[petsc-dev] Something changed with SBAIJ on april 17?
Éric Chamberland
Eric.Chamberland at giref.ulaval.ca
Mon Apr 22 15:42:11 CDT 2019
Hi Stefano,
ok, it will be tested tonight.
Meanwhile, I ran on example to extract some information you asked for:
Le 19-04-22 à 18:42, Stefano Zampini a écrit :
> Eric,
>
> I have update (force pushed) the branch. It should be fixed now, Can
> you please confirm?
>
> Thanks
>
> Il giorno lun 22 apr 2019 alle ore 09:00 Stefano Zampini
> <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> ha scritto:
>
> Eric
>
> I'll try to reproduce your setting.
> Few questions.
>
> Is your AIJ matrix lA symmetric?
>
No, it is not.
>
> Does it have any block size set?
>
No, block size is 1.
>
> Do you get the error the first time you do mat copy? Or in
> subsequent ones?
>
At the first MatCopy... which is following the MatConvert...
Thanks,
Eric
>
>
> Il Lun 22 Apr 2019, 08:41 Éric Chamberland via petsc-dev
> <petsc-dev at mcs.anl.gov <mailto: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: Seehttp://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 <http://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
>>> <mailto: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 <mailto: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
>>>> <mailto: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
>>>> <http://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
>>>> <http://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
>
>
>
> --
> Stefano
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