[petsc-dev] Something changed with SBAIJ on april 17?
Éric Chamberland
Eric.Chamberland at giref.ulaval.ca
Tue Apr 23 00:40:37 CDT 2019
Hi Stefano,
I confirm that your commit 0a16297aeba2de71 fixed all bugs we got since
april 17!
Thanks a lot!!! :)
Eric
Le 19-04-22 à 22:42, Éric Chamberland via petsc-dev a écrit :
>
> 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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