[petsc-users] [petsc-maint] DMSwarm on multiple processors
Matthew Knepley
knepley at gmail.com
Thu Oct 26 14:34:49 CDT 2023
Okay, there were a few problems:
1) You overwrote the bounds on string loc_grid_gen[]
2) You destroyed the coordinate DA
I fixed these and it runs for me fine on several processes. I am including
my revised source since I check a lot more error values. I converted it to
C because that is easier for me, although C has a problem with your sqrt()
in a compile-time constant.
Thanks,
Matt
On Thu, Oct 26, 2023 at 10:59 AM Barry Smith <bsmith at petsc.dev> wrote:
>
> Please run with -malloc_debug option or even better run under Valgrind
> https://petsc.org/release/faq/
>
>
>
> On Oct 26, 2023, at 10:35 AM, Joauma Marichal via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
> Hello,
>
> Here is a very simple version where I have issues.
>
> Which I run as follows:
>
> cd Grid_generation
> make clean
> make all
> ./grid_generation
> cd ..
> make clean
> make all
> ./cobpor # on 1 proc
> # OR
> mpiexec ./cobpor -ksp_type cg -pc_type pfmg -dm_mat_type hyprestruct
> -pc_pfmg_skip_relax 1 -pc_pfmg_rap_time non-Galerkin # on multiple procs
>
> The error that I get is the following:
> munmap_chunk(): invalid pointer
> [cns266:2552391] *** Process received signal ***
> [cns266:2552391] Signal: Aborted (6)
> [cns266:2552391] Signal code: (-6)
> [cns266:2552391] [ 0] /lib64/libc.so.6(+0x4eb20)[0x7fd7fd194b20]
> [cns266:2552391] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7fd7fd194a9f]
> [cns266:2552391] [ 2] /lib64/libc.so.6(abort+0x127)[0x7fd7fd167e05]
> [cns266:2552391] [ 3] /lib64/libc.so.6(+0x91037)[0x7fd7fd1d7037]
> [cns266:2552391] [ 4] /lib64/libc.so.6(+0x9819c)[0x7fd7fd1de19c]
> [cns266:2552391] [ 5] /lib64/libc.so.6(+0x9844c)[0x7fd7fd1de44c]
> [cns266:2552391] [ 6] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(PetscFreeAlign+0xe)[0x7fd7fe63d50e]
> [cns266:2552391] [ 7] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(DMSetMatType+0x3d)[0x7fd7feab87ad]
> [cns266:2552391] [ 8] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(DMSetFromOptions+0x109)[0x7fd7feab8b59]
> [cns266:2552391] [ 9] ./cobpor[0x402df9]
> [cns266:2552391] [10] /lib64/libc.so
> .6(__libc_start_main+0xf3)[0x7fd7fd180cf3]
> [cns266:2552391] [11] ./cobpor[0x40304e]
> [cns266:2552391] *** End of error message ***
>
>
> Thanks a lot for your help.
>
> Best regards,
>
> Joauma
>
>
>
>
> *De : *Matthew Knepley <knepley at gmail.com>
> *Date : *mercredi, 25 octobre 2023 à 14:45
> *À : *Joauma Marichal <joauma.marichal at uclouvain.be>
> *Cc : *petsc-maint at mcs.anl.gov <petsc-maint at mcs.anl.gov>,
> petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Objet : *Re: [petsc-maint] DMSwarm on multiple processors
> On Wed, Oct 25, 2023 at 8:32 AM Joauma Marichal via petsc-maint <
> petsc-maint at mcs.anl.gov> wrote:
>
> Hello,
>
> I am using the DMSwarm library in some Eulerian-Lagrangian approach to
> have vapor bubbles in water.
> I have obtained nice results recently and wanted to perform bigger
> simulations. Unfortunately, when I increase the number of processors used
> to run the simulation, I get the following error:
>
>
> free(): invalid size
>
> [cns136:590327] *** Process received signal ***
>
> [cns136:590327] Signal: Aborted (6)
>
> [cns136:590327] Signal code: (-6)
>
> [cns136:590327] [ 0] /lib64/libc.so.6(+0x4eb20)[0x7f56cd4c9b20]
>
> [cns136:590327] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7f56cd4c9a9f]
>
> [cns136:590327] [ 2] /lib64/libc.so.6(abort+0x127)[0x7f56cd49ce05]
>
> [cns136:590327] [ 3] /lib64/libc.so.6(+0x91037)[0x7f56cd50c037]
>
> [cns136:590327] [ 4] /lib64/libc.so.6(+0x9819c)[0x7f56cd51319c]
>
> [cns136:590327] [ 5] /lib64/libc.so.6(+0x99aac)[0x7f56cd514aac]
>
> [cns136:590327] [ 6] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(PetscSFSetUpRanks+0x4c4)[0x7f56cea71e64]
>
> [cns136:590327] [ 7] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(+0x841642)[0x7f56cea83642]
>
> [cns136:590327] [ 8] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(PetscSFSetUp+0x9e)[0x7f56cea7043e]
>
> [cns136:590327] [ 9] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(VecScatterCreate+0x164e)[0x7f56cea7bbde]
>
> [cns136:590327] [10] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(DMSetUp_DA_3D+0x3e38)[0x7f56cee84dd8]
>
> [cns136:590327] [11] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(DMSetUp_DA+0xd8)[0x7f56cee9b448]
>
> [cns136:590327] [12] /gpfs/home/acad/ucl-tfl/marichaj/marha/lib_petsc/lib/
> libpetsc.so.3.019(DMSetUp+0x20)[0x7f56cededa20]
>
> [cns136:590327] [13] ./cobpor[0x4418dc]
>
> [cns136:590327] [14] ./cobpor[0x408b63]
>
> [cns136:590327] [15] /lib64/libc.so
> .6(__libc_start_main+0xf3)[0x7f56cd4b5cf3]
>
> [cns136:590327] [16] ./cobpor[0x40bdee]
>
> [cns136:590327] *** End of error message ***
>
> --------------------------------------------------------------------------
>
> Primary job terminated normally, but 1 process returned
>
> a non-zero exit code. Per user-direction, the job has been aborted.
>
> --------------------------------------------------------------------------
>
> --------------------------------------------------------------------------
>
> mpiexec noticed that process rank 84 with PID 590327 on node cns136 exited
> on signal 6 (Aborted).
>
> --------------------------------------------------------------------------
>
> When I reduce the number of processors the error disappears and when I run
> my code without the vapor bubbles it also works.
> The problem seems to take place at this moment:
>
> DMCreate(PETSC_COMM_WORLD,swarm);
> DMSetType(*swarm,DMSWARM);
> DMSetDimension(*swarm,3);
> DMSwarmSetType(*swarm,DMSWARM_PIC);
> DMSwarmSetCellDM(*swarm,*dmcell);
>
>
> Thanks a lot for your help.
>
>
> Things that would help us track this down:
>
> 1) The smallest example where it fails
>
> 2) The smallest number of processes where it fails
>
> 3) A stack trace of the failure
>
> 4) A simple example that we can run that also fails
>
> Thanks,
>
> Matt
>
>
> Best regards,
>
> Joauma
>
>
>
> --
> 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/>
>
>
>
--
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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