[petsc-users] unsorted local columns in 3.8?
Hong
hzhang at mcs.anl.gov
Fri Nov 10 09:38:09 CST 2017
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_memcheck-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_memcheck-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_memcheck-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_memcheck-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
>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20171110/bf87339a/attachment-0001.html>
More information about the petsc-users
mailing list