[petsc-users] unsorted local columns in 3.8?
Satish Balay
balay at mcs.anl.gov
Fri Nov 10 17:04:55 CST 2017
I don't see any changes hzhang/fix-submat_samerowdist in past few
days. So how did this error get fixed?
please do not merge yet.
Satish
On Fri, 10 Nov 2017, Mark Adams wrote:
> I don't see a problem with this. As far as what branch to merge it into,
> that is a Barry/Satish/etc decision.
>
> On Fri, Nov 10, 2017 at 5:17 PM, Hong <hzhang at mcs.anl.gov> wrote:
>
> > 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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