[petsc-users] Valgrind Issue With Ghosted Vectors

[Zhang, Junchao]

Thanks to Stefano for fixing this bug.  His fix is easy to apply (two-line change) and therefore should be tried first.

--Junchao Zhang


On Thu, Mar 21, 2019 at 3:02 AM Stefano Zampini <stefano.zampini at gmail.com<mailto:stefano.zampini at gmail.com>> wrote:
Derek

I have fixed the optimized plan few weeks ago

https://bitbucket.org/petsc/petsc/commits/c3caad8634d376283f7053f3b388606b45b3122c

Maybe this will fix your problem too?

Stefano


Il Gio 21 Mar 2019, 04:21 Zhang, Junchao via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> ha scritto:
Hi, Derek,
  Try to apply this tiny (but dirty) patch on your version of PETSc to disable the VecScatterMemcpyPlan optimization to see if it helps.
  Thanks.
--Junchao Zhang

On Wed, Mar 20, 2019 at 6:33 PM Junchao Zhang <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>> wrote:
Did you see the warning with small scale runs?  Is it possible to provide a test code?
You mentioned "changing PETSc now would be pretty painful". Is it because it will affect your performance (but not your code)?  If yes, could you try PETSc master and run you code with or without -vecscatter_type sf.  I want to isolate the problem and see if it is due to possible bugs in VecScatter.
If the above suggestion is not feasible, I will disable VecScatterMemcpy. It is an optimization I added. Sorry I did not have an option to turn off it because I thought it was always useful:)  I will provide you a patch later to disable it. With that you can run again to isolate possible bugs in VecScatterMemcpy.
Thanks.
--Junchao Zhang


On Wed, Mar 20, 2019 at 5:40 PM Derek Gaston via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Trying to track down some memory corruption I'm seeing on larger scale runs (3.5B+ unknowns).  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

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