[petsc-dev] Something changed with SBAIJ on april 17?
Stefano Zampini
stefano.zampini at gmail.com
Tue Apr 23 15:48:37 CDT 2019
Eric,
Is in maint and master now
> On Apr 23, 2019, at 9:22 AM, Smith, Barry F. via petsc-dev <petsc-dev at mcs.anl.gov> wrote:
>
>
> Great, thanks Stefano for fixing them all
>
>
>> On Apr 23, 2019, at 12:40 AM, Éric Chamberland via petsc-dev <petsc-dev at mcs.anl.gov> wrote:
>>
>> 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> 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> 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/
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Stefano
>>>>
>>>>
>>>> --
>>>> Stefano
>
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