[petsc-users] [EXTERNAL] PETSc Installation Assistance
Pierre Jolivet
pierre.jolivet at lip6.fr
Mon Jul 17 14:11:21 CDT 2023
> On 17 Jul 2023, at 9:00 PM, Ferrand, Jesus A. <FERRANJ2 at my.erau.edu> wrote:
>
> Pierre:
> Setting the environment variable allows make check to complete without errors.
> It only seems to run three checks.
> I recall that in the past, make check would run 100+ tests.
You are probably thinking of make test, which is running thousands of tests indeed.
> This is what I get from make check:
> =========================================================================
> Running check examples to verify correct installation
> Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug
> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
> C/C++ example src/vec/vec/tests/ex47 run successfully with hdf5
> Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
> Completed test examples
> =========================================================================
>
> Anyhow, some of the APIs that worked before now break.
> For example "DMPlexCreateGmshFromFile()" breaks when I read simple test mesh.
> I tried configuring and installing both the newest release of PETSc and that tarball of version 3.18.3.
> Both seem to be breaking APIs that used to work in the older OS.
There has been some internal changes to the behavior of DMPlex, they should be documented in the change log.
But you are saying that with the same version, just by switching OS, you get a different behavior?
Do as Satish suggested then, because it’s unlikely that the root cause is in the library itself.
Thanks,
Pierre
> =========================================================================
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple
> xnatural.c:21
> [0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)
> - process 0
> :
> system msg for write_line failure : Bad file descriptor
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple
> xnatural.c:21
> [0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)
> - process 0
> :
> system msg for write_line failure : Bad file descriptor
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u
> tils/eventlog.c:622
> [0]PETSC ERROR: #2 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog
> .c:802
> [0]PETSC ERROR: #3 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface
> /dlregisvec.c:187
> [0]PETSC ERROR: #4 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.
> c:32
> [0]PETSC ERROR: #5 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm
> /interface/dmi.c:80
> [0]PETSC ERROR: #6 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex
> /plexcreate.c:4432
> [0]PETSC ERROR: #7 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:
> 1056
> [0]PETSC ERROR: #8 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms
> h.c:1933
> [0]PETSC ERROR: #9 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex
> /plexgmsh.c:1433
> [0]PETSC ERROR: #10 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)
> - process 0
> :
> system msg for write_line failure : Bad file descriptor
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 PetscStrcasecmp() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/utils/str.c:285
> [0]PETSC ERROR: #2 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u
> tils/eventlog.c:622
> [0]PETSC ERROR: #3 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog
> .c:802
> [0]PETSC ERROR: #4 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface
> /dlregisvec.c:188
> [0]PETSC ERROR: #5 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.
> c:32
> [0]PETSC ERROR: #6 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm
> /interface/dmi.c:80
> [0]PETSC ERROR: #7 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex
> /plexcreate.c:4432
> [0]PETSC ERROR: #8 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:
> 1056
> [0]PETSC ERROR: #9 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms
> h.c:1933
> [0]PETSC ERROR: #10 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/ple
> x/plexgmsh.c:1433
> [0]PETSC ERROR: #11 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)
> - process 0
> :
> system msg for write_line failure : Bad file descriptor
> --------------------------------------------------------------------------
> mpiexec detected that one or more processes exited with non-zero status, thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[33478,1],2]
> Exit code: 15
> ===========================================================================
>
> Here are the options I give ./configure:
>
> ./configure --download-mpich=yes --download-viennacl=yes --download-hdf5=yes --download-chaco=yes --download-metis=yes --download-parmetis=yes --download-cgns=yes
> From: Pierre Jolivet <pierre.jolivet at lip6.fr <mailto:pierre.jolivet at lip6.fr>>
> Sent: Monday, July 17, 2023 1:58 PM
> To: Ferrand, Jesus A. <FERRANJ2 at my.erau.edu <mailto:FERRANJ2 at my.erau.edu>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: [EXTERNAL] Re: [petsc-users] PETSc Installation Assistance
>
> CAUTION: This email originated outside of Embry-Riddle Aeronautical University. Do not click links or open attachments unless you recognize the sender and know the content is safe.
>
> https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean
>
> Thanks,
> Pierre
>
>> On 17 Jul 2023, at 7:51 PM, Ferrand, Jesus A. <FERRANJ2 at my.erau.edu <mailto:FERRANJ2 at my.erau.edu>> wrote:
>>
>> Greetings.
>>
>> I recently changed operating systems (Ubuntu 20.04 -> Debian 12 "Bookworm") and tried to reinstall PETSc.
>> I tried doing the usual as described in (https://petsc.org/release/install/download/#recommended-obtain-release-version-with-git):
>> git clone/pull
>> ./configure --<option_1> ... --<option_N>
>> make install
>> make check
>> Everything proceeds smoothly until the "make check" step, where I get the following error:
>> ==============================================================================
>> Running check examples to verify correct installation
>> Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug
>> Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>> Number of SNES iterations = 2
>> Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>> Number of SNES iterations = 2
>> 0a1,3
>> > hwloc/linux: Ignoring PCI device with non-16bit domain.
>> > Pass --enable-32bits-pci-domain to configure to support such devices
>> > (warning: it would break the library ABI, don't enable unless really needed).
>> /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests
>> Possible problem with ex47 running with hdf5, diffs above
>> =========================================
>> Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> Number of SNES iterations = 3
>> Completed test examples
>> Error while running make check
>> gmake[1]: *** [makefile:123: check] Error 1
>> make: *** [GNUmakefile:17: check] Error 2
>> ==============================================================================
>>
>>
>> I tried reinstalling the same version I was able to use prior to changing OS's (PETSc 3.18.3, via tarball) and get a similar error.
>> ==============================================================================
>> make PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_P
>> arty/newPETSC/petsc-3.18.3 PETSC_ARCH=arch-linux-c-debug check
>> Running check examples to verify correct installation
>> Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug
>> Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>> Number of SNES iterations = 2
>> Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>> Number of SNES iterations = 2
>> 0a1,3
>> > hwloc/linux: Ignoring PCI device with non-16bit domain.
>> > Pass --enable-32bits-pci-domain to configure to support such devices
>> > (warning: it would break the library ABI, don't enable unless really needed).
>> /home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests
>> Possible problem with ex47 running with hdf5, diffs above
>> =========================================
>> Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
>> See https://petsc.org/release/faq/
>> hwloc/linux: Ignoring PCI device with non-16bit domain.
>> Pass --enable-32bits-pci-domain to configure to support such devices
>> (warning: it would break the library ABI, don't enable unless really needed).
>> Number of SNES iterations = 3
>> Completed test examples
>> Error while running make check
>> gmake[1]: *** [makefile:149: check] Error 1
>> make: *** [GNUmakefile:17: check] Error 2
>> ==============================================================================
>>
>>
>> I checked the FAQs (https://petsc.org/release/faq/#table-of-contents) and tried the suggestions there (specifically the points underhttps://petsc.org/release/faq/#what-does-it-mean-when-make-check-hangs-or-errors-on-petscoptionsinsertfile) to no avail.
>> I don't use a VPN.
>> I tried running make check with Wifi disabled.
>> Ran ./configure with --download-mpich-device=ch3:nemesis --download-mpich
>>
>> Surprisingly, I can compile my PETSc programs using a makefile, and run them.
>> However, the programs are now broken (I get SIGSEGV originating from within DM/DMPlex APIs).
>>
>>
>> Sincerely:
>>
>> J.A. Ferrand
>> Embry-Riddle Aeronautical University - Daytona Beach - FL
>> Ph.D. Candidate, Aerospace Engineering
>> M.Sc. Aerospace Engineering
>> B.Sc. Aerospace Engineering
>> B.Sc. Computational Mathematics
>>
>> Phone: (386)-843-1829
>> Email(s): ferranj2 at my.erau.edu <mailto:ferranj2 at my.erau.edu>
>> jesus.ferrand at gmail.com <mailto:jesus.ferrand at gmail.com>
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