<div dir="ltr"><div dir="ltr"><div dir="ltr">Eric</div><div dir="ltr"><br></div><div dir="ltr">I have opened a PRmay fix the issues you reported <a href="https://bitbucket.org/petsc/petsc/pull-requests/1571/fix-sbaij/diff">https://bitbucket.org/petsc/petsc/pull-requests/1571/fix-sbaij/diff</a><br></div><div>Could you please try <a href="https://bitbucket.org/petsc/petsc/branch/stefano_zampini/fix-matcopy-sbaij">https://bitbucket.org/petsc/petsc/branch/stefano_zampini/fix-matcopy-sbaij</a>? (off maint)</div><div><br></div><div>Thanks</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno ven 19 apr 2019 alle ore 23:26 Éric Chamberland via petsc-dev <<a href="mailto:petsc-dev@mcs.anl.gov">petsc-dev@mcs.anl.gov</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi,</p>
<p>ok, I will try do to one, but since I am on vacation right now, I
will try to do it at my return in a week.</p>
<p>I wanted to report the bug asap, so you may figure out the
problem quickly.</p>
<p>Thanks,</p>
<p>Eric</p>
<p><br>
</p>
<div class="gmail-m_7466304462959273877moz-cite-prefix">Le 19-04-19 à 19:10, Stefano Zampini
via petsc-dev a écrit :<br>
</div>
<blockquote type="cite">
<div dir="auto">Can you please send a MWE to reproduce the errors
so that I can provide a fix?</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Il Ven 19 Apr 2019, 17:00
Matthew Knepley via petsc-dev <<a href="mailto:petsc-dev@mcs.anl.gov" target="_blank">petsc-dev@mcs.anl.gov</a>>
ha scritto:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">On Fri, Apr 19, 2019 at 9:40 AM Balay,
Satish via petsc-dev <<a href="mailto:petsc-dev@mcs.anl.gov" rel="noreferrer" target="_blank">petsc-dev@mcs.anl.gov</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">There were a few
merges in the the past few days.<br>
<br>
For ex: <a href="https://bitbucket.org/petsc/petsc/pull-requests/1547/add-support-for-zeroing-rows-and-columns/diff" rel="noreferrer noreferrer" target="_blank">https://bitbucket.org/petsc/petsc/pull-requests/1547/add-support-for-zeroing-rows-and-columns/diff</a><br>
<br>
Perhaps you can narrow down to the commit that
triggered this change with git bisect.<br>
</blockquote>
<div><br>
</div>
<div>I think its this commit:</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/commits/2b4bbc58b197e97e85869bd03594884bbca73c67" rel="noreferrer" target="_blank">https://bitbucket.org/petsc/petsc/commits/2b4bbc58b197e97e85869bd03594884bbca73c67</a></div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
cc: Stefano<br>
<br>
Satish<br>
<br>
On Fri, 19 Apr 2019, Éric Chamberland via petsc-dev
wrote:<br>
<br>
> Hi,<br>
> <br>
> Looks like something pushed on master change or
broke some sbaij usages. I<br>
> have two kind off errors with MatCopy:<br>
> <br>
> 1) MatCopy error saying: No support for this
operation for this object type<br>
> <br>
> [0]PETSC ERROR: --------------------- Error
Message<br>
>
--------------------------------------------------------------<br>
> [0]PETSC ERROR: No support for this operation for
this object type<br>
> [0]PETSC ERROR: MatGetRow is not supported for
SBAIJ matrix format. Getting<br>
> the upper triangular part of row, run with
-mat_getrow_uppertriangular, call<br>
>
MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE)
or<br>
> MatGetRowUpperTriangular()<br>
> [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for<br>
> trouble shooting.<br>
> [0]PETSC ERROR: Petsc Development GIT revision:
v3.11.1-277-g63b3610 GIT<br>
> Date: 2019-04-18 08:33:56 -0500<br>
> [0]PETSC ERROR:<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/BIB/bin/<a href="http://Test.deliMEFPP.dev" rel="noreferrer
noreferrer" target="_blank">Test.deliMEFPP.dev</a><br>
> on a named compile by Unknown Fri Apr 19
03:19:09 2019<br>
> [0]PETSC ERROR: Configure options
--prefix=/opt/petsc-master_debug<br>
> --with-mpi-compilers=1
--with-mpi-dir=/opt/openmpi-1.10.2<br>
> --with-cxx-dialect=C++11 --with-make-np=12
--with-shared-libraries=1<br>
> --with-debugging=yes --with-memalign=64
--with-visibility=0<br>
> --with-64-bit-indices=0 --download-ml=yes
--download-mumps=yes<br>
> --download-superlu=yes
--download-superlu_dist=yes --download-parmetis=yes<br>
> --download-ptscotch=yes --download-metis=yes
--download-suitesparse=yes<br>
> --download-hypre=yes<br>
>
--with-blaslapack-dir=/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64<br>
>
--with-mkl_pardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl<br>
>
--with-mkl_cpardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl<br>
> --with-scalapack=1<br>
>
--with-scalapack-include=/opt/intel/composer_xe_2015.2.164/mkl/include<br>
>
--with-scalapack-lib="-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64<br>
> -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"<br>
> [0]PETSC ERROR: #1 MatGetRow_SeqSBAIJ() line 281
in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/sbaij/seq/sbaij.c<br>
> [0]PETSC ERROR: #2 MatGetRow() line 574 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> [0]PETSC ERROR: #3 MatAXPY_Basic_Preallocate()
line 138 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #4 MatAXPY() line 95 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #5 MatAYPX() line 384 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #6 MatCopy_Basic() line 4056 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> [0]PETSC ERROR: #7 MatCopy_SeqAIJ() line 2844 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/aij/seq/aij.c<br>
> [0]PETSC ERROR: #8 MatCopy() line 4110 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> <br>
> 2) MatCopy error saying:<br>
> <br>
> Argument out of range: New nonzero at (6,7)
caused a malloc<br>
> <br>
> [0]PETSC ERROR: --------------------- Error
Message<br>
>
--------------------------------------------------------------<br>
> [0]PETSC ERROR: Argument out of range<br>
> [0]PETSC ERROR: New nonzero at (6,7) caused a
malloc<br>
> Use MatSetOption(A,
MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
off<br>
> this check<br>
> [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for<br>
> trouble shooting.<br>
> [0]PETSC ERROR: Petsc Development GIT revision:
v3.11.1-277-g63b3610 GIT<br>
> Date: 2019-04-18 08:33:56 -0500<br>
> [0]PETSC ERROR:<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/BIB/bin/<a href="http://Test.BIBProblemeGD.dev" rel="noreferrer
noreferrer" target="_blank">Test.BIBProblemeGD.dev</a><br>
> on a named compile by Unknown Fri Apr 19
03:22:25 2019<br>
> [0]PETSC ERROR: Configure options
--prefix=/opt/petsc-master_debug<br>
> --with-mpi-compilers=1
--with-mpi-dir=/opt/openmpi-1.10.2<br>
> --with-cxx-dialect=C++11 --with-make-np=12
--with-shared-libraries=1<br>
> --with-debugging=yes --with-memalign=64
--with-visibility=0<br>
> --with-64-bit-indices=0 --download-ml=yes
--download-mumps=yes<br>
> --download-superlu=yes
--download-superlu_dist=yes --download-parmetis=yes<br>
> --download-ptscotch=yes --download-metis=yes
--download-suitesparse=yes<br>
> --download-hypre=yes<br>
>
--with-blaslapack-dir=/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64<br>
>
--with-mkl_pardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl<br>
>
--with-mkl_cpardiso-dir=/opt/intel/composer_xe_2015.2.164/mkl<br>
> --with-scalapack=1<br>
>
--with-scalapack-include=/opt/intel/composer_xe_2015.2.164/mkl/include<br>
>
--with-scalapack-lib="-L/opt/intel/composer_xe_2015.2.164/mkl/lib/intel64<br>
> -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"<br>
> [0]PETSC ERROR: #1 MatSetValues_SeqSBAIJ() line
990 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/sbaij/seq/sbaij.c<br>
> [0]PETSC ERROR: #2 MatSetValues() line 1404 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> [0]PETSC ERROR: #3
MatAXPY_BasicWithPreallocation() line 209 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #4 MatAXPY() line 96 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #5 MatAYPX() line 384 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/utils/axpy.c<br>
> [0]PETSC ERROR: #6 MatCopy_Basic() line 4056 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> [0]PETSC ERROR: #7 MatCopy_SeqAIJ() line 2844 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/impls/aij/seq/aij.c<br>
> [0]PETSC ERROR: #8 MatCopy() line 4110 in<br>
>
/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c<br>
> <br>
> Here are my installation logs as of april 18, at
02h00:<br>
> <br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_configure.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_configure.log</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make.log</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_default.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_default.log</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_RDict.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_RDict.log</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_CMakeLists.txt" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_CMakeLists.txt</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_test.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_test.log</a><br>
> <a href="http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_streams.log" rel="noreferrer noreferrer" target="_blank">http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2019.04.18.02h00m01s_make_streams.log</a><br>
> <br>
> Thanks,<br>
> <br>
> Eric<br>
> <br>
> <br>
> <br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail-m_7466304462959273877m_-9048173619379337331gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for granted
before they begin their experiments is
infinitely more interesting than any results
to which their experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="http://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature">Stefano</div>