[petsc-users] Valgrind Issue With Ghosted Vectors

[Derek Gaston]

It sounds like you already tracked this down... but for completeness here
is what track-origins gives:

==262923== Conditional jump or move depends on uninitialised value(s)
==262923==    at 0x73C6548: VecScatterMemcpyPlanCreate_Index (vscat.c:294)
==262923==    by 0x73DBD97: VecScatterMemcpyPlanCreate_PtoP
(vpscat_mpi1.c:312)
==262923==    by 0x73DE6AE: VecScatterCreateCommon_PtoS_MPI1
(vpscat_mpi1.c:2328)
==262923==    by 0x73DFFEA: VecScatterCreateLocal_PtoS_MPI1
(vpscat_mpi1.c:2202)
==262923==    by 0x73C7A51: VecScatterCreate_PtoS (vscat.c:608)
==262923==    by 0x73C9E8A: VecScatterSetUp_vectype_private (vscat.c:857)
==262923==    by 0x73CBE5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)
==262923==    by 0x7413D39: VecScatterSetUp (vscatfce.c:212)
==262923==    by 0x7412D73: VecScatterCreateWithData (vscreate.c:333)
==262923==    by 0x747A232: VecCreateGhostWithArray (pbvec.c:685)
==262923==    by 0x747A90D: VecCreateGhost (pbvec.c:741)
==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)
==262923==  Uninitialised value was created by a heap allocation
==262923==    at 0x402DDC6: memalign (vg_replace_malloc.c:899)
==262923==    by 0x7359702: PetscMallocAlign (mal.c:41)
==262923==    by 0x7359C70: PetscMallocA (mal.c:390)
==262923==    by 0x73DECF0: VecScatterCreateLocal_PtoS_MPI1
(vpscat_mpi1.c:2061)
==262923==    by 0x73C7A51: VecScatterCreate_PtoS (vscat.c:608)
==262923==    by 0x73C9E8A: VecScatterSetUp_vectype_private (vscat.c:857)
==262923==    by 0x73CBE5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)
==262923==    by 0x7413D39: VecScatterSetUp (vscatfce.c:212)
==262923==    by 0x7412D73: VecScatterCreateWithData (vscreate.c:333)
==262923==    by 0x747A232: VecCreateGhostWithArray (pbvec.c:685)
==262923==    by 0x747A90D: VecCreateGhost (pbvec.c:741)
==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)


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!).

But: It sounds like my digging may have uncovered something real here... so
it wasn't completely useless :-)

Thanks for your help everyone!

Derek



On Thu, Mar 21, 2019 at 10:38 AM Stefano Zampini <stefano.zampini at gmail.com>
wrote:

>
>
> Il giorno mer 20 mar 2019 alle ore 23:40 Derek Gaston via petsc-users <
> petsc-users at mcs.anl.gov> ha scritto:
>
>> Trying to track down some memory corruption I'm seeing on larger scale
>> runs (3.5B+ unknowns).
>>
>
> Uhm.... are you using 32bit indices? is it possible there's integer
> overflow somewhere?
>
>
>
>> 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:
>>
>> ==87695== Conditional jump or move depends on uninitialised value(s)
>> ==87695==    at 0x73236D3: PetscMallocAlign (mal.c:28)
>> ==87695==    by 0x7323C70: PetscMallocA (mal.c:390)
>> ==87695==    by 0x739048E: VecScatterMemcpyPlanCreate_Index (vscat.c:284)
>> ==87695==    by 0x73A5D97: VecScatterMemcpyPlanCreate_PtoP
>> (vpscat_mpi1.c:312)
>> ==64730==    by 0x7393E8A: VecScatterSetUp_vectype_private (vscat.c:857)
>> ==64730==    by 0x7395E5D: VecScatterSetUp_MPI1 (vpscat_mpi1.c:2543)
>> ==64730==    by 0x73DDD39: VecScatterSetUp (vscatfce.c:212)
>> ==64730==    by 0x73DCD73: VecScatterCreateWithData (vscreate.c:333)
>> ==64730==    by 0x7444232: VecCreateGhostWithArray (pbvec.c:685)
>> ==64730==    by 0x744490D: VecCreateGhost (pbvec.c:741)
>>
>> ==133582== Conditional jump or move depends on uninitialised value(s)
>> ==133582==    at 0x4030384: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:1034)
>> ==133582==    by 0x739E4F9: PetscMemcpy (petscsys.h:1649)
>> ==133582==    by 0x739E4F9: VecScatterMemcpyPlanExecute_Pack
>> (vecscatterimpl.h:150)
>> ==133582==    by 0x739E4F9: VecScatterBeginMPI1_1 (vpscat_mpi1.h:69)
>> ==133582==    by 0x73DD964: VecScatterBegin (vscatfce.c:110)
>> ==133582==    by 0x744E195: VecGhostUpdateBegin (commonmpvec.c:225)
>>
>> 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!).
>>
>> Any ideas?  Is it possible it's in my code?  Is it possible that there
>> are later PETSc commits that already fix this?
>>
>> Thanks for any help,
>> Derek
>>
>>
>
> --
> Stefano
>
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