[petsc-users] Bus Error
Mark Lohry
mlohry at gmail.com
Mon Aug 24 10:15:28 CDT 2020
>
> Do you ever use regular malloc()? PETSc malloc aligns automatically, but
> the system one does not.
Indirectly via new, yes.
On Mon, Aug 24, 2020 at 11:10 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Mon, Aug 24, 2020 at 10:56 AM Mark Lohry <mlohry at gmail.com> wrote:
>
>> 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?
>>
>
> Do you ever use regular malloc()? PETSc malloc aligns automatically, but
> the system one does not.
>
> Thanks,
>
> Matt
>
>
>> 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/>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>
>
> --
> 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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