[petsc-users] A bad commit affects MOOSE
Fande Kong
fdkong.jd at gmail.com
Tue Apr 3 10:43:38 CDT 2018
On Tue, Apr 3, 2018 at 9:12 AM, Stefano Zampini <stefano.zampini at gmail.com>
wrote:
>
> On Apr 3, 2018, at 4:58 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
> 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].
>
>
> You’re right; however, it was the same before the commit.
> I don’t understand how this specific commit is related with this issue,
> being the error not in the MPI_Comm_Dup which is inside MatCreate_MATHYPRE.
> Actually, the error comes from MPI_Comm_create
>
>
>
>
>
> * frame #5: 0x00000001068defd4 libmpi.12.dylib`MPI_Comm_create +
> 3492 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] frame #7: 0x000000010618f8ba
> libpetsc.3.07.dylib`hypre_GaussElimSetup(amg_data=0x00007fe7ff857a00,
> level=<unavailable>, relax_type=9) + 74 at par_relax.c:4209 [opt] frame
> #8: 0x0000000106140e93
> libpetsc.3.07.dylib`hypre_BoomerAMGSetup(amg_vdata=<unavailable>,
> A=0x00007fe80842aff0, f=0x00007fe80842a980, u=0x00007fe80842a510) + 17699
> at par_amg_setup.c:2108 [opt] frame #9: 0x0000000105ec773c
> libpetsc.3.07.dylib`PCSetUp_HYPRE(pc=<unavailable>) + 2540 at hypre.c:226
> [opt*
>
> How did you perform the bisection? make clean + make all ? Which version
> of HYPRE are you using?
>
I did more aggressively.
"rm -rf arch-darwin-c-opt-bisect "
"./configure --optionsModule=config.compilerOptions -with-debugging=no
--with-shared-libraries=1 --with-mpi=1 --download-fblaslapack=1
--download-metis=1 --download-parmetis=1 --download-superlu_dist=1
--download-hypre=1 --download-mumps=1 --download-scalapack=1
PETSC_ARCH=arch-darwin-c-opt-bisect"
HYPRE verison:
self.gitcommit = 'v2.11.1-55-g2ea0e43'
self.download = ['git://https://github.com/LLNL/hypre','
https://github.com/LLNL/hypre/archive/'+self.gitcommit+'.tar.gz']
I do not think this is caused by HYPRE.
Fande,
>
> 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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