[petsc-users] Valgrind Issue With Ghosted Vectors

[Balay, Satish]

Ok - cherrypicked and pushed to maint.

Satish

On Thu, 21 Mar 2019, Zhang, Junchao via petsc-users wrote:

> Yes, it does.  It is a bug.
> --Junchao Zhang
> 
> 
> On Thu, Mar 21, 2019 at 11:16 AM Balay, Satish <balay at mcs.anl.gov<mailto:balay at mcs.anl.gov>> wrote:
> Does maint also need this fix?
> 
> Satish
> 
> On Thu, 21 Mar 2019, Stefano Zampini via petsc-users 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
> > >>>
> > >>>
> >
> 
>