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 <mfad...@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 <mfad...@lbl.gov> wrote: > >> This is comming from blas. How did you configure blas? >> >> On Fri, Nov 10, 2017 at 10:38 AM, Hong <hzh...@mcs.anl.gov> wrote: >> >>> Using petsc machine, I get >>> hzhang@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 <mfad...@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 <mfad...@lbl.gov> wrote: >>>> >>>>> >>>>> >>>>> On Thu, Nov 9, 2017 at 1:56 PM, Hong <hzh...@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 >>>>> >>>>> >>>>> >>>> >>> >> >