[petsc-dev] Something changed with SBAIJ on april 17?
Éric Chamberland
Eric.Chamberland at giref.ulaval.ca
Mon Apr 22 00:40:43 CDT 2019
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 <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
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