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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: > >> >> Mark, >> >> Can you run in valgrind? >> >> Exactly what BLAS are you using? >> >> Barry >> >> >> On Aug 24, 2020, at 7:54 AM, Mark Lohry <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >>>>> wrote: >>>>> >>>>> On Wed, Aug 12, 2020 at 7:53 AM Mark Lohry <[email protected]> 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/> >>>>> >>>>> >>>>> >>>> >> >
