[petsc-dev] Fwd: [petsc-users] How to correctly call MatXAIJSetPreallocation for MATIS?
Barry Smith
bsmith at petsc.dev
Wed Nov 11 12:03:46 CST 2020
Maybe we should rename MatXAIJSetPreallocation(), it is now a super confusing name. And get rid of all the specialized versions from the API (deprecate).
MatSetPreallocation()?
I'm guessing it won't work for MatNest but will for pretty much all the rest?
Barry
> Begin forwarded message:
>
> From: Stefano Zampini <stefano.zampini at gmail.com>
> Subject: Re: [petsc-users] How to correctly call MatXAIJSetPreallocation for MATIS?
> Date: November 11, 2020 at 5:47:36 AM CST
> To: Barry Smith <bsmith at petsc.dev>
> Cc: Eric Chamberland <Eric.Chamberland at giref.ulaval.ca>, petsc-users <petsc-users at mcs.anl.gov>, Wing Hong Félix Kwok <felix.kwok at mat.ulaval.ca>
> Message-Id: <CAGPUisinaZRtUqCdRDKwmkV2Ee6iHvw5_6xHSFztpG_Nf1BmjQ at mail.gmail.com>
>
> Eric
>
> just use the same arrays you provide for the other matrix types. The purpose of having support for MATIS in MatXAIJSetPreallocation is exactly to not preallocate the local matrices, but treat the matrix as if it was in "assembled" (AIJ) form. The MATIS code does the local preallocation for you (a little bit overestimated), see here https://gitlab.com/petsc/petsc/-/blob/master/src/mat/impls/is/matis.c#L1686 <https://gitlab.com/petsc/petsc/-/blob/master/src/mat/impls/is/matis.c#L1686>
> You need to provide the local2global map object before calling the preallocation routine
>
> Let me know if something is still unclear
>
> Stefano
>
> Il giorno mer 11 nov 2020 alle ore 12:06 Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> ha scritto:
>
>
> > On Nov 10, 2020, at 11:10 PM, Eric Chamberland <Eric.Chamberland at giref.ulaval.ca <mailto:Eric.Chamberland at giref.ulaval.ca>> wrote:
> >
> > Hi,
> >
> > I am trying to add support for MATIS in our code to be able to use PCBDDC and others.
> >
> > So far, I have modify our matrix creation to add a call to MatSetLocalToGlobalMapping and also modified our non-zeros count to be able to give "local" non-zeros to MatXAIJSetPreallocation.
> >
> > When I run with, don't laugh, 1 process, everything is fine! So far so good. ;)
> >
> > When I run with 2 processes, fine also...
> >
> > When I run with 3 processes, I have process rank 1 and 2 giving errors:
> >
> > [1]PETSC ERROR: New nonzero at (7,5) caused a malloc
> >
> > and
> >
> > [2]PETSC ERROR: New nonzero at (10,2) caused a malloc
> >
> > I understand that these new nonzero indices are *local* indices. The global indices I am trying to do assembly on are:
> >
> > proc 1:
> >
> > global Line 3 (local 7)
> > global Columns: 3 7 10 15 *16* 17 (local 7 9 10 4 *5* 6) // *x* is faulty column, meaning only 4 nnz have been allocated!?
>
> Because the local column indices may not be set "in order" it doesn't mean for sure that it thinks there are only 4 column slots available, it could
> be it filled up column slots with local columns larger than 5 and hence used up all the available space.
>
> Unfortunately we don't have any code in place to display what is happening when the error occurs. So I suggest the following.
>
> Stop putting in values just before the first problematic value.
>
> At that point in your code call MatAssemblyBegin/End()
>
> Then call MatView()
>
> This will show you what columns have been filled up in each local matrix and can help you determine if either
>
> 1) some other column entries are getting in there that you didn't expect. or
>
> 2) somehow the preallocation is not properly being determined and is smaller than you expect.
>
> Good luck,
>
> Barry
>
>
> >
> > proc2 :
> >
> > (global Line 16 (local 10)
> > (global Columns: 3 8 16 17 *20* 22 23 24 (local 8 11 10 12 *2* 4 5 6) // *x* is faulty column, , meaning only 4 nnz have been allocated!?
> >
> > The error is returned at the moment we do the first assembly.
> >
> > After verifying my number of nnz, I just can't find why PETSc complains about a malloc, since as I can verify, I counted them well...
> >
> > Global matrix "size": 25 x 25 (given to MatSetSizes)
> >
> > Here are the non-zeros given to MatXAIJSetPreallocation followed by mapping used when creating ISLocalToGlobalMapping:
> >
> > =============
> >
> > Process 0:
> >
> > nnz_d[Local:0]=4
> > nnz_d[Local:1]=6
> > nnz_d[Local:2]=4
> > nnz_d[Local:3]=4
> > nnz_d[Local:4]=6
> > nnz_d[Local:5]=4
> > nnz_d[Local:6]=6
> > nnz_d[Local:7]=8
> > nnz_d[Local:8]=6
> > nnz_d[Local:9]=9
> > nnz_d[Local:10]=4
> >
> > Local,Global:
> >
> > 0,0
> > 1,1
> > 2,2
> > 3,3
> > 4,4
> > 5,5
> > 6,6
> > 7,7
> > 8,8
> > 9,9
> > 10,10
> >
> > =============
> >
> > Process 1:
> >
> >
> > nnz_d[Local:0]=4
> > nnz_d[Local:1]=6
> > nnz_d[Local:2]=6
> > nnz_d[Local:3]=4
> > nnz_d[Local:4]=9
> > nnz_d[Local:5]=4
> > nnz_d[Local:6]=6
> > nnz_d[Local:7]=6
> > nnz_d[Local:8]=4
> > nnz_d[Local:9]=4
> > nnz_d[Local:10]=8
> >
> > Local,Global:
> >
> > 0,11
> > 1,12
> > 2,13
> > 3,14
> > 4,15
> > 5,16
> > 6,17
> > 7,3
> > 8,5
> > 9,7
> > 10,10
> >
> > =============
> >
> > Process 2:
> >
> > nnz_d[Local:0]=4
> > nnz_d[Local:1]=4
> > nnz_d[Local:2]=6
> > nnz_d[Local:3]=6
> > nnz_d[Local:4]=6
> > nnz_d[Local:5]=6
> > nnz_d[Local:6]=9
> > nnz_d[Local:7]=4
> > nnz_d[Local:8]=4
> > nnz_d[Local:9]=4
> > nnz_d[Local:10]=8
> > nnz_d[Local:11]=6
> > nnz_d[Local:12]=6
> >
> > Local,Global:
> > 0,18
> > 1,19
> > 2,20
> > 3,21
> > 4,22
> > 5,23
> > 6,24
> > 7,2
> > 8,3
> > 9,14
> > 10,16
> > 11,8
> > 12,17
> >
> > =============
> >
> > I have ran with valgrind, everything is ok.
> >
> > So, why don't I have enough values reserved on local line 7 of rank 1? and 10 of rank 2?
> >
> > Thanks for your insights,
> >
> > Eric
> >
> > ps: Here is the backtrace:
> >
> > [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > [1]PETSC ERROR: Argument out of range
> > [1]PETSC ERROR: New nonzero at (7,5) caused a malloc
> > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check
> > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> > [1]PETSC ERROR: Petsc Release Version 3.11.2, May, 18, 2019
> > [1]PETSC ERROR: Test.MEF++.dev on a named rohan by ericc Tue Nov 10 23:39:47 2020
> > [1]PETSC ERROR: Configure options --prefix=/opt/petsc-3.11.2_debug_openmpi-4.0.1 --with-mpi-compilers=1 --with-mpi-dir=/opt/openmpi-4.0.1 --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"
> > [1]PETSC ERROR: #1 MatSetValues_SeqAIJ() line 481 in /home/mefpp_ericc/depots_prepush/cpetssc/ompi-opt/petsc-3.11.2-debug/src/mat/impls/aij/seq/aij.c
> > [1]PETSC ERROR: #2 MatSetValues() line 1407 in /home/mefpp_ericc/depots_prepush/cpetssc/ompi-opt/petsc-3.11.2-debug/src/mat/interface/matrix.c
> > [1]PETSC ERROR: #3 MatSetValuesBlocked() line 1919 in /home/mefpp_ericc/depots_prepush/cpetssc/ompi-opt/petsc-3.11.2-debug/src/mat/interface/matrix.c
> > [1]PETSC ERROR: #4 MatSetValuesBlocked_IS() line 2609 in /home/mefpp_ericc/depots_prepush/cpetssc/ompi-opt/petsc-3.11.2-debug/src/mat/impls/is/matis.c
> > [1]PETSC ERROR: #5 MatSetValuesBlocked() line 1898 in /home/mefpp_ericc/depots_prepush/cpetssc/ompi-opt/petsc-3.11.2-debug/src/mat/interface/matrix.c
> > _GIREF_ASSERTION(false)
> > voir fichier /home/mefpp_ericc/depots_prepush/GIREF/src/commun/Petsc/MatricePETSc.cc:858
> > ----> ERREUR FATALE: Erreur PETSc
> >
> >
> > --
> > Eric Chamberland, ing., M. Ing
> > Professionnel de recherche
> > GIREF/Université Laval
> > (418) 656-2131 poste 41 22 42
> >
>
>
>
> --
> Stefano
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