[petsc-users] Bus Error
Mark Lohry
mlohry at gmail.com
Mon Aug 24 09:54:57 CDT 2020
Thanks Barry, I'll give -malloc_debug a shot.
I know this is not necessarily a reasonable test but if you run the exact
> same thing twice does it crash at the same location in terms of iterations
> or does it seem to crash eventually "randomly" just after a long time?
>
Crashes after a different number of iterations, seemingly random.
>
> I understand the frustration with this kind of crash, it just shouldn't
> happen because the same BLAS calls have been made in the same way thousands
> of times and yet suddenly trouble and very hard to debug.
>
Eventually makes for a good war story.
Thinking back, I have seen some disturbing memory behavior that I think
falls back to my use of eigen... e.g. in the past when running my full test
suite a particular case would fail with NaNs, but if I ran that case in
isolation it passes. I wonder if some object isn't getting properly aligned
and at some point some kind of corruption occurs?
On Mon, Aug 24, 2020 at 10:35 AM Barry Smith <bsmith at petsc.dev> wrote:
>
> Mark,
>
> Ok, I'd generally trust the stock BLAS for not failing over OpenBLAS.
>
> Since valgrind is not viable have you tried with -malloc_debug with the
> bad case it will be a little bit slower but not to bad and can find some
> memory corruption issues.
>
> It might be useful to get the stack trace inside the BLAS to see exactly
> where it crashes. If you ./configure with debugging and use
> --download-fblaslapack or --download-f2cblaslapack it will compile the BLAS
> with debugging, but just running a batch job still won't display the stack
> frames inside the BLAS call.
>
> We have an option -on_error_attach_debugger which is useful for longer
> many rank runs that attaches the debugger ONLY when the error is detected
> but it may not play well with batch systems. But if you can make your run
> on a non-batch system it might be able, along with the
> --download-fblaslapack or --download-f2cblaslapack to get the exact stack
> frames. And in the debugger look at the variables and address points to try
> to determine how it could have gone wrong.
>
> I know this is not necessarily a reasonable test but if you run the
> exact same thing twice does it crash at the same location in terms of
> iterations or does it seem to crash eventually "randomly" just after a long
> time?
>
> I understand the frustration with this kind of crash, it just shouldn't
> happen because the same BLAS calls have been made in the same way thousands
> of times and yet suddenly trouble and very hard to debug.
>
> Barry
>
>
>
>
> On Aug 24, 2020, at 9:15 AM, Mark Lohry <mlohry at gmail.com> wrote:
>
> valgrind: I ran a much smaller case and didn't see any issues in valgrind.
> I'm only seeing this bus error on several hundred cores a few hours
> wallclock in, so it might not be feasible to run that in valgrind.
>
> blas: i'm not entirely sure -- it's the stock one in PUIAS linux (red hat
> derivative), libblas.so.3.4.2.. i'm going to try with intel and if that
> fails use the openblas downloaded via petsc and see if it alleviates itself.
>
>
>
> On Mon, Aug 24, 2020 at 9:48 AM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>> Mark,
>>
>> Can you run in valgrind?
>>
>> Exactly what BLAS are you using?
>>
>> Barry
>>
>>
>> On Aug 24, 2020, at 7:54 AM, Mark Lohry <mlohry at gmail.com> wrote:
>>
>> 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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