[petsc-users] unsorted local columns in 3.8?

Fri Nov 10 09:56:50 CST 2017

This is comming from blas. How did you configure blas?

On Fri, Nov 10, 2017 at 10:38 AM, Hong <hzhang at mcs.anl.gov> wrote:

> Using petsc machine, I get
> hzhang at petsc /sandbox/hzhang/petsc/src/snes/examples/tutorials
> (hzhang/fix-submat_samerowdist)
> $ mpiexec -n 2 valgrind ./ex56 -cells 2,2,1 -max_conv_its 3
> -petscspace_order 2 -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol
> 1.e-11 -ksp_norm_type unpreconditioned -snes_rtol 1.e-10 -pc_type gamg
> -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -snes_converged_reason
> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type jacobi
> -pc_gamg_mat_partitioning_type parmetis -mat_block_size 3 -run_type 1
>
> ==28811== Memcheck, a memory error detector
> ==28811== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
> ==28811== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright
> info
> ==28811== Command: ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order 2
> -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type
> unpreconditioned -snes_rtol 1.e-10 -pc_type gamg -pc_gamg_type agg
> -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -snes_converged_reason
> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type jacobi
> -pc_gamg_mat_partitioning_type parmetis -mat_block_size 3 -run_type 1
> ...
> ==28811== Invalid read of size 16
> ==28811==    at 0x8550946: dswap_k_NEHALEM (in /usr/lib/openblas-base/
> libblas.so.3)
> ==28811==    by 0x7C6797F: dswap_ (in /usr/lib/openblas-base/libblas.so.3)
> ==28811==    by 0x75B33B2: dgetri_ (in /usr/lib/lapack/liblapack.so.3.0)
> ==28811==    by 0x5E3CA5C: PetscFESetUp_Basic (dtfe.c:4012)
> ==28811==    by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==28811==    by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==28811==    by 0x41056E: main (ex56.c:395)
> ==28811==  Address 0xdc650d0 is 52,480 bytes inside a block of size 52,488
> alloc'd
> ==28811==    at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_
> memcheck-amd64-linux.so)
> ==28811==    by 0x51590F6: PetscMallocAlign (mal.c:39)
> ==28811==    by 0x5E3C169: PetscFESetUp_Basic (dtfe.c:3983)
> ==28811==    by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==28811==    by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==28811==    by 0x41056E: main (ex56.c:395)
> ==28811==
> ==28812== Invalid read of size 16
> ==28812==    at 0x8550946: dswap_k_NEHALEM (in /usr/lib/openblas-base/
> libblas.so.3)
> ==28812==    by 0x7C6797F: dswap_ (in /usr/lib/openblas-base/libblas.so.3)
> ==28812==    by 0x75B33B2: dgetri_ (in /usr/lib/lapack/liblapack.so.3.0)
> ==28812==    by 0x5E3CA5C: PetscFESetUp_Basic (dtfe.c:4012)
> ==28812==    by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==28812==    by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==28812==    by 0x41056E: main (ex56.c:395)
> ==28812==  Address 0xd9c7600 is 52,480 bytes inside a block of size 52,488
> alloc'd
> ==28812==    at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_
> memcheck-amd64-linux.so)
> ==28812==    by 0x51590F6: PetscMallocAlign (mal.c:39)
> ==28812==    by 0x5E3C169: PetscFESetUp_Basic (dtfe.c:3983)
> ==28812==    by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==28812==    by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==28812==    by 0x41056E: main (ex56.c:395)
> ==28812==
> ==28811== Invalid read of size 16
> ==28811==    at 0x8550A55: dswap_k_NEHALEM (in /usr/lib/openblas-base/
> libblas.so.3)
> ==28811==    by 0x7C6797F: dswap_ (in /usr/lib/openblas-base/libblas.so.3)
> ==28811==    by 0x7675179: dsteqr_ (in /usr/lib/lapack/liblapack.so.3.0)
> ==28811==    by 0x5DFFA22: PetscDTGaussQuadrature (dt.c:508)
> ==28811==    by 0x5E00BD8: PetscDTGaussTensorQuadrature (dt.c:582)
> ==28811==    by 0x5E57D7A: PetscFECreateDefault (dtfe.c:6763)
> ==28811==    by 0x41056E: main (ex56.c:395)
> ==28811==  Address 0xd99cbe0 is 64 bytes inside a block of size 72 alloc'd
> ==28811==    at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_
> memcheck-amd64-linux.so)
> ==28811==    by 0x51590F6: PetscMallocAlign (mal.c:39)
> ==28811==    by 0x5DFF766: PetscDTGaussQuadrature (dt.c:504)
> ==28811==    by 0x5E00BD8: PetscDTGaussTensorQuadrature (dt.c:582)
> ==28811==    by 0x5E57D7A: PetscFECreateDefault (dtfe.c:6763)
> ==28811==    by 0x41056E: main (ex56.c:395)
> ==28811==
> ==28812== Invalid read of size 16
> ==28812==    at 0x8550A55: dswap_k_NEHALEM (in /usr/lib/openblas-base/
> libblas.so.3)
> ==28812==    by 0x7C6797F: dswap_ (in /usr/lib/openblas-base/libblas.so.3)
> ==28812==    by 0x7675179: dsteqr_ (in /usr/lib/lapack/liblapack.so.3.0)
> ==28812==    by 0x5DFFA22: PetscDTGaussQuadrature (dt.c:508)
> ==28812==    by 0x5E00BD8: PetscDTGaussTensorQuadrature (dt.c:582)
> ==28812==    by 0x5E57D7A: PetscFECreateDefault (dtfe.c:6763)
> ==28812==    by 0x41056E: main (ex56.c:395)
> ==28812==  Address 0xdc11f30 is 64 bytes inside a block of size 72 alloc'd
> ==28812==    at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_
> memcheck-amd64-linux.so)
> ==28812==    by 0x51590F6: PetscMallocAlign (mal.c:39)
> ==28812==    by 0x5DFF766: PetscDTGaussQuadrature (dt.c:504)
> ==28812==    by 0x5E00BD8: PetscDTGaussTensorQuadrature (dt.c:582)
> ==28812==    by 0x5E57D7A: PetscFECreateDefault (dtfe.c:6763)
> ==28812==    by 0x41056E: main (ex56.c:395)
> ==28812==
> [0] 27 global equations, 9 vertices
> [0] 27 equations in vector, 9 vertices
> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
> [0] 441 global equations, 147 vertices
> [0] 441 equations in vector, 147 vertices
>
> hangs here ...
>
> Hong
>
> On Fri, Nov 10, 2017 at 8:57 AM, Mark Adams <mfadams at lbl.gov> wrote:
>
>> This printed a little funny in gmail, snes/ex56 is running clean in the
>> first few loops (appended), but the last one is the one with a reduced
>> processor set. Still waiting. This is with 32 bit integers. I'm running
>> another with 64 bit integers.
>>
>>    ...
>> [0] 27 global equations, 9 vertices
>> [0] 27 equations in vector, 9 vertices
>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>> [0] 441 global equations, 147 vertices
>> [0] 441 equations in vector, 147 vertices
>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>> [0] 4725 global equations, 1575 vertices
>> [0] 4725 equations in vector, 1575 vertices
>>
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Nov 10, 2017 at 9:06 AM, Mark Adams <mfadams at lbl.gov> wrote:
>>
>>>
>>>
>>> On Thu, Nov 9, 2017 at 1:56 PM, Hong <hzhang at mcs.anl.gov> wrote:
>>>
>>>> Mark:
>>>>
>>>>> OK, well, just go with the Linux machine for the regression test. I
>>>>> will keep trying to reproduce this on my Mac with an O build.
>>>>>
>>>>
>>>> Valgrind error occurs on linux machines with g-build. I cannot merge
>>>> this branch to maint until the bug is fixed.
>>>>
>>>
>>> Valgrind is failing on this run on my Mac. Moving to cg, like you I
>>> suppose. This takes forever. This is what I have so far. Did you get this
>>> far?
>>>
>>> 07:48 hzhang/fix-submat_samerowdist *= /sandbox/adams/petsc/src/snes/examples/tutorials$
>>> make PETSC_DIR=/sandbox/adams/petsc PETSC_ARCH=arch-linux2-c-dbg32 val
>>> /sandbox/adams/petsc/arch-linux2-c-dbg32/bin/mpiexec -n 2 valgrind
>>> ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order 2 -snes_max_it 2
>>> -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type
>>> unpreconditioned -snes_rtol 1.e-10 -pc_type gamg -pc_gamg_type agg
>>> -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
>>> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
>>> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -snes_converged_reason
>>> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
>>> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
>>> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type jacobi
>>> -pc_gamg_mat_partitioning_type parmetis -mat_block_size 3 -run_type 1
>>> ==12414== Memcheck, a memory error detector
>>> ==12414== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
>>> ==12414== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright
>>> info
>>> ==12415== Memcheck, a memory error detector
>>> ==12415== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
>>> ==12415== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright
>>> info
>>> ==12415== Command: ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order
>>> 2 -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11
>>> -ksp_norm_type unpreconditioned -snes_rtol 1.e-10 -pc_type gamg
>>> -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
>>> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
>>> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -snes_converged_reason
>>> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
>>> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
>>> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type jacobi
>>> -pc_gamg_mat_partitioning_type parmetis -mat_block_size 3 -run_type 1
>>> ==12415==
>>> ==12414== Command: ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order
>>> 2 -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11
>>> -ksp_norm_type unpreconditioned -snes_rtol 1.e-10 -pc_type gamg
>>> -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
>>> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
>>> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -snes_converged_reason
>>> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
>>> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
>>> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type jacobi
>>> -pc_gamg_mat_partitioning_type parmetis -mat_block_size 3 -run_type 1
>>> ==12414==
>>> [0] 27 global equations, 9 vertices
>>> [0] 27 equations in vector, 9 vertices
>>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>>> [0] 441 global equations, 147 vertices
>>> [0] 441 equations in vector, 147 vertices
>>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>>> [0] 4725 global equations, 1575 vertices
>>> [0] 4725 equations in vector, 1575 vertices
>>>
>>>
>>>
>>
>
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