[petsc-users] unsorted local columns in 3.8?

Fri Nov 10 09:59:07 CST 2017

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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