[petsc-dev] Something changed with SBAIJ on april 17?

Smith, Barry F. bsmith at mcs.anl.gov
Tue Apr 23 01:22:52 CDT 2019 

  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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