[petsc-users] unsorted local columns in 3.8?
Hong
hzhang at mcs.anl.gov
Fri Nov 10 16:17:12 CST 2017
Mark:
> I would add:
>
> '--download-fblaslapack=1',
>
> This is what I have on my Linux machine (cg at ANL) and it runs clean.
>
I do not see any error report from nightly tests for ex56. Should I merge
this branch to maint?
Hong
>
> On Fri, Nov 10, 2017 at 11:03 AM, Hong <hzhang at mcs.anl.gov> wrote:
>
>> 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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