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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 > > > > > <[email protected] <[email protected]>>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, > > > > > > > > > > > > > > > > > > > >
