[petsc-users] Bus Error
Mark Lohry
mlohry at gmail.com
Mon Aug 24 07:54:07 CDT 2020
Reran with debug mode and got a stack trace for this bus error, looks like
it's happening in BLASgemv, see pasted below. I did take care of the
ISColoring leak mentioned previously, although that was a very small amount
of data and I don't think is relevant here.
At this point it's happily run 222 timesteps prior to this, so I'm a little
mystified. Any ideas?
Thanks,
Mark
222 TS dt 0.03 time 6.66
0 SNES Function norm 4.124287265556e+02
0 KSP Residual norm 4.124287265556e+02
1 KSP Residual norm 4.123248052318e+02
2 KSP Residual norm 4.123173350456e+02
3 KSP Residual norm 4.118769044110e+02
4 KSP Residual norm 4.094856150740e+02
5 KSP Residual norm 4.006000788078e+02
6 KSP Residual norm 3.787922969183e+02
[clip]
Linear solve converged due to CONVERGED_RTOL iterations 9
Line search: Using full step: fnorm 4.015236590684e+01 gnorm
3.173434863784e+00
2 SNES Function norm 3.173434863784e+00
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 2
0 SNES Function norm 5.842010710080e+02
0 KSP Residual norm 5.842010710080e+02
1 KSP Residual norm 5.840526408234e+02
2 KSP Residual norm 5.840431857354e+02
3 KSP Residual norm 5.834351392302e+02
4 KSP Residual norm 5.800901047861e+02
5 KSP Residual norm 5.675562288567e+02
6 KSP Residual norm 5.366287895681e+02
7 KSP Residual norm 4.725811521866e+02
[911]PETSC ERROR:
------------------------------------------------------------------------
[911]PETSC ERROR: Caught signal number 7 BUS: Bus Error, possibly illegal
memory access
[911]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[911]PETSC ERROR: or see
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[911]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
X to find memory corruption errors
[911]PETSC ERROR: likely location of problem given in stack below
[911]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[911]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[911]PETSC ERROR: INSTEAD the line number of the start of the function
[911]PETSC ERROR: is given.
[911]PETSC ERROR: [911] BLASgemv line 1393
/home/mlohry/build/external/petsc/src/mat/impls/baij/seq/baijfact.c
[911]PETSC ERROR: [911] MatSolve_SeqBAIJ_N_NaturalOrdering line 1378
/home/mlohry/build/external/petsc/src/mat/impls/baij/seq/baijfact.c
[911]PETSC ERROR: [911] MatSolve line 3354
/home/mlohry/build/external/petsc/src/mat/interface/matrix.c
[911]PETSC ERROR: [911] PCApply_ILU line 201
/home/mlohry/build/external/petsc/src/ksp/pc/impls/factor/ilu/ilu.c
[911]PETSC ERROR: [911] PCApply line 426
/home/mlohry/build/external/petsc/src/ksp/pc/interface/precon.c
[911]PETSC ERROR: [911] KSP_PCApply line 279
/home/mlohry/build/external/petsc/include/petsc/private/kspimpl.h
[911]PETSC ERROR: [911] KSPSolve_PREONLY line 16
/home/mlohry/build/external/petsc/src/ksp/ksp/impls/preonly/preonly.c
[911]PETSC ERROR: [911] KSPSolve_Private line 590
/home/mlohry/build/external/petsc/src/ksp/ksp/interface/itfunc.c
[911]PETSC ERROR: [911] KSPSolve line 848
/home/mlohry/build/external/petsc/src/ksp/ksp/interface/itfunc.c
[911]PETSC ERROR: [911] PCApply_ASM line 441
/home/mlohry/build/external/petsc/src/ksp/pc/impls/asm/asm.c
[911]PETSC ERROR: [911] PCApply line 426
/home/mlohry/build/external/petsc/src/ksp/pc/interface/precon.c
[911]PETSC ERROR: [911] KSP_PCApply line 279
/home/mlohry/build/external/petsc/include/petsc/private/kspimpl.h
[911]PETSC ERROR: [911] KSPFGMRESCycle line 108
/home/mlohry/build/external/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
[911]PETSC ERROR: [911] KSPSolve_FGMRES line 274
/home/mlohry/build/external/petsc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c
[911]PETSC ERROR: [911] KSPSolve_Private line 590
/home/mlohry/build/external/petsc/src/ksp/ksp/interface/itfunc.c
[911]PETSC ERROR: [911] KSPSolve line 848
/home/mlohry/build/external/petsc/src/ksp/ksp/interface/itfunc.c
[911]PETSC ERROR: [911] SNESSolve_NEWTONLS line 144
/home/mlohry/build/external/petsc/src/snes/impls/ls/ls.c
[911]PETSC ERROR: [911] SNESSolve line 4403
/home/mlohry/build/external/petsc/src/snes/interface/snes.c
[911]PETSC ERROR: [911] TSStep_ARKIMEX line 728
/home/mlohry/build/external/petsc/src/ts/impls/arkimex/arkimex.c
[911]PETSC ERROR: [911] TSStep line 3682
/home/mlohry/build/external/petsc/src/ts/interface/ts.c
[911]PETSC ERROR: [911] TSSolve line 4005
/home/mlohry/build/external/petsc/src/ts/interface/ts.c
[911]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[911]PETSC ERROR: Signal received
[911]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.
[911]PETSC ERROR: Petsc Release Version 3.13.3, Jul 01, 2020
[911]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h20c2n20 by
mlohry Sun Aug 23 19:54:21 2020
[911]PETSC ERROR: Configure options
PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
--with-cc=/usr/local/openmpi/3.1.3/gcc/x8
[911]PETSC ERROR: #1 User provided function() line 0 in unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 911 in communicator MPI_COMM_WORLD
On Wed, Aug 12, 2020 at 8:19 PM Mark Lohry <mlohry at gmail.com> wrote:
> Perhaps you are calling ISColoringGetIS() and not calling
>> ISColoringRestoreIS()?
>>
>
> I have matching ISColoringGet/Restore here, and it's only used prior to
> the first iteration so at least it doesn't seem to be growing. At the
> bottom I pasted the malloc_view and malloc_debug output from running 1 time
> step.
>
> I'm sort of thinking this might be a red herring -- is it possible the
> rank 0 process is chewing up dramatically more memory than others, like
> with logging or something? Like I mentioned earlier the total memory usage
> is well under the machine limits. I'll spring in some
> PetscMemoryGetMaximumUsage logging at every time step and try to get a big
> job going again.
>
>
>
> Are you using Fortran?
>>
>
> C++
>
>
>
> [ 0]1408 bytes PetscSplitReductionCreate() line 63 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/vec/utils/comb.c
> [ 0]80 bytes PetscSplitReductionCreate() line 57 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/vec/utils/comb.c
> [ 0]16 bytes PetscCommBuildTwoSided_Allreduce() line 169 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/mpits.c
> [ 0]16 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]272 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]880 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]960 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]976 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]1024 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]1024 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]1040 bytes ISGeneralSetIndices_General() line 578 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]16 bytes PetscLayoutSetUp() line 269 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]80 bytes PetscLayoutCreate() line 55 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
> [ 0]16 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]32 bytes PetscStrallocpy() line 187 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
> [ 0]16 bytes ISCreate_General() line 647 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
> [ 0]896 bytes ISCreate() line 37 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
> [ 0]64 bytes ISColoringGetIS() line 266 in
> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/utils/iscoloring.c
> [ 0]32 bytes PetscCommDuplicate() line 129 in
> /home/mlohry/dev/cmake-build/external/petsc/src/sys/objects/tagm.c
> [0] Maximum memory PetscMalloc()ed 610153776 maximum size of entire
> process 719073280
> [0] Memory usage sorted by function
> [0] 6 192 DMCoarsenHookAdd()
> [0] 2 9984 DMCreate()
> [0] 2 128 DMCreate_Shell()
> [0] 2 64 DMDSEnlarge_Static()
> [0] 1 672 DMKSPCreate()
> [0] 3 96 DMRefineHookAdd()
> [0] 3 2064 DMSNESCreate()
> [0] 4 128 DMSubDomainHookAdd()
> [0] 1 768 DMTSCreate()
> [0] 2 96 ISColoringCreate()
> [0] 8 12608 ISColoringGetIS()
> [0] 1 307200 ISConcatenate()
> [0] 29 25984 ISCreate()
> [0] 25 400 ISCreate_General()
> [0] 4 64 ISCreate_Stride()
> [0] 20 338016 ISGeneralSetIndices_General()
> [0] 3 921600 ISGetIndices_Stride()
> [0] 2 307232 ISGlobalToLocalMappingSetUp_Basic()
> [0] 1 6144 ISInvertPermutation_General()
> [0] 3 308576 ISLocalToGlobalMappingCreate()
> [0] 2 32 KSPConvergedDefaultCreate()
> [0] 2 2816 KSPCreate()
> [0] 1 224 KSPCreate_FGMRES()
> [0] 1 8016 KSPGMRESClassicalGramSchmidtOrthogonalization()
> [0] 2 16032 KSPSetUp_FGMRES()
> [0] 4 16084160 KSPSetUp_GMRES()
> [0] 2 36864 MatColoringApply_SL()
> [0] 1 656 MatColoringCreate()
> [0] 6 17088 MatCreate()
> [0] 1 16 MatCreateMFFD_WP()
> [0] 1 16 MatCreateSubMatrices_SeqBAIJ()
> [0] 1 12288 MatCreateSubMatrix_SeqBAIJ()
> [0] 3 32320 MatCreateSubMatrix_SeqBAIJ_Private()
> [0] 2 1472 MatCreate_MFFD()
> [0] 1 416 MatCreate_SeqAIJ()
> [0] 3 864 MatCreate_SeqBAIJ()
> [0] 2 416 MatCreate_Shell()
> [0] 1 784 MatFDColoringCreate()
> [0] 2 12288 MatFDColoringDegreeSequence_Minpack()
> [0] 6 30859392 MatFDColoringSetUp_SeqXAIJ()
> [0] 3 42512 MatGetColumnIJ_SeqAIJ()
> [0] 4 72720 MatGetColumnIJ_SeqBAIJ_Color()
> [0] 1 6144 MatGetOrdering_Natural()
> [0] 2 36384 MatGetRowIJ_SeqAIJ()
> [0] 7 210626000 MatILUFactorSymbolic_SeqBAIJ()
> [0] 2 313376 MatIncreaseOverlap_SeqBAIJ()
> [0] 2 30740608 MatLUFactorNumeric_SeqBAIJ_N()
> [0] 1 6144 MatMarkDiagonal_SeqAIJ()
> [0] 1 6144 MatMarkDiagonal_SeqBAIJ()
> [0] 8 256 MatRegisterRootName()
> [0] 1 6160 MatSeqAIJCheckInode()
> [0] 4 115216 MatSeqAIJSetPreallocation_SeqAIJ()
> [0] 4 302779424 MatSeqBAIJSetPreallocation_SeqBAIJ()
> [0] 13 576 MatSolverTypeRegister()
> [0] 1 16 PCASMCreateSubdomains()
> [0] 2 1664 PCCreate()
> [0] 1 160 PCCreate_ASM()
> [0] 1 192 PCCreate_ILU()
> [0] 5 307264 PCSetUp_ASM()
> [0] 2 416 PetscBTCreate()
> [0] 2 3216 PetscClassPerfLogCreate()
> [0] 2 1616 PetscClassRegLogCreate()
> [0] 2 32 PetscCommBuildTwoSided_Allreduce()
> [0] 2 64 PetscCommDuplicate()
> [0] 2 1888 PetscDSCreate()
> [0] 2 26416 PetscEventPerfLogCreate()
> [0] 2 158400 PetscEventPerfLogEnsureSize()
> [0] 2 1616 PetscEventRegLogCreate()
> [0] 2 9600 PetscEventRegLogRegister()
> [0] 8 102400 PetscFreeSpaceGet()
> [0] 474 15168 PetscFunctionListAdd_Private()
> [0] 2 528 PetscIntStackCreate()
> [0] 142 11360 PetscLayoutCreate()
> [0] 56 896 PetscLayoutSetUp()
> [0] 59 9440 PetscObjectComposedDataIncreaseReal()
> [0] 2 576 PetscObjectListAdd()
> [0] 33 768 PetscOptionsGetEList()
> [0] 1 16 PetscOptionsHelpPrintedCreate()
> [0] 1 32 PetscPushSignalHandler()
> [0] 7 6944 PetscSFCreate()
> [0] 3 432 PetscSFCreate_Basic()
> [0] 2 1472 PetscSFLinkCreate()
> [0] 11 1229040 PetscSFSetUpRanks()
> [0] 7 614512 PetscSFSetUp_Basic()
> [0] 4 20096 PetscSegBufferCreate()
> [0] 2 1488 PetscSplitReductionCreate()
> [0] 2 3008 PetscStageLogCreate()
> [0] 1148 23872 PetscStrallocpy()
> [0] 6 13056 PetscStrreplace()
> [0] 9 3456 PetscTableCreate()
> [0] 1 16 PetscViewerASCIIOpen()
> [0] 6 96 PetscViewerAndFormatCreate()
> [0] 1 752 PetscViewerCreate()
> [0] 1 96 PetscViewerCreate_ASCII()
> [0] 2 1424 SNESCreate()
> [0] 1 16 SNESCreate_NEWTONLS()
> [0] 1 1008 SNESLineSearchCreate()
> [0] 1 16 SNESLineSearchCreate_BT()
> [0] 16 1824 SNESMSRegister()
> [0] 46 9056 TSARKIMEXRegister()
> [0] 1 1264 TSAdaptCreate()
> [0] 8 384 TSBasicSymplecticRegister()
> [0] 1 2160 TSCreate()
> [0] 1 224 TSCreate_Theta()
> [0] 48 5968 TSGLEERegister()
> [0] 41 7728 TSRKRegister()
> [0] 89 14736 TSRosWRegister()
> [0] 71 110192 VecCreate()
> [0] 1 307200 VecCreateGhostWithArray()
> [0] 123 36874080 VecCreate_MPI_Private()
> [0] 7 4300800 VecCreate_Seq()
> [0] 8 256 VecCreate_Seq_Private()
> [0] 6 400 VecDuplicateVecs_Default()
> [0] 3 2352 VecScatterCreate()
> [0] 7 1843296 VecScatterSetUp_SF()
> [0] 126 2016 VecStashCreate_Private()
> [0] 1 3072 mapBlockColoringToJacobian()
>
> On Wed, Aug 12, 2020 at 4:22 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>> Yes, there are some PETSc objects or arrays that you are not freeing
>> so they are printed at the end of the run. For small runs this harmless but
>> if new objects/memory is allocated at each iteration and not suitably freed
>> it will eventually add up.
>>
>> Run with -malloc_view (small problem with say 2 iterations) it will
>> print everything allocated and might be helpful.
>>
>> Perhaps you are calling ISColoringGetIS() and not calling
>> ISColoringRestoreIS()?
>>
>> It is also possible it is a leak in PETSc, but that is unlikely since
>> we test for them.
>>
>> Are you using Fortran?
>>
>> Barry
>>
>>
>> On Aug 12, 2020, at 1:29 PM, Mark Lohry <mlohry at gmail.com> wrote:
>>
>> Thanks Matt and Barry. At Matt's suggestion I ran a smaller
>> representative case with valgrind and didn't see anything alarming (apart
>> from a small leak in an older boost version I was using:
>> https://github.com/boostorg/serialization/issues/104 although I don't
>> think this was causing the issue).
>>
>> -malloc_debug dumps quite a lot, this is supposed to be empty right?
>> Output pasted below. It looks like the same sequence of calls is repeated 8
>> times, which is how many nonlinear solves occurred in this particular run.
>> Thoughts?
>>
>>
>>
>> [ 0]1408 bytes PetscSplitReductionCreate() line 63 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/vec/utils/comb.c
>> [ 0]80 bytes PetscSplitReductionCreate() line 57 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/vec/utils/comb.c
>> [ 0]16 bytes PetscCommBuildTwoSided_Allreduce() line 169 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/mpits.c
>> [ 0]16 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]272 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]880 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]960 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]976 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]1024 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]1024 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]1040 bytes ISGeneralSetIndices_General() line 578 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]16 bytes PetscLayoutSetUp() line 269 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]80 bytes PetscLayoutCreate() line 55 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/utils/pmap.c
>> [ 0]16 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 255 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]32 bytes PetscStrallocpy() line 187 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/utils/str.c
>> [ 0]32 bytes PetscFunctionListAdd_Private() line 222 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/dll/reg.c
>> [ 0]16 bytes ISCreate_General() line 647 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/impls/general/general.c
>> [ 0]896 bytes ISCreate() line 37 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/interface/isreg.c
>> [ 0]64 bytes ISColoringGetIS() line 266 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/vec/is/is/utils/iscoloring.c
>> [ 0]32 bytes PetscCommDuplicate() line 129 in
>> /home/mlohry/dev/cmake-build/external/petsc/src/sys/objects/tagm.c
>>
>>
>>
>> On Wed, Aug 12, 2020 at 1:46 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>> Mark.
>>>
>>> When valgrind is not feasible (like on many centrally controlled
>>> batch systems) you can run PETSc with an extra flag to do some memory error
>>> checks
>>> -malloc_debug
>>>
>>> this
>>>
>>> 1) fills all malloced memory with Nan so if the code is using
>>> uninitialized memory it may be detected and
>>> 2) checks the beginning and end of each alloced memory region for
>>> out-of-bounds writes at each malloc and free.
>>>
>>> it will slow the code down a little bit but generally not a huge amount.
>>>
>>> It is no where near as good as valgrind or other memory corruption tools
>>> but it has the advantage you can run it anywhere on any size job.
>>>
>>>
>>> Barry
>>>
>>>
>>>
>>>
>>>
>>> On Aug 12, 2020, at 7:46 AM, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>> On Wed, Aug 12, 2020 at 7:53 AM Mark Lohry <mlohry at gmail.com> wrote:
>>>
>>>> I'm getting seemingly random failures of late:
>>>> Caught signal number 7 BUS: Bus Error, possibly illegal memory access
>>>>
>>>
>>> The first thing I would do is run valgrind on as wide an array of tests
>>> as you can. This will find problems
>>> on things that run completely fine.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Symptoms:
>>>> 1) Seems to only happen (so far) on larger cases, 400-2000 cores
>>>> 2) It doesn't happen right away -- this was running happily for several
>>>> hours over several hundred time steps with no indication of bad health in
>>>> the numerics
>>>> 3) At least the total memory consumption seems to be within bounds,
>>>> though I'm not sure about individual processes. e.g. slurm here reported
>>>> Memory Efficiency: 75.23% of 1.76 TB (180.00 GB/node)
>>>> 4) running the same setup twice it fails at different points
>>>>
>>>> Any suggestions on what to look for? This is a bit painful to work on
>>>> as I can only reproduce it on large runs and then it's seemingly random.
>>>>
>>>>
>>>> Thanks,
>>>> Mark
>>>>
>>>
>>>
>>> --
>>> 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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