Wed, May 12, 2021 at 5:51 AM Antonio T. sagitter < sagitter(a)fedoraproject.org> wrote: > Hi all. > > I'm sorry if using python-3.10 is not in your plan yet and this mail is > inappropriate now. > > This is an error from a build of PETSc-3.15 in a Python-3.10.0b1 (on > Fedora 35 > , GCC-11.1.1): > > + make V=1 MAKE_NP=2 > PETSC_DIR=/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0 > PETSC_ARCH=x86_64 all > We need makefile parsing, which is currently in distutils. Casual Googling does not find it in any other packages. Where has Python moved it? I am assuming they have not just dropped it on the floor. Thanks, Matt > /usr/bin/python3 ./config/gmakegen.py --petsc-arch=x86_64 > > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py:4: > DeprecationWarning: The distutils package is deprecated and slated for > removal in Python 3.12. Use setuptools or check PEP 632 for potential > alternatives > > from distutils.sysconfig import parse_makefile > > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py:4: > DeprecationWarning: The distutils.sysconfig module is deprecated, use > sysconfig instead > > from distutils.sysconfig import parse_makefile > > Traceback (most recent call last): > > File > "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", > line 345, in <module> > > main(petsc_arch=opts.petsc_arch, pkg_dir=opts.pkg_dir, > pkg_name=opts.pkg_name, pkg_arch=opts.pkg_arch, pkg_pkgs=opts.pkg_pkgs, > output=opts.output, verbose=opts.verbose) > > File > "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", > line 328, in main > > petsc.summary() > > File > "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", > line 255, in summary > > self.mistakes.summary() > > File > "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", > line 79, in summary > > raise RuntimeError('PETSc makefiles contain mistakes or files are > missing on filesystem.\n%s\nPossible reasons:\n\t1. Files were deleted > locally, try "hg revert filename" or "git checkout filename".\n\t2. > Files were deleted from repository, but were not removed from makefile. > Send mail to petsc-maint(a)mcs.anl.gov.\n\t3. Someone forgot to "add" new > files to the repository. Send mail to petsc-maint(a)mcs.anl.gov.' % > ('\n'.join(self.mistakes))) > > RuntimeError: PETSc makefiles contain mistakes or files are missing on > filesystem. > > Makefile contains directory not on filesystem: > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/sys: ['\\'] > > Makefile contains directory not on filesystem: > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/mat/impls/aij/seq: > ['\\'] > > Makefile contains directory not on filesystem: > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/ksp/ksp/impls: ['\\'] > > Makefile contains directory not on filesystem: > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/ksp/pc/impls: ['ml\\'] > > Makefile contains directory not on filesystem: > /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/tao/complementarity/impls: > > ['#', 'isls', 'rscs'] > > Possible reasons: > > 1. Files were deleted locally, try "hg revert filename" or "git > checkout filename". > > 2. Files were deleted from repository, but were not removed from > makefile. Send mail to petsc-maint(a)mcs.anl.gov. > > 3. Someone forgot to "add" new files to the repository. Send mail > to > petsc-maint(a)mcs.anl.gov. > > gmakefile:67: x86_64/lib/petsc/conf/files: No such file or directory > > Can you say me what's cause it? (Same configuration works with Python-3.9)? > > > Regards. > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keys.gnupg.net/ > -- 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.cse.buffalo.edu/~knepley/>

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Error of petsc-3.15 with python-3.10
by Antonio T. sagitter 12 May '21

12 May '21

Hi all. I'm sorry if using python-3.10 is not in your plan yet and this mail is inappropriate now. This is an error from a build of PETSc-3.15 in a Python-3.10.0b1 (on Fedora 35 , GCC-11.1.1): + make V=1 MAKE_NP=2 PETSC_DIR=/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0 PETSC_ARCH=x86_64 all /usr/bin/python3 ./config/gmakegen.py --petsc-arch=x86_64 /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py:4: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.sysconfig import parse_makefile /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py:4: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils.sysconfig import parse_makefile Traceback (most recent call last): File "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", line 345, in <module> main(petsc_arch=opts.petsc_arch, pkg_dir=opts.pkg_dir, pkg_name=opts.pkg_name, pkg_arch=opts.pkg_arch, pkg_pkgs=opts.pkg_pkgs, output=opts.output, verbose=opts.verbose) File "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", line 328, in main petsc.summary() File "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", line 255, in summary self.mistakes.summary() File "/builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/./config/gmakegen.py", line 79, in summary raise RuntimeError('PETSc makefiles contain mistakes or files are missing on filesystem.\n%s\nPossible reasons:\n\t1. Files were deleted locally, try "hg revert filename" or "git checkout filename".\n\t2. Files were deleted from repository, but were not removed from makefile. Send mail to petsc-maint(a)mcs.anl.gov.\n\t3. Someone forgot to "add" new files to the repository. Send mail to petsc-maint(a)mcs.anl.gov.' % ('\n'.join(self.mistakes))) RuntimeError: PETSc makefiles contain mistakes or files are missing on filesystem. Makefile contains directory not on filesystem: /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/sys: ['\\'] Makefile contains directory not on filesystem: /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/mat/impls/aij/seq: ['\\'] Makefile contains directory not on filesystem: /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/ksp/ksp/impls: ['\\'] Makefile contains directory not on filesystem: /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/ksp/pc/impls: ['ml\\'] Makefile contains directory not on filesystem: /builddir/build/BUILD/petsc-3.15.0/petsc-3.15.0/src/tao/complementarity/impls: ['#', 'isls', 'rscs'] Possible reasons: 1. Files were deleted locally, try "hg revert filename" or "git checkout filename". 2. Files were deleted from repository, but were not removed from makefile. Send mail to petsc-maint(a)mcs.anl.gov. 3. Someone forgot to "add" new files to the repository. Send mail to petsc-maint(a)mcs.anl.gov. gmakefile:67: x86_64/lib/petsc/conf/files: No such file or directory Can you say me what's cause it? (Same configuration works with Python-3.9)? Regards. -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keys.gnupg.net/

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Re: [petsc-dev] [petsc4py] missing DMPlexCreateMedFromFile interface
by Matthew Knepley 11 May '21

11 May '21

On Tue, May 11, 2021 at 10:19 AM TARDIEU Nicolas <nicolas.tardieu(a)edf.fr> wrote: > Dear PETSc team, > > I cannot find the interface to DMPlexCreateMedFromFile in petsc4py. > Am I missing something ? Could it be added to the python module ? > Hi Nicolas, You can just use DMPlexCreateFromFile() since it handles all supported file types automatically. Thanks, Matt > > Best regards, > Nicolas > > -- > Nicolas Tardieu > > > > > > > Ce message et toutes les pièces jointes (ci-après le 'Message') sont > établis à l'intention exclusive des destinataires et les informations qui y > figurent sont strictement confidentielles. Toute utilisation de ce Message > non conforme à sa destination, toute diffusion ou toute publication totale > ou partielle, est interdite sauf autorisation expresse. > > Si vous n'êtes pas le destinataire de ce Message, il vous est interdit de > le copier, de le faire suivre, de le divulguer ou d'en utiliser tout ou > partie. Si vous avez reçu ce Message par erreur, merci de le supprimer de > votre système, ainsi que toutes ses copies, et de n'en garder aucune trace > sur quelque support que ce soit. Nous vous remercions également d'en > avertir immédiatement l'expéditeur par retour du message. > > Il est impossible de garantir que les communications par messagerie > électronique arrivent en temps utile, sont sécurisées ou dénuées de toute > erreur ou virus. > ____________________________________________________ > > This message and any attachments (the 'Message') are intended solely for > the addressees. The information contained in this Message is confidential. > Any use of information contained in this Message not in accord with its > purpose, any dissemination or disclosure, either whole or partial, is > prohibited except formal approval. > > If you are not the addressee, you may not copy, forward, disclose or use > any part of it. If you have received this message in error, please delete > it and all copies from your system and notify the sender immediately by > return message. > > E-mail communication cannot be guaranteed to be timely secure, error or > virus-free. > -- 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.cse.buffalo.edu/~knepley/>

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[petsc4py] missing DMPlexCreateMedFromFile interface
by TARDIEU Nicolas 11 May '21

11 May '21

Dear PETSc team, I cannot find the interface to DMPlexCreateMedFromFile in petsc4py. Am I missing something ? Could it be added to the python module ? Best regards, Nicolas -- Nicolas Tardieu Ce message et toutes les pièces jointes (ci-après le 'Message') sont établis à l'intention exclusive des destinataires et les informations qui y figurent sont strictement confidentielles. Toute utilisation de ce Message non conforme à sa destination, toute diffusion ou toute publication totale ou partielle, est interdite sauf autorisation expresse. Si vous n'êtes pas le destinataire de ce Message, il vous est interdit de le copier, de le faire suivre, de le divulguer ou d'en utiliser tout ou partie. Si vous avez reçu ce Message par erreur, merci de le supprimer de votre système, ainsi que toutes ses copies, et de n'en garder aucune trace sur quelque support que ce soit. Nous vous remercions également d'en avertir immédiatement l'expéditeur par retour du message. Il est impossible de garantir que les communications par messagerie électronique arrivent en temps utile, sont sécurisées ou dénuées de toute erreur ou virus. ____________________________________________________ This message and any attachments (the 'Message') are intended solely for the addressees. The information contained in this Message is confidential. Any use of information contained in this Message not in accord with its purpose, any dissemination or disclosure, either whole or partial, is prohibited except formal approval. If you are not the addressee, you may not copy, forward, disclose or use any part of it. If you have received this message in error, please delete it and all copies from your system and notify the sender immediately by return message. E-mail communication cannot be guaranteed to be timely secure, error or virus-free.

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Re: [petsc-dev] should plexgeometry.c check for divide by zero?
by Barry Smith 09 May '21

09 May '21

I saw it when running src/dm/impls/plex/tests ex5 without setting the -displacement_petscspace_degree 1 and using -fp_trap ./ex5 -fp_trap -dim 2 -faulttraction_petscspace_degree 1 -orig_dm_plex_check_all -dm_plex_check_all -displacement_petscspace_degree 1 -faulttraction_petscspace_degree 1 -petscds_view -local_section_view -local_solution_view -local_residual_view -local_jacobian_view It looks like the degree may be defaulting to 0?? which then results in bogus information passed to the geometry routines; without the -fp_trap it keeps running but presumably generating nonsense. Barry > On May 9, 2021, at 12:12 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Sun, May 9, 2021 at 12:06 PM Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: > > Matt, > > > if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); > csum[d] /= (tdim+1)*vsum; > > Also > > for (d = 0; d < dim; d++) n[d] /= norm; > etc > > Would adding (some/all) tests detect errors in the geometry information earlier then later strange behavior that happens because of the infinities in the arrays? > > We could perhaps benefit from earlier checks. Here however all points would have to be the same in order for vsum == 0. which is a generacy I have never seen. > > Thanks, > > 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 > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] should plexgeometry.c check for divide by zero?
by Matthew Knepley 09 May '21

09 May '21

On Sun, May 9, 2021 at 12:06 PM Barry Smith <bsmith(a)petsc.dev> wrote: > > Matt, > > > if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); > csum[d] /= (tdim+1)*vsum; > > Also > > for (d = 0; d < dim; d++) n[d] /= norm; > etc > > Would adding (some/all) tests detect errors in the geometry information > earlier then later strange behavior that happens because of the infinities > in the arrays? > We could perhaps benefit from earlier checks. Here however all points would have to be the same in order for vsum == 0. which is a generacy I have never seen. Thanks, 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 https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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should plexgeometry.c check for divide by zero?
by Barry Smith 09 May '21

09 May '21

Matt, if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); csum[d] /= (tdim+1)*vsum; Also for (d = 0; d < dim; d++) n[d] /= norm; etc Would adding (some/all) tests detect errors in the geometry information earlier then later strange behavior that happens because of the infinities in the arrays?

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