[petsc-users] A bad commit affects MOOSE

Smith, Barry F. bsmith at mcs.anl.gov
Tue Apr 3 02:17:24 CDT 2018 

   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.

    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_JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&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,
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>>

More information about the petsc-users mailing list