[petsc-dev] Something changed with SBAIJ on april 17?
Eric Chamberland
Eric.Chamberland at giref.ulaval.ca
Wed Apr 24 05:20:01 CDT 2019
Perfect!
I confirm the master branch is working again for me!
Thanks a lot! :)
Eric
On 2019-04-23 10:48 p.m., Stefano Zampini wrote:
> 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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