[petsc-users] PetscAllreduceBarrierCheck is valgrind clean?
Fande Kong
fdkong.jd at gmail.com
Wed Jan 13 14:18:05 CST 2021
On Wed, Jan 13, 2021 at 11:49 AM Barry Smith <bsmith at petsc.dev> wrote:
>
> Fande,
>
> Look at
> https://scm.mvapich.cse.ohio-state.edu/svn/mpi/mvapich2/trunk/src/mpid/ch3/channels/common/src/detect/arch/mv2_arch_detect.c
>
> cpubind_set = hwloc_bitmap_alloc();
>
> but I don't find a corresponding hwloc_bitmap_free(cpubind_set ); in
> get_socket_bound_info().
>
Thanks. I added hwloc_bitmap_free(cpubind_set ) to the end
of get_socket_bound_info(). And then these valgrind messages disappeared.
Will ask mvapich developers to fix this.
Thanks,
Fande,
>
>
> Barry
>
>
> >
>
> > On Jan 13, 2021, at 12:32 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
> >
> > Hi All,
> >
> > I ran valgrind with mvapich-2.3.5 for a moose simulation. The
> motivation was that we have a few non-deterministic parallel simulations in
> moose. I want to check if we have any memory issues. I got some complaints
> from PetscAllreduceBarrierCheck
> >
> > Thanks,
> >
> >
> > Fande
> >
> >
> >
> > ==98001== 88 (24 direct, 64 indirect) bytes in 1 blocks are definitely
> lost in loss record 31 of 54
> > ==98001== at 0x4C29F73: malloc (vg_replace_malloc.c:307)
> > ==98001== by 0xDAE1D5E: hwloc_bitmap_alloc (bitmap.c:74)
> > ==98001== by 0xDA7523F: get_socket_bound_info (mv2_arch_detect.c:898)
> > ==98001== by 0xD93C87A: create_intra_sock_comm
> (create_2level_comm.c:593)
> > ==98001== by 0xD93BEBA: create_2level_comm (create_2level_comm.c:1762)
> > ==98001== by 0xD59A894: mv2_increment_shmem_coll_counter
> (ch3_shmem_coll.c:2183)
> > ==98001== by 0xD4E4CBB: PMPI_Allreduce (allreduce.c:912)
> > ==98001== by 0x99F1766: PetscAllreduceBarrierCheck (pbarrier.c:26)
> > ==98001== by 0x99F70BE: PetscSplitOwnership (psplit.c:84)
> > ==98001== by 0x9C5C26B: PetscLayoutSetUp (pmap.c:262)
> > ==98001== by 0xA08C66B: MatMPIAdjSetPreallocation_MPIAdj
> (mpiadj.c:630)
> > ==98001== by 0xA08EB9A: MatMPIAdjSetPreallocation (mpiadj.c:856)
> > ==98001== by 0xA08F6D3: MatCreateMPIAdj (mpiadj.c:904)
> >
> >
> > ==98001== 88 (24 direct, 64 indirect) bytes in 1 blocks are definitely
> lost in loss record 32 of 54
> > ==98001== at 0x4C29F73: malloc (vg_replace_malloc.c:307)
> > ==98001== by 0xDAE1D5E: hwloc_bitmap_alloc (bitmap.c:74)
> > ==98001== by 0xDA7523F: get_socket_bound_info (mv2_arch_detect.c:898)
> > ==98001== by 0xD93C87A: create_intra_sock_comm
> (create_2level_comm.c:593)
> > ==98001== by 0xD93BEBA: create_2level_comm (create_2level_comm.c:1762)
> > ==98001== by 0xD59A9A4: mv2_increment_allgather_coll_counter
> (ch3_shmem_coll.c:2218)
> > ==98001== by 0xD4E4CE4: PMPI_Allreduce (allreduce.c:917)
> > ==98001== by 0xCD9D74D: libparmetis__gkMPI_Allreduce (gkmpi.c:103)
> > ==98001== by 0xCDBB663: libparmetis__ComputeParallelBalance
> (stat.c:87)
> > ==98001== by 0xCDA4FE0: libparmetis__KWayFM (kwayrefine.c:352)
> > ==98001== by 0xCDA21ED: libparmetis__Global_Partition (kmetis.c:222)
> > ==98001== by 0xCDA20B2: libparmetis__Global_Partition (kmetis.c:191)
> > ==98001== by 0xCDA20B2: libparmetis__Global_Partition (kmetis.c:191)
> > ==98001== by 0xCDA20B2: libparmetis__Global_Partition (kmetis.c:191)
> > ==98001== by 0xCDA20B2: libparmetis__Global_Partition (kmetis.c:191)
> > ==98001== by 0xCDA2748: ParMETIS_V3_PartKway (kmetis.c:94)
> > ==98001== by 0xA2D6B39: MatPartitioningApply_Parmetis_Private
> (pmetis.c:145)
> > ==98001== by 0xA2D77D9: MatPartitioningApply_Parmetis (pmetis.c:219)
> > ==98001== by 0xA2CD46A: MatPartitioningApply (partition.c:332)
> >
> >
> > ==98001== 88 (24 direct, 64 indirect) bytes in 1 blocks are definitely
> lost in loss record 33 of 54
> > ==98001== at 0x4C29F73: malloc (vg_replace_malloc.c:307)
> > ==98001== by 0xDAE1D5E: hwloc_bitmap_alloc (bitmap.c:74)
> > ==98001== by 0xDA7523F: get_socket_bound_info (mv2_arch_detect.c:898)
> > ==98001== by 0xD93C87A: create_intra_sock_comm
> (create_2level_comm.c:593)
> > ==98001== by 0xD93BEBA: create_2level_comm (create_2level_comm.c:1762)
> > ==98001== by 0xD59A894: mv2_increment_shmem_coll_counter
> (ch3_shmem_coll.c:2183)
> > ==98001== by 0xD4E4CBB: PMPI_Allreduce (allreduce.c:912)
> > ==98001== by 0x99F1766: PetscAllreduceBarrierCheck (pbarrier.c:26)
> > ==98001== by 0x99F733E: PetscSplitOwnership (psplit.c:91)
> > ==98001== by 0x9C5C26B: PetscLayoutSetUp (pmap.c:262)
> > ==98001== by 0x9C5DB0D: PetscLayoutCreateFromSizes (pmap.c:112)
> > ==98001== by 0x9D9A018: ISGeneralSetIndices_General (general.c:568)
> > ==98001== by 0x9D9AB44: ISGeneralSetIndices (general.c:554)
> > ==98001== by 0x9D9ADC4: ISCreateGeneral (general.c:529)
> > ==98001== by 0x9B431E6: VecCreateGhostWithArray (pbvec.c:692)
> > ==98001== by 0x9B43A33: VecCreateGhost (pbvec.c:748)
> >
> >
> > ==98001== 88 (24 direct, 64 indirect) bytes in 1 blocks are definitely
> lost in loss record 34 of 54
> > =98001== at 0x4C29F73: malloc (vg_replace_malloc.c:307)
> > ==98001== by 0xDAE1D5E: hwloc_bitmap_alloc (bitmap.c:74)
> > ==98001== by 0xDA7523F: get_socket_
> > =
> > bound_info (mv2_arch_detect.c:898)
> > ==98001== by 0xD93C87A: create_intra_sock_comm
> (create_2level_comm.c:593)
> > ==98001== by 0xD93BEBA: create_2level_comm (create_2level_comm.c:1762)
> > ==98001== by 0xD59A894: mv2_increment_shmem_coll_counter
> (ch3_shmem_coll.c:2183)
> > ==98001== by 0xD4E4CBB: PMPI_Allreduce (allreduce.c:912)
> > ==98001== by 0x9B0B5F3: VecSetSizes (vector.c:1318)
> > ==98001== by 0x9B42DDC: VecCreateMPIWithArray (pbvec.c:625)
> > ==98001== by 0xA7CF280: PCSetUp_Redundant (redundant.c:125)
> > ==98001== by 0xA7BB0CE: PCSetUp (precon.c:1009)
> > ==98001== by 0xAA2A9B9: KSPSetUp (itfunc.c:406)
> > ==98001== by 0xA92C490: PCSetUp_MG (mg.c:907)
> > ==98001== by 0xA93CAE9: PCSetUp_HMG (hmg.c:220)
> > ==98001== by 0xA7BB0CE: PCSetUp (precon.c:1009)
> > ==98001== by 0xAA2A9B9: KSPSetUp (itfunc.c:406)
> > ==98001== by 0xAA2B2E9: KSPSolve_Private (itfunc.c:658)
> > ==98001== by 0xAA2E8B7: KSPSolve (itfunc.c:889)
> > ==98001== by 0xAC33950: SNESSolve_NEWTONLS (ls.c:225)
> > ==98001== by 0xABD95AA: SNESSolve (snes.c:4569)
> >
> >
> > ==98001== 176 (48 direct, 128 indirect) bytes in 2 blocks are definitely
> lost in loss record 39 of 54
> > ==98001== at 0x4C29F73: malloc (vg_replace_malloc.c:307)
> > ==98001== by 0xDAE1D5E: hwloc_bitmap_alloc (bitmap.c:74)
> > ==98001== by 0xDA7523F: get_socket_bound_info (mv2_arch_detect.c:898)
> > ==98001== by 0xD93C87A: create_intra_sock_comm
> (create_2level_comm.c:593)
> > ==98001== by 0xD93BEBA: create_2level_comm (create_2level_comm.c:1762)
> > ==98001== by 0xD59A894: mv2_increment_shmem_coll_counter
> (ch3_shmem_coll.c:2183)
> > ==98001== by 0xD4E4CBB: PMPI_Allreduce (allreduce.c:912)
> > ==98001== by 0xBAB3848: hypre_MPI_Allreduce (mpistubs.c:1180)
> > ==98001== by 0xB96093E: hypre_ParCSRMatrixSetNumNonzeros_core
> (par_csr_matrix.c:383)
> > ==98001== by 0xB960A11: hypre_ParCSRMatrixSetDNumNonzeros
> (par_csr_matrix.c:413)
> > ==98001== by 0xB8B32DF: hypre_BoomerAMGSetup (par_amg_setup.c:2784)
> > ==98001== by 0xB8A0D26: HYPRE_BoomerAMGSetup (HYPRE_parcsr_amg.c:47)
> > ==98001== by 0xA9EDB17: PCSetUp_HYPRE (hypre.c:408)
> > ==98001== by 0xA7BB0CE: PCSetUp (precon.c:1009)
> > ==98001== by 0xA93B2DB: PCSetUp_HMG (hmg.c:161)
> > ==98001== by 0xA7BB0CE: PCSetUp (precon.c:1009)
> > ==98001== by 0xAA2A9B9: KSPSetUp (itfunc.c:406)
> > ==98001== by 0xAA2B2E9: KSPSolve_Private (itfunc.c:658)
> > ==98001== by 0xAA2E8B7: KSPSolve (itfunc.c:889)
> > ==98001== by 0xAC33950: SNESSolve_NEWTONLS (ls.c:225)
> >
> >
> >
> >
>
>
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