[petsc-users] unsorted local columns in 3.8?
Satish Balay
balay at mcs.anl.gov
Fri Nov 10 19:30:04 CST 2017
Ok - I just ran this example with valgrind (and parmetis) on my laptop
- and got no valgrind errors.
Will have a build tonight of this branch in next-tmp - and then look
at merging it tomorrow.
BTW: if the destination for this branch is maint - then its best to
use the name 'hzhang/fix-submat_samerowdist/maint' to make it more
obvious.
Satish
On Fri, 10 Nov 2017, Hong wrote:
> Satish :
>
> > I don't see any changes hzhang/fix-submat_samerowdist in past few
> > days. So how did this error get fixed?
> >
>
> I've never seen valgrind error for ex56 from nightly tests.
> Mark told me about Valgrind error on his mac, and I reproduced it on our
> linux machine with my own configure,
> which directs to lapack.
>
> >
> > please do not merge yet.
> >
> Sure.
>
> Hong
>
> >
> > 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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