[petsc-users] Valgrind Issue With Ghosted Vectors

[Derek Gaston]

Stefano: the stupidity was all mine and had nothing to do with PETSc.
Valgrind helped me track down a memory corruption issue that ultimately was
just about a bad input file to my code (and obviously not enough error
checking for input files!).

The issue is fixed.

Now - I'd like to understand a bit more about what happened here on the
PETSc side.  Was this valgrind issue something that was known and you
already had a fix for it - but it wasn't on maint yet?  Or was it just that
I was using too old of a version of PETSc so I didn't have the fix?

Derek

On Fri, Mar 22, 2019 at 4:29 AM Stefano Zampini <stefano.zampini at gmail.com>
wrote:

>
>
> On Mar 21, 2019, at 7:59 PM, Derek Gaston <friedmud at gmail.com> wrote:
>
> 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 :-)
>
>
> Derek,
>
> I don’t understand. Is your problem fixed or not? Would be nice to
> understand what was the “some stupidity on your part”, and if it was still
> leading to valid PETSc code or just to a broken setup.
> In the first case, then we should investigate the valgrind error you
> reported.
> In the second case, this is not a PETSc issue.
>
>
> 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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