Hello,
I'm getting some valgrind errors in my PETSc code that looks like it's related
to MatTranspose(). I just figured I was doing something wrong. But I ran one
of the examples (snes/ex70) which uses MatTranpose() through valgrind and see
the same errors there as well. It seems that when the result of a MatTranspose
is used as input to a MatMatMult() call valgrind is unhappy.
Here's the valgrind output. I'm not concerned with the first MPI uninitialized
error. But that invalid read of size 8 in mpiaij.c looks a bit concerning.
I'm probably doing something wrong. Any ideas?
Thanks,
James
bash-4.1$ valgrind ./ex70
==21117== Memcheck, a memory error detector
==21117== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==21117== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
==21117== Command: ./ex70
==21117==
==21117== Syscall param writev(vector[...]) points to uninitialised byte(s)
==21117== at 0x39898E0B2B: writev (in /lib64/libc-2.12.so)
==21117== by 0x8996F16: mca_oob_tcp_msg_send_handler (oob_tcp_msg.c:249)
==21117== by 0x8997F3C: mca_oob_tcp_peer_send (oob_tcp_peer.c:204)
==21117== by 0x899A2DC: mca_oob_tcp_send_nb (oob_tcp_send.c:167)
==21117== by 0x8388955: orte_rml_oob_send (rml_oob_send.c:136)
==21117== by 0x8388B9F: orte_rml_oob_send_buffer (rml_oob_send.c:270)
==21117== by 0x8DA4F97: modex (grpcomm_bad_module.c:573)
==21117== by 0x6E31E6A: ompi_mpi_init (ompi_mpi_init.c:541)
==21117== by 0x6E4860F: PMPI_Init_thread (pinit_thread.c:84)
==21117== by 0x4DAA379: PetscInitialize (pinit.c:781)
==21117== by 0x409E29: main (ex70.c:668)
==21117== Address 0x9c7e261 is 161 bytes inside a block of size 256 alloc'd
==21117== at 0x4A06C9C: realloc (vg_replace_malloc.c:687)
==21117== by 0x6EB7FF2: opal_dss_buffer_extend (dss_internal_functions.c:63)
==21117== by 0x6EB81B4: opal_dss_copy_payload (dss_load_unload.c:164)
==21117== by 0x6E90C36: orte_grpcomm_base_pack_modex_entries
(grpcomm_base_modex.c:861)
==21117== by 0x8DA4F4C: modex (grpcomm_bad_module.c:563)
==21117== by 0x6E31E6A: ompi_mpi_init (ompi_mpi_init.c:541)
==21117== by 0x6E4860F: PMPI_Init_thread (pinit_thread.c:84)
==21117== by 0x4DAA379: PetscInitialize (pinit.c:781)
==21117== by 0x409E29: main (ex70.c:668)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E504: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5220)
==21117== by 0x557D53D: MatMatMultSymbolic_MPIAIJ_MPIAIJ
(mpimatmatmult.c:677)
==21117== by 0x55758FC: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:33)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd420 is 0 bytes after a block of size 48 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A8A: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E516: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5221)
==21117== by 0x557D53D: MatMatMultSymbolic_MPIAIJ_MPIAIJ
(mpimatmatmult.c:677)
==21117== by 0x55758FC: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:33)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3d0 is not stack'd, malloc'd or (recently) free'd
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E64D: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5226)
==21117== by 0x557D53D: MatMatMultSymbolic_MPIAIJ_MPIAIJ
(mpimatmatmult.c:677)
==21117== by 0x55758FC: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:33)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3b0 is 0 bytes after a block of size 16 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A58: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E66B: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5228)
==21117== by 0x557D53D: MatMatMultSymbolic_MPIAIJ_MPIAIJ
(mpimatmatmult.c:677)
==21117== by 0x55758FC: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:33)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3b8 is 8 bytes after a block of size 16 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A58: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E504: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5220)
==21117== by 0x557C680: MatMatMultNumeric_MPIAIJ_MPIAIJ_Scalable
(mpimatmatmult.c:560)
==21117== by 0x5575BBE: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:39)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd420 is 0 bytes after a block of size 48 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A8A: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E516: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5221)
==21117== by 0x557C680: MatMatMultNumeric_MPIAIJ_MPIAIJ_Scalable
(mpimatmatmult.c:560)
==21117== by 0x5575BBE: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:39)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3d0 is not stack'd, malloc'd or (recently) free'd
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E64D: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5226)
==21117== by 0x557C680: MatMatMultNumeric_MPIAIJ_MPIAIJ_Scalable
(mpimatmatmult.c:560)
==21117== by 0x5575BBE: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:39)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3b0 is 0 bytes after a block of size 16 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A58: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
==21117== Invalid read of size 8
==21117== at 0x553E66B: MatGetBrowsOfAoCols_MPIAIJ (mpiaij.c:5228)
==21117== by 0x557C680: MatMatMultNumeric_MPIAIJ_MPIAIJ_Scalable
(mpimatmatmult.c:560)
==21117== by 0x5575BBE: MatMatMult_MPIAIJ_MPIAIJ (mpimatmatmult.c:39)
==21117== by 0x5601808: MatMatMult (matrix.c:8714)
==21117== by 0x4067D0: StokesSetupApproxSchur (ex70.c:379)
==21117== by 0x406DB5: StokesSetupMatrix (ex70.c:399)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117== Address 0x9cdd3b8 is 8 bytes after a block of size 16 alloc'd
==21117== at 0x4A055DC: memalign (vg_replace_malloc.c:755)
==21117== by 0x4D42117: PetscMallocAlign (mal.c:27)
==21117== by 0x5016A58: VecScatterCreate (vscat.c:1168)
==21117== by 0x5547B10: MatSetUpMultiply_MPIAIJ (mmaij.c:116)
==21117== by 0x5509F30: MatAssemblyEnd_MPIAIJ (mpiaij.c:702)
==21117== by 0x55D978A: MatAssemblyEnd (matrix.c:4901)
==21117== by 0x551D7AD: MatTranspose_MPIAIJ (mpiaij.c:2024)
==21117== by 0x55D394A: MatTranspose (matrix.c:4382)
==21117== by 0x405CE4: StokesSetupMatBlock10 (ex70.c:337)
==21117== by 0x406C60: StokesSetupMatrix (ex70.c:396)
==21117== by 0x40A0D3: main (ex70.c:679)
==21117==
residual u = 3.56267e-06
residual p = 1.14951e-05
residual [u,p] = 1.20346e-05
discretization error u = 0.0106477
discretization error p = 1.85783
discretization error [u,p] = 1.85786
==21117==
==21117== HEAP SUMMARY:
==21117== in use at exit: 345,301 bytes in 3,773 blocks
==21117== total heap usage: 24,730 allocs, 20,957 frees, 16,608,714 bytes
allocated
==21117==
==21117== LEAK SUMMARY:
==21117== definitely lost: 42,743 bytes in 40 blocks
==21117== indirectly lost: 11,134 bytes in 28 blocks
==21117== possibly lost: 0 bytes in 0 blocks
==21117== still reachable: 291,424 bytes in 3,705 blocks
==21117== suppressed: 0 bytes in 0 blocks
==21117== Rerun with --leak-check=full to see details of leaked memory
==21117==
==21117== For counts of detected and suppressed errors, rerun with: -v
==21117== Use --track-origins=yes to see where uninitialised values come from
==21117== ERROR SUMMARY: 9 errors from 9 contexts (suppressed: 6 from 6)
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