[petsc-dev] Something changed with SBAIJ on april 17?

Matthew Knepley knepley at gmail.com
Fri Apr 19 08:59:24 CDT 2019 

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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20190419/d48dc17d/attachment-0001.html>

More information about the petsc-dev mailing list