[petsc-dev] Something changed with SBAIJ on april 17?
Stefano Zampini
stefano.zampini at gmail.com
Mon Apr 22 01:00:15 CDT 2019
Eric
I'll try to reproduce your setting.
Few questions.
Is your AIJ matrix lA symmetric?
Does it have any block size set?
Do you get the error the first time you do mat copy? Or in subsequent ones?
Il Lun 22 Apr 2019, 08:41 Éric Chamberland via petsc-dev <
petsc-dev at mcs.anl.gov> ha scritto:
> Hi,
>
> the patch fixed the 1st kind of error I got ("No support for this
> operation for this object type"), but I still have all the same faulty
> tests now returning the 2nd error I reported:
>
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: New nonzero at (0,1) 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 Release Version 3.11.1, unknown
> [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 Sun Apr 21 18:14:41 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 992 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 1407 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 171 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 52 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 348 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 4044 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 4098 in /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/src/mat/interface/matrix.c
>
>
> We are calling a MatCopy from an aij (lA) to sbaij (lB) matrix with
> DIFFERENT_NONZERO_PATTERN option.
>
> But on first call, the SBAIJ matrix has first been created then filled
> with MatConvert call:
>
> MatConvert(lA,MATSBAIJ, MAT_INITIAL_MATRIX, &lB);
>
> I just noticed we then do a:
> MatSetOption(lA, MAT_SYMMETRIC, PETSC_FALSE);
> (I have to find why???....)
>
> and on other calls, we call the "faulty" MatCopy with previously created
> matrices:
>
> MatCopy(lA,lB,DIFFERENT_NONZERO_PATTERN);
>
> which gives the "Argument out of range" error...
>
> Thanks,
>
> Eric
>
> Le 19-04-21 à 22:52, Éric Chamberland via petsc-dev a écrit :
>
> Hi Stefano,
>
> sure!
>
> configuration is running with your branch and tests will begin later. I
> will see and share the results tomorrow.
>
> thanks! :)
>
> Eric
>
>
> Le 19-04-21 à 17:21, Stefano Zampini a écrit :
>
> Eric
>
> I have opened a PRmay fix the issues you reported
> https://bitbucket.org/petsc/petsc/pull-requests/1571/fix-sbaij/diff
> Could you please try
> https://bitbucket.org/petsc/petsc/branch/stefano_zampini/fix-matcopy-sbaij?
> (off maint)
>
> Thanks
>
> Il giorno ven 19 apr 2019 alle ore 23:26 Éric Chamberland via petsc-dev <
> petsc-dev at mcs.anl.gov> ha scritto:
>
>> Hi,
>>
>> 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.
>>
>> I wanted to report the bug asap, so you may figure out the problem
>> quickly.
>>
>> Thanks,
>>
>> Eric
>>
>>
>> Le 19-04-19 à 19:10, Stefano Zampini via petsc-dev a écrit :
>>
>> 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/>
>>>
>>
>
> --
> Stefano
>
>
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