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<div dir="ltr" class="gmail_attr">On Thu, Mar 21, 2019 at 1:57 PM Derek Gaston via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:<br>
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<div>It sounds like you already tracked this down... but for completeness here is what track-origins gives:</div>
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<div>==262923== Conditional jump or move depends on uninitialised value(s)<br>
==262923== at 0x73C6548: VecScatterMemcpyPlanCreate_Index (vscat.c:294)<br>
==262923== by 0x73DBD97: VecScatterMemcpyPlanCreate_PtoP (vpscat_mpi1.c:312)<br>
==262923== by 0x73DE6AE: VecScatterCreateCommon_PtoS_MPI1 (vpscat_mpi1.c:2328)<br>
==262923== by 0x73DFFEA: VecScatterCreateLocal_PtoS_MPI1 (vpscat_mpi1.c:2202)<br>
==262923== by 0x73C7A51: VecScatterCreate_PtoS (vscat.c:608)<br>
==262923== by 0x73C9E8A: VecScatterSetUp_vectype_private (vscat.c:857)<br>
==262923== by 0x73CBE5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)<br>
==262923== by 0x7413D39: VecScatterSetUp (vscatfce.c:212)<br>
==262923== by 0x7412D73: VecScatterCreateWithData (vscreate.c:333)<br>
==262923== by 0x747A232: VecCreateGhostWithArray (pbvec.c:685)<br>
==262923== by 0x747A90D: VecCreateGhost (pbvec.c:741)<br>
==262923== by 0x5C7FFD6: libMesh::PetscVector<double>::init(unsigned long, unsigned long, std::vector<unsigned long, std::allocator<unsigned long> > const&, bool, libMesh::ParallelType) (petsc_vector.h:752)<br>
==262923== Uninitialised value was created by a heap allocation<br>
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<div>I checked the code but could not figure out what was wrong. Perhaps you should use 64-bit integers and see whether the warning still exists. Please remember to incorporate Stefano's bug fix. </div>
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<div>==262923== at 0x402DDC6: memalign (vg_replace_malloc.c:899)<br>
==262923== by 0x7359702: PetscMallocAlign (mal.c:41)<br>
==262923== by 0x7359C70: PetscMallocA (mal.c:390)<br>
==262923== by 0x73DECF0: VecScatterCreateLocal_PtoS_MPI1 (vpscat_mpi1.c:2061)<br>
==262923== by 0x73C7A51: VecScatterCreate_PtoS (vscat.c:608)<br>
==262923== by 0x73C9E8A: VecScatterSetUp_vectype_private (vscat.c:857)<br>
==262923== by 0x73CBE5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)<br>
==262923== by 0x7413D39: VecScatterSetUp (vscatfce.c:212)<br>
==262923== by 0x7412D73: VecScatterCreateWithData (vscreate.c:333)<br>
==262923== by 0x747A232: VecCreateGhostWithArray (pbvec.c:685)<br>
==262923== by 0x747A90D: VecCreateGhost (pbvec.c:741)<br>
==262923== by 0x5C7FFD6: libMesh::PetscVector<double>::init(unsigned long, unsigned long, std::vector<unsigned long, std::allocator<unsigned long> > const&, bool, libMesh::ParallelType) (petsc_vector.h:752)</div>
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<div>BTW: This turned out not to be my actual problem. My actual problem was just some stupidity on my part... just a simple input parameter issue to my code (should have had better error checking!).</div>
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<div>But: It sounds like my digging may have uncovered something real here... so it wasn't completely useless :-)<br>
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<div>Thanks for your help everyone!</div>
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<div>Derek</div>
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<div dir="ltr" class="gmail_attr">On Thu, Mar 21, 2019 at 10:38 AM Stefano Zampini <<a href="mailto:stefano.zampini@gmail.com" target="_blank">stefano.zampini@gmail.com</a>> wrote:<br>
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<div dir="ltr" class="gmail_attr">Il giorno mer 20 mar 2019 alle ore 23:40 Derek Gaston via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> ha scritto:<br>
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<div>Trying to track down some memory corruption I'm seeing on larger scale runs (3.5B+ unknowns).</div>
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<div>Uhm.... are you using 32bit indices? is it possible there's integer overflow somewhere?</div>
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<div>Was able to run Valgrind on it... and I'm seeing quite a lot of uninitialized value errors coming from ghost updating. Here are some of the traces:</div>
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<div>==87695== Conditional jump or move depends on uninitialised value(s)<br>
==87695== at 0x73236D3: PetscMallocAlign (mal.c:28)<br>
==87695== by 0x7323C70: PetscMallocA (mal.c:390)<br>
==87695== by 0x739048E: VecScatterMemcpyPlanCreate_Index (vscat.c:284)<br>
==87695== by 0x73A5D97: VecScatterMemcpyPlanCreate_PtoP (vpscat_mpi1.c:312)<br>
==64730== by 0x7393E8A: VecScatterSetUp_vectype_private (vscat.c:857)<br>
==64730== by 0x7395E5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)<br>
==64730== by 0x73DDD39: VecScatterSetUp (vscatfce.c:212)<br>
==64730== by 0x73DCD73: VecScatterCreateWithData (vscreate.c:333)<br>
==64730== by 0x7444232: VecCreateGhostWithArray (pbvec.c:685)<br>
==64730== by 0x744490D: VecCreateGhost (pbvec.c:741)<br>
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<div>==133582== Conditional jump or move depends on uninitialised value(s)<br>
==133582== at 0x4030384: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:1034)<br>
==133582== by 0x739E4F9: PetscMemcpy (petscsys.h:1649)<br>
==133582== by 0x739E4F9: VecScatterMemcpyPlanExecute_Pack (vecscatterimpl.h:150)<br>
==133582== by 0x739E4F9: VecScatterBeginMPI1_1 (vpscat_mpi1.h:69)<br>
==133582== by 0x73DD964: VecScatterBegin (vscatfce.c:110)<br>
==133582== by 0x744E195: VecGhostUpdateBegin (commonmpvec.c:225)<br>
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<div>This is from a Git checkout of PETSc... the hash I branched from is: 0e667e8fea4aa from December 23rd (updating would be really hard at this point as I've completed 90% of my dissertation with this version... and changing PETSc now would be pretty painful!).</div>
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<div>Any ideas? Is it possible it's in my code? Is it possible that there are later PETSc commits that already fix this?</div>
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<div>Thanks for any help,</div>
<div>Derek<br>
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-- <br>
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Stefano</div>
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