[petsc-dev] Something changed with SBAIJ on april 17?
Stefano Zampini
stefano.zampini at gmail.com
Fri Apr 19 12:10:08 CDT 2019
Can you please send a MWE to reproduce the errors so that I can provide a
fix?
Il Ven 19 Apr 2019, 17:00 Matthew Knepley via petsc-dev <
petsc-dev at mcs.anl.gov> ha scritto:
> On Fri, Apr 19, 2019 at 9:40 AM Balay, Satish via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
>> There were a few merges in the the past few days.
>>
>> For ex:
>> https://bitbucket.org/petsc/petsc/pull-requests/1547/add-support-for-zeroing-rows-and-columns/diff
>>
>> Perhaps you can narrow down to the commit that triggered this change with
>> git bisect.
>>
>
> I think its this commit:
>
>
> https://bitbucket.org/petsc/petsc/commits/2b4bbc58b197e97e85869bd03594884bbca73c67
>
> Matt
>
>
>> cc: Stefano
>>
>> Satish
>>
>> On Fri, 19 Apr 2019, Éric Chamberland via petsc-dev wrote:
>>
>> > Hi,
>> >
>> > Looks like something pushed on master change or broke some sbaij
>> usages. I
>> > have two kind off errors with MatCopy:
>> >
>> > 1) MatCopy error saying: No support for this operation for this object
>> type
>> >
>> > [0]PETSC ERROR: --------------------- Error Message
>> > --------------------------------------------------------------
>> > [0]PETSC ERROR: No support for this operation for this object type
>> > [0]PETSC ERROR: MatGetRow is not supported for SBAIJ matrix format.
>> Getting
>> > the upper triangular part of row, run with -mat_getrow_uppertriangular,
>> call
>> > MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE) or
>> > MatGetRowUpperTriangular()
>> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for
>> > trouble shooting.
>> > [0]PETSC ERROR: Petsc Development GIT revision: v3.11.1-277-g63b3610
>> GIT
>> > Date: 2019-04-18 08:33:56 -0500
>> > [0]PETSC ERROR:
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/BIB/bin/
>> Test.deliMEFPP.dev
>> > on a named compile by Unknown Fri Apr 19 03:19:09 2019
>> > [0]PETSC ERROR: Configure options --prefix=/opt/petsc-master_debug
>> > --with-mpi-compilers=1 --with-mpi-dir=/opt/openmpi-1.10.2
>> > --with-cxx-dialect=C++11 --with-make-np=12 --with-shared-libraries=1
>> > --with-debugging=yes --with-memalign=64 --with-visibility=0
>> > --with-64-bit-indices=0 --download-ml=yes --download-mumps=yes
>> > --download-superlu=yes --download-superlu_dist=yes
>> --download-parmetis=yes
>> > --download-ptscotch=yes --download-metis=yes --download-suitesparse=yes
>> > --download-hypre=yes
>> > --with-blaslapack-dir=/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> > --with-mkl_pardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl
>> > --with-mkl_cpardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl
>> > --with-scalapack=1
>> > --with-scalapack-include=/opt/intel/composer_xe_2015.2.164/mkl/include
>> >
>> --with-scalapack-lib="-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> > -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"
>> > [0]PETSC ERROR: #1 MatGetRow_SeqSBAIJ() line 281 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/sbaij/seq/sbaij.c
>> > [0]PETSC ERROR: #2 MatGetRow() line 574 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: #3 MatAXPY_Basic_Preallocate() line 138 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #4 MatAXPY() line 95 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #5 MatAYPX() line 384 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #6 MatCopy_Basic() line 4056 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: #7 MatCopy_SeqAIJ() line 2844 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/aij/seq/aij.c
>> > [0]PETSC ERROR: #8 MatCopy() line 4110 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> >
>> > 2) MatCopy error saying:
>> >
>> > Argument out of range: New nonzero at (6,7) caused a malloc
>> >
>> > [0]PETSC ERROR: --------------------- Error Message
>> > --------------------------------------------------------------
>> > [0]PETSC ERROR: Argument out of range
>> > [0]PETSC ERROR: New nonzero at (6,7) caused a malloc
>> > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
>> turn off
>> > this check
>> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for
>> > trouble shooting.
>> > [0]PETSC ERROR: Petsc Development GIT revision: v3.11.1-277-g63b3610
>> GIT
>> > Date: 2019-04-18 08:33:56 -0500
>> > [0]PETSC ERROR:
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/BIB/bin/
>> Test.BIBProblemeGD.dev
>> > on a named compile by Unknown Fri Apr 19 03:22:25 2019
>> > [0]PETSC ERROR: Configure options --prefix=/opt/petsc-master_debug
>> > --with-mpi-compilers=1 --with-mpi-dir=/opt/openmpi-1.10.2
>> > --with-cxx-dialect=C++11 --with-make-np=12 --with-shared-libraries=1
>> > --with-debugging=yes --with-memalign=64 --with-visibility=0
>> > --with-64-bit-indices=0 --download-ml=yes --download-mumps=yes
>> > --download-superlu=yes --download-superlu_dist=yes
>> --download-parmetis=yes
>> > --download-ptscotch=yes --download-metis=yes --download-suitesparse=yes
>> > --download-hypre=yes
>> > --with-blaslapack-dir=/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> > --with-mkl_pardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl
>> > --with-mkl_cpardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl
>> > --with-scalapack=1
>> > --with-scalapack-include=/opt/intel/composer_xe_2015.2.164/mkl/include
>> >
>> --with-scalapack-lib="-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64
>> > -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"
>> > [0]PETSC ERROR: #1 MatSetValues_SeqSBAIJ() line 990 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/sbaij/seq/sbaij.c
>> > [0]PETSC ERROR: #2 MatSetValues() line 1404 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: #3 MatAXPY_BasicWithPreallocation() line 209 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #4 MatAXPY() line 96 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #5 MatAYPX() line 384 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c
>> > [0]PETSC ERROR: #6 MatCopy_Basic() line 4056 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: #7 MatCopy_SeqAIJ() line 2844 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/aij/seq/aij.c
>> > [0]PETSC ERROR: #8 MatCopy() line 4110 in
>> >
>> /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>> >
>> > Here are my installation logs as of april 18, at 02h00:
>> >
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_configure.log
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make.log
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_default.log
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_RDict.log
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_CMakeLists.txt
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_test.log
>> >
>> http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_streams.log
>> >
>> > Thanks,
>> >
>> > Eric
>> >
>> >
>> >
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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