[petsc-users] A bad commit affects MOOSE

Satish Balay balay at mcs.anl.gov
Tue Apr 3 09:58:00 CDT 2018 

On Tue, 3 Apr 2018, Kong, Fande wrote:

> On Tue, Apr 3, 2018 at 1:17 AM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> 
> >
> >    Each external package definitely needs its own duplicated communicator;
> > cannot share between packages.
> >
> >    The only problem with the dups below is if they are in a loop and get
> > called many times.
> >
> 
> 
> The "standard test" that has this issue actually has 1K fields. MOOSE
> creates its own field-split preconditioner (not based on the PETSc
> fieldsplit), and each filed is associated with one PC HYPRE.  If PETSc
> duplicates communicators, we should easily reach the limit 2048.
> 
> I also want to confirm what extra communicators are introduced in the bad
> commit.

To me it looks like there is 1 extra comm created [for MATHYPRE] for each PCHYPRE that is created [which also creates one comm for this object].

But you might want to verify [by linking with mpi trace library?]


There are some debugging hints at https://lists.mpich.org/pipermail/discuss/2012-December/000148.html [wrt mpich] - which I haven't checked..

Satish

> 
> 
> Fande,
> 
> 
> 
> >
> >     To debug the hypre/duplication issue in MOOSE I would run in the
> > debugger with a break point in MPI_Comm_dup() and see
> > who keeps calling it an unreasonable amount of times. (My guess is this is
> > a new "feature" in hypre that they will need to fix but only debugging will
> > tell)
> >
> >    Barry
> >
> >
> > > On Apr 2, 2018, at 7:44 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
> > >
> > > We do a MPI_Comm_dup() for objects related to externalpackages.
> > >
> > > Looks like we added a new mat type MATHYPRE - in 3.8 that PCHYPRE is
> > > using. Previously there was one MPI_Comm_dup() PCHYPRE - now I think
> > > is one more for MATHYPRE - so more calls to MPI_Comm_dup in 3.8 vs 3.7
> > >
> > > src/dm/impls/da/hypre/mhyp.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)B),&(ex->hcomm));CHKERRQ(ierr);
> > > src/dm/impls/da/hypre/mhyp.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)B),&(ex->hcomm));CHKERRQ(ierr);
> > > src/dm/impls/swarm/data_ex.c:  ierr = MPI_Comm_dup(comm,&d->comm);
> > CHKERRQ(ierr);
> > > src/ksp/pc/impls/hypre/hypre.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)pc),&(jac->comm_hypre));CHKERRQ(ierr);
> > > src/ksp/pc/impls/hypre/hypre.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)pc),&(ex->hcomm));CHKERRQ(ierr);
> > > src/ksp/pc/impls/hypre/hypre.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)pc),&(ex->hcomm));CHKERRQ(ierr);
> > > src/ksp/pc/impls/spai/ispai.c:  ierr      =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)pc),&(ispai->comm_
> > spai));CHKERRQ(ierr);
> > > src/mat/examples/tests/ex152.c:  ierr   = MPI_Comm_dup(MPI_COMM_WORLD,
> > &comm);CHKERRQ(ierr);
> > > src/mat/impls/aij/mpi/mkl_cpardiso/mkl_cpardiso.c:  ierr =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(mat_mkl_
> > cpardiso->comm_mkl_cpardiso));CHKERRQ(ierr);
> > > src/mat/impls/aij/mpi/mumps/mumps.c:  ierr =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(mumps->comm_
> > mumps));CHKERRQ(ierr);
> > > src/mat/impls/aij/mpi/pastix/pastix.c:    ierr =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(lu->pastix_
> > comm));CHKERRQ(ierr);
> > > src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:  ierr =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(lu->comm_
> > superlu));CHKERRQ(ierr);
> > > src/mat/impls/hypre/mhypre.c:  ierr = MPI_Comm_dup(PetscObjectComm((
> > PetscObject)B),&hB->comm);CHKERRQ(ierr);
> > > src/mat/partition/impls/pmetis/pmetis.c:    ierr   =
> > MPI_Comm_dup(pcomm,&comm);CHKERRQ(ierr);
> > > src/sys/mpiuni/mpi.c:    MPI_COMM_SELF, MPI_COMM_WORLD, and a
> > MPI_Comm_dup() of each of these (duplicates of duplicates return the same
> > communictor)
> > > src/sys/mpiuni/mpi.c:int MPI_Comm_dup(MPI_Comm comm,MPI_Comm *out)
> > > src/sys/objects/pinit.c:      ierr = MPI_Comm_dup(MPI_COMM_WORLD,&
> > local_comm);CHKERRQ(ierr);
> > > src/sys/objects/pinit.c:      ierr = MPI_Comm_dup(MPI_COMM_WORLD,&
> > local_comm);CHKERRQ(ierr);
> > > src/sys/objects/tagm.c:      ierr = MPI_Comm_dup(comm_in,comm_out)
> > ;CHKERRQ(ierr);
> > > src/sys/utils/mpiu.c:  ierr = MPI_Comm_dup(comm,&local_comm)
> > ;CHKERRQ(ierr);
> > > src/ts/impls/implicit/sundials/sundials.c:  ierr =
> > MPI_Comm_dup(PetscObjectComm((PetscObject)ts),&(cvode->comm_
> > sundials));CHKERRQ(ierr);
> > >
> > > Perhaps we need a PetscCommDuplicateExternalPkg() to somehow avoid
> > these MPI_Comm_dup() calls?
> > >
> > > Satish
> > >
> > > On Tue, 3 Apr 2018, Smith, Barry F. wrote:
> > >
> > >>
> > >>  Are we sure this is a PETSc comm issue and not a hypre comm
> > duplication issue
> > >>
> > >> frame #6: 0x00000001061345d9 libpetsc.3.07.dylib`hypre_
> > GenerateSubComm(comm=-1006627852, participate=<unavailable>,
> > new_comm_ptr=<unavailable>) + 409 at gen_redcs_mat.c:531 [opt]
> > >>
> > >> Looks like hypre is needed to generate subcomms, perhaps it generates
> > too many?
> > >>
> > >>   Barry
> > >>
> > >>
> > >>> On Apr 2, 2018, at 7:07 PM, Derek Gaston <friedmud at gmail.com> wrote:
> > >>>
> > >>> I’m working with Fande on this and I would like to add a bit more.
> > There are many circumstances where we aren’t working on COMM_WORLD at all
> > (e.g. working on a sub-communicator) but PETSc was initialized using
> > MPI_COMM_WORLD (think multi-level solves)… and we need to create
> > arbitrarily many PETSc vecs/mats/solvers/preconditioners and solve.  We
> > definitely can’t rely on using PETSC_COMM_WORLD to avoid triggering
> > duplication.
> > >>>
> > >>> Can you explain why PETSc needs to duplicate the communicator so much?
> > >>>
> > >>> Thanks for your help in tracking this down!
> > >>>
> > >>> Derek
> > >>>
> > >>> On Mon, Apr 2, 2018 at 5:44 PM Kong, Fande <fande.kong at inl.gov> wrote:
> > >>> Why we do not use user-level MPI communicators directly? What are
> > potential risks here?
> > >>>
> > >>>
> > >>> Fande,
> > >>>
> > >>> On Mon, Apr 2, 2018 at 5:08 PM, Satish Balay <balay at mcs.anl.gov>
> > wrote:
> > >>> PETSC_COMM_WORLD [via PetscCommDuplicate()] attempts to minimize calls
> > to MPI_Comm_dup() - thus potentially avoiding such errors
> > >>>
> > >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.
> > anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Sys_
> > PetscCommDuplicate.html&d=DwIBAg&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB_
> > _aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmi
> > CY&m=jgv7gpZ3K52d_FWMgkK9yEScbLA7pkrWydFuJnYflsU&s=_
> > zpWRcyk3kHuEHoq02NDqYExnXIohXpNnjyabYnnDjU&e=
> > >>>
> > >>>
> > >>> Satish
> > >>>
> > >>> On Mon, 2 Apr 2018, Kong, Fande wrote:
> > >>>
> > >>>> On Mon, Apr 2, 2018 at 4:23 PM, Satish Balay <balay at mcs.anl.gov>
> > wrote:
> > >>>>
> > >>>>> Does this 'standard test' use MPI_COMM_WORLD' to crate PETSc objects?
> > >>>>>
> > >>>>> If so - you could try changing to PETSC_COMM_WORLD
> > >>>>>
> > >>>>
> > >>>>
> > >>>> I do not think we are using PETSC_COMM_WORLD when creating PETSc
> > objects.
> > >>>> Why we can not use MPI_COMM_WORLD?
> > >>>>
> > >>>>
> > >>>> Fande,
> > >>>>
> > >>>>
> > >>>>>
> > >>>>> Satish
> > >>>>>
> > >>>>>
> > >>>>> On Mon, 2 Apr 2018, Kong, Fande wrote:
> > >>>>>
> > >>>>>> Hi All,
> > >>>>>>
> > >>>>>> I am trying to upgrade PETSc from 3.7.6 to 3.8.3 for MOOSE and its
> > >>>>>> applications. I have a error message for a standard test:
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> *preconditioners/pbp.lots_of_variables: MPI had an
> > >>>>>> errorpreconditioners/pbp.lots_of_variables:
> > >>>>>> ------------------------------------------------
> > >>>>> preconditioners/pbp.lots_of_variables:
> > >>>>>> Other MPI error, error stack:preconditioners/pbp.lots_of_variables:
> > >>>>>> PMPI_Comm_dup(177)..................: MPI_Comm_dup(comm=0x84000001,
> > >>>>>> new_comm=0x97d1068) failedpreconditioners/pbp.lots_of_variables:
> > >>>>>> PMPI_Comm_dup(162)..................:
> > >>>>>> preconditioners/pbp.lots_of_variables:
> > >>>>>> MPIR_Comm_dup_impl(57)..............:
> > >>>>>> preconditioners/pbp.lots_of_variables:
> > >>>>>> MPIR_Comm_copy(739).................:
> > >>>>>> preconditioners/pbp.lots_of_variables:
> > >>>>>> MPIR_Get_contextid_sparse_group(614): Too many communicators
> > (0/2048
> > >>>>> free
> > >>>>>> on this process; ignore_id=0)*
> > >>>>>>
> > >>>>>>
> > >>>>>> I did "git bisect', and the following commit introduces this issue:
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> *commit 49a781f5cee36db85e8d5b951eec29f10ac13593Author: Stefano
> > Zampini
> > >>>>>> <stefano.zampini at gmail.com <stefano.zampini at gmail.com>>Date:   Sat
> > Nov 5
> > >>>>>> 20:15:19 2016 +0300    PCHYPRE: use internal Mat of type MatHYPRE
> > >>>>>> hpmat already stores two HYPRE vectors*
> > >>>>>>
> > >>>>>> Before I debug line-by-line, anyone has a clue on this?
> > >>>>>>
> > >>>>>>
> > >>>>>> Fande,
> > >>>>>>
> > >>>>>
> > >>>>>
> > >>>>
> > >>>
> > >>
> >
> >
>

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