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

Re: [petsc-dev] Test parsing
by Jacob Faibussowitsch 28 Oct '21

28 Oct '21

Alternatively, we could run dos2unix over all the tests during configure stage and error if this makes a diff. https://linux.die.net/man/1/dos2unix Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) > On Oct 28, 2021, at 08:22, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > > Fix is trivial, we just need to replace ‘\n’ with os.linesep everywhere. > > https://docs.python.org/3/library/os.html#os.linesep <https://docs.python.org/3/library/os.html#os.linesep> > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > >> On Oct 28, 2021, at 08:12, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >> >> I just found a loophole in the test parsing happening here: >> >> https://gitlab.com/petsc/petsc/-/blob/main/config/testparse.py#L530 <https://gitlab.com/petsc/petsc/-/blob/main/config/testparse.py#L530> >> >> If your file was produced on Windows (CRLF), then the parsing fails and tests >> are silently ignored. This took me some time to find and could be confusing >> for others. I think we should either: >> >> a) Fix the parser to work with CRLF as well >> >> or >> >> b) Fail immediately for CRLF files >> >> What do you think? >> >> 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] Test parsing
by Jacob Faibussowitsch 28 Oct '21

28 Oct '21

Fix is trivial, we just need to replace ‘\n’ with os.linesep everywhere. https://docs.python.org/3/library/os.html#os.linesep <https://docs.python.org/3/library/os.html#os.linesep> Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) > On Oct 28, 2021, at 08:12, Matthew Knepley <knepley(a)gmail.com> wrote: > > I just found a loophole in the test parsing happening here: > > https://gitlab.com/petsc/petsc/-/blob/main/config/testparse.py#L530 <https://gitlab.com/petsc/petsc/-/blob/main/config/testparse.py#L530> > > If your file was produced on Windows (CRLF), then the parsing fails and tests > are silently ignored. This took me some time to find and could be confusing > for others. I think we should either: > > a) Fix the parser to work with CRLF as well > > or > > b) Fail immediately for CRLF files > > What do you think? > > 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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Test parsing
by Matthew Knepley 28 Oct '21

28 Oct '21

I just found a loophole in the test parsing happening here: https://gitlab.com/petsc/petsc/-/blob/main/config/testparse.py#L530 If your file was produced on Windows (CRLF), then the parsing fails and tests are silently ignored. This took me some time to find and could be confusing for others. I think we should either: a) Fix the parser to work with CRLF as well or b) Fail immediately for CRLF files What do you think? 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] Anyone run STREAMS on an Apple M1 system?
by Jed Brown 25 Oct '21

25 Oct '21

This shows 240 GB/s using 10 cores (8 performance + 2 efficiency) and 224 GB/s with 8 cores (as you'd most likely run HPC apps). Good, but far from the theoretical 400 GB/s headline. https://www.anandtech.com/show/17024/apple-m1-max-performance-review/2 Barry Smith <bsmith(a)petsc.dev> writes: > Thanks, presumably we'll see the new Mac's there in a few days. BTW: the old streams benchmark page should point to this site; google is worthless. > > I get 24 on my Intel MacBook Pro and it also saturates with 1 core. > > Barry > > >> On Oct 18, 2021, at 4:48 PM, Jed Brown <jed(a)jedbrown.org> wrote: >> >> I don't have one, but this suggests it gets about 40 GB/s and can be saturated by a single core. I believe it uses two channels of LPDDR4X-4266, which has a theoretical peak of 68 GB/s. >> >> https://browser.geekbench.com/v3/cpu/8931693 >> >> The press release claims up to 400 GB/s on the Max using DDR5. I assume that's calculated based on 8 channels of LPDDR5-6400, which seems like a surprisingly big step and I'm skeptical of what will actually be realized. >> >> Barry Smith <bsmith(a)petsc.dev> writes: >> >>> Can anyone who owns an Apple M1 system run the MPI streams benchmark? Make sure the -O3 (or something) optimization flags are turned on. >>> >>> Thanks >>> >>> Barry

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Re: [petsc-dev] PETSCTEST_VALGRIND
by Scott Kruger 25 Oct '21

25 Oct '21

Adding this as a feature would add some ugly code logic for something that only affects 2 tests out of the thousands that we have. Instead, MR !4500 enables one to filter out that test. So: make -f gmakefile test s='snes_tutorials-ex19_' i='\!*logviewmemory' VALGRIND=1 does every ex19 test *except* for the problematic test. I might be able to figure out a better way of hard-coding runtime behavior per test, but I think for now this offers a general-purpose workaround. If you still don't like that, you could just create a local modification to `config/gmakegentest.py`: if self.petsc_arch.find('valgrind') >= 0: self.conf['PETSCTEST_VALGRIND']=1 to self.conf['PETSCTEST_VALGRIND']=1 This means that the `logviewmemory` test would never be run, but that might be OK for your needs. Scott On 2021-10-25 09:22, Pierre Jolivet did write: > Hello, > I think I’m asking too much of test harness, but is there a way to automatically deactivate a test when running with VALGRIND=1 without having to play around with PETSC_RUNNING_ON_VALGRIND in the code? > I see the variable PETSCTEST_VALGRIND, but it seems rather static and set depending on PETSC_ARCH. > So even if there is src/snes/tutorials/ex19.c: requires: defined(PETSC_USE_LOG) !defined(PETSCTEST_VALGRIND), > Running make -f gmakefile test s='snes*logviewmemory' VALGRIND=1 on my machine (without valgrind in the PETSC_ARCH) gets the test going. > > Thanks, > Pierre -- 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] [petsc-maint] PETSc () -- MPI -- Versions Conflict on Mac 1
by Ahmed Galal 25 Oct '21

25 Oct '21

Hello Barry, Not existent. Here is what I got: bash-3.2$ otool -L libdeal_II.g.9.3.0.dylib error: otool: can't open file: libdeal_II.g.9.3.0.dylib (No such file or directory) bash-3.2$ otool -L libslepc.3.15.dylib error: otool: can't open file: libslepc.3.15.dylib (No such file or directory) bash-3.2$ otool -L libpetsc.3.15.dylib error: otool: can't open file: libpetsc.3.15.dylib (No such file or directory) bash-3.2$ ls Kind regards, Ahmed On Mon, Oct 25, 2021 at 9:55 AM Barry Smith <bsmith(a)petsc.dev> wrote: > > Send the output from > > otool -L libdeal_II.g.9.3.0.dylib > > otool -L libslepc.3.15.dylib > > otool -L libpetsc.3.15.dylib > > You will need to find the directories of these libraries and include > them in the otool command. > > > > On Oct 25, 2021, at 10:00 AM, Ahmed Galal <ahmed.galal8591(a)gmail.com> > wrote: > > Hello, > > I tried to run Step-17 in Dealii, a PETSc Dependenant software, but I got > the following error. Given I have two versions of PETSc. I use the other > one for another software. > > I googled and found that the issue is solved by commenting out the line > "ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")" in > "cmake/checks/check_01_compiler_features.cmake", make test, worked. > --- > > https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1https://groups.go… > > --- > > Any suggestions for how to get around that error "PETSc Error --- > Application was linked against both OpenMPI and MPICH based MPI libraries > and will not run correctly" in the new version of DealII.9.3 as I could > not find a .cmake similar file to edit? > > Thanks in advance! > Ahmed > > Error: > ------------------------ > > PETSc Error --- Application was linked against both OpenMPI and MPICH > based MPI libraries and will not run correctly > > [----] *** Process received signal *** > > [----] Signal: Segmentation fault: 11 (11) > > [----] Signal code: Address not mapped (1) > > [----] Failing at address: 0x68 > > [----] [ 0] 0 libsystem_platform.dylib 0x00007fff2041cd7d > _sigtramp + 29 > > [----] [ 1] 0 ??? 0x0000000060b9d791 > 0x0 + 1622792081 > > [----] [ 2] 0 libsystem_c.dylib 0x00007fff202edfcc > vfprintf_l + 28 > > [----] [ 3] 0 libsystem_c.dylib 0x00007fff202e69a2 > fprintf + 160 > > [----] [ 4] 0 libpetsc.3.15.dylib 0x000000014c224f0d > PetscVFPrintfDefault + 685 > > [ 5] 0 libpetsc.3.15.dylib 0x000000014c2280d6 > PetscFPrintf + 726 > > [ 6] 0 libpetsc.3.15.dylib 0x000000014c21d537 > PetscErrorPrintfDefault + 375 > > [ 7] 0 libpetsc.3.15.dylib 0x000000014c21d66a > PetscTraceBackErrorHandler + 154 > > [ 8] 0 libpetsc.3.15.dylib 0x000000014c21713c > PetscError + 716 > > [ 9] 0 libslepc.3.15.dylib 0x000000014bc9cc8c > SlepcInitialize + 428 > > [10] 0 libdeal_II.g.9.3.0.dylib 0x00000001151ae627 > _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC2ERiRPPcj + 135 > > [11] 0 libdeal_II.g.9.3.0.dylib 0x00000001151aece9 > _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC1ERiRPPcj + 9 > > [12] 0 step-17 0x000000010f244892 main + 82 > > [13] 0 libdyld.dylib 0x00007fff203f2f3d start + 1 > > [14] 0 ??? 0x0000000000000001 0x0 + 1 > > *** End of error message *** > > make[3]: *** [CMakeFiles/run] Segmentation fault: 11 > > make[2]: *** [CMakeFiles/run.dir/all] Error 2 > > make[1]: *** [CMakeFiles/run.dir/rule] Error 2 > > make: *** [run] Error 2 > > bash-3.2$ > > >

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Re: [petsc-dev] [petsc-maint] PETSc () -- MPI -- Versions Conflict on Mac 1
by Barry Smith 25 Oct '21

25 Oct '21

Send the output from otool -L libdeal_II.g.9.3.0.dylib otool -L libslepc.3.15.dylib otool -L libpetsc.3.15.dylib You will need to find the directories of these libraries and include them in the otool command. > On Oct 25, 2021, at 10:00 AM, Ahmed Galal <ahmed.galal8591(a)gmail.com> wrote: > > Hello, > > I tried to run Step-17 in Dealii, a PETSc Dependenant software, but I got the following error. Given I have two versions of PETSc. I use the other one for another software. > > I googled and found that the issue is solved by commenting out the line "ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")" in "cmake/checks/check_01_compiler_features.cmake", make test, worked. > --- > https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1https://groups.go… <https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1https://groups.go…> > --- > > Any suggestions for how to get around that error "PETSc Error --- Application was linked against both OpenMPI and MPICH based MPI libraries and will not run correctly" in the new version of DealII.9.3 as I could not find a .cmake similar file to edit? > > Thanks in advance! > Ahmed > > Error: > ------------------------ > > PETSc Error --- Application was linked against both OpenMPI and MPICH based MPI libraries and will not run correctly > > [----] *** Process received signal *** > > [----] Signal: Segmentation fault: 11 (11) > > [----] Signal code: Address not mapped (1) > > [----] Failing at address: 0x68 > > [----] [ 0] 0 libsystem_platform.dylib 0x00007fff2041cd7d _sigtramp + 29 > > [----] [ 1] 0 ??? 0x0000000060b9d791 0x0 + 1622792081 > > [----] [ 2] 0 libsystem_c.dylib 0x00007fff202edfcc vfprintf_l + 28 > > [----] [ 3] 0 libsystem_c.dylib 0x00007fff202e69a2 fprintf + 160 > > [----] [ 4] 0 libpetsc.3.15.dylib 0x000000014c224f0d PetscVFPrintfDefault + 685 > > [ 5] 0 libpetsc.3.15.dylib 0x000000014c2280d6 PetscFPrintf + 726 > > [ 6] 0 libpetsc.3.15.dylib 0x000000014c21d537 PetscErrorPrintfDefault + 375 > > [ 7] 0 libpetsc.3.15.dylib 0x000000014c21d66a PetscTraceBackErrorHandler + 154 > > [ 8] 0 libpetsc.3.15.dylib 0x000000014c21713c PetscError + 716 > > [ 9] 0 libslepc.3.15.dylib 0x000000014bc9cc8c SlepcInitialize + 428 > > [10] 0 libdeal_II.g.9.3.0.dylib 0x00000001151ae627 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC2ERiRPPcj + 135 > > [11] 0 libdeal_II.g.9.3.0.dylib 0x00000001151aece9 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC1ERiRPPcj + 9 > > [12] 0 step-17 0x000000010f244892 main + 82 > > [13] 0 libdyld.dylib 0x00007fff203f2f3d start + 1 > > [14] 0 ??? 0x0000000000000001 0x0 + 1 > > *** End of error message *** > > make[3]: *** [CMakeFiles/run] Segmentation fault: 11 > > make[2]: *** [CMakeFiles/run.dir/all] Error 2 > > make[1]: *** [CMakeFiles/run.dir/rule] Error 2 > > make: *** [run] Error 2 > > bash-3.2$ >

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PETSc () -- MPI -- Versions Conflict on Mac 1
by Ahmed Galal 25 Oct '21

25 Oct '21

Hello, I tried to run Step-17 in Dealii, a PETSc Dependenant software, but I got the following error. Given I have two versions of PETSc. I use the other one for another software. I googled and found that the issue is solved by commenting out the line "ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")" in "cmake/checks/check_01_compiler_features.cmake", make test, worked. --- https://groups.google.com/u/1/g/dealii/c/JxUOyd_4eFM?pli=1https://groups.go… --- Any suggestions for how to get around that error "PETSc Error --- Application was linked against both OpenMPI and MPICH based MPI libraries and will not run correctly" in the new version of DealII.9.3 as I could not find a .cmake similar file to edit? Thanks in advance! Ahmed Error: ------------------------ PETSc Error --- Application was linked against both OpenMPI and MPICH based MPI libraries and will not run correctly [----] *** Process received signal *** [----] Signal: Segmentation fault: 11 (11) [----] Signal code: Address not mapped (1) [----] Failing at address: 0x68 [----] [ 0] 0 libsystem_platform.dylib 0x00007fff2041cd7d _sigtramp + 29 [----] [ 1] 0 ??? 0x0000000060b9d791 0x0 + 1622792081 [----] [ 2] 0 libsystem_c.dylib 0x00007fff202edfcc vfprintf_l + 28 [----] [ 3] 0 libsystem_c.dylib 0x00007fff202e69a2 fprintf + 160 [----] [ 4] 0 libpetsc.3.15.dylib 0x000000014c224f0d PetscVFPrintfDefault + 685 [ 5] 0 libpetsc.3.15.dylib 0x000000014c2280d6 PetscFPrintf + 726 [ 6] 0 libpetsc.3.15.dylib 0x000000014c21d537 PetscErrorPrintfDefault + 375 [ 7] 0 libpetsc.3.15.dylib 0x000000014c21d66a PetscTraceBackErrorHandler + 154 [ 8] 0 libpetsc.3.15.dylib 0x000000014c21713c PetscError + 716 [ 9] 0 libslepc.3.15.dylib 0x000000014bc9cc8c SlepcInitialize + 428 [10] 0 libdeal_II.g.9.3.0.dylib 0x00000001151ae627 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC2ERiRPPcj + 135 [11] 0 libdeal_II.g.9.3.0.dylib 0x00000001151aece9 _ZN6dealii9Utilities3MPI16MPI_InitFinalizeC1ERiRPPcj + 9 [12] 0 step-17 0x000000010f244892 main + 82 [13] 0 libdyld.dylib 0x00007fff203f2f3d start + 1 [14] 0 ??? 0x0000000000000001 0x0 + 1 *** End of error message *** make[3]: *** [CMakeFiles/run] Segmentation fault: 11 make[2]: *** [CMakeFiles/run.dir/all] Error 2 make[1]: *** [CMakeFiles/run.dir/rule] Error 2 make: *** [run] Error 2 bash-3.2$

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PETSCTEST_VALGRIND
by Pierre Jolivet 25 Oct '21

25 Oct '21

Hello, I think I’m asking too much of test harness, but is there a way to automatically deactivate a test when running with VALGRIND=1 without having to play around with PETSC_RUNNING_ON_VALGRIND in the code? I see the variable PETSCTEST_VALGRIND, but it seems rather static and set depending on PETSC_ARCH. So even if there is src/snes/tutorials/ex19.c: requires: defined(PETSC_USE_LOG) !defined(PETSCTEST_VALGRIND), Running make -f gmakefile test s='snes*logviewmemory' VALGRIND=1 on my machine (without valgrind in the PETSC_ARCH) gets the test going. Thanks, Pierre

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Tutorial videos
by Matthew Knepley 22 Oct '21

22 Oct '21

Where did we move the page with tutorial videos? 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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