[petsc-users] unsorted local columns in 3.8?
Hong
hzhang at mcs.anl.gov
Fri Nov 10 10:03:33 CST 2017
I use
Using configure Options: --download-metis --download-mpich --download-mumps
--download-parmetis --download-scalapack --download-superlu
--download-superlu_dist --download-suitesparse --download-hypre
--download-ptscotch --download-chaco --with-ctable=1 --download-cmake
--with-cc=gcc --with-cxx=g++ --with-debugging=1 --with-visibility=0
--with-fc=gfortran
Hong
On Fri, Nov 10, 2017 at 9:59 AM, Mark Adams <mfadams at lbl.gov> wrote:
> This must be a configure issue. I don't see these warning:
>
> #!/usr/bin/python
> if __name__ == '__main__':
> import sys
> import os
> sys.path.insert(0, os.path.abspath('config'))
> import configure
> configure_options = [
> '--with-cc=clang',
> '--with-cc++=clang++',
> '--download-mpich=1',
> '--download-metis=1',
> '--download-superlu=1',
> '--download-superlu_dist=1',
> '--download-parmetis=1',
> '--download-fblaslapack=1',
> '--download-p4est=1',
> '--with-debugging=1',
> '--with-batch=0',
> 'PETSC_ARCH=arch-linux2-c-dbg32',
> '--with-openmp=0',
> '--download-p4est=0'
> ]
> configure.petsc_configure(configure_options)
>
> ~
>
>
>
>
>
> On Fri, Nov 10, 2017 at 10:56 AM, Mark Adams <mfadams at lbl.gov> wrote:
>
>> 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_me
>>> mcheck-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_me
>>> mcheck-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_me
>>> mcheck-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_me
>>> mcheck-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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