[petsc-users] Cholesky: matrix ordering with aij? Bug with debugging=1 for ordering on sbaij?

Eric Chamberland Eric.Chamberland at giref.ulaval.ca
Thu Nov 27 12:52:36 CST 2014 

Hi,

Using petsc 3.5.2.

------------------------
Question #1:
------------------------

I configured a cholesky like this:

KSP Object:(o_slin) 1 MPI processes
   type: preonly
   maximum iterations=4000, initial guess is zero
   tolerances:  relative=1e-12, absolute=1e-20, divergence=1e+30
   left preconditioning
   using NONE norm type for convergence test
PC Object:(o_slin) 1 MPI processes
   type: cholesky
     Cholesky: out-of-place factorization
     tolerance for zero pivot 2.22045e-14
     matrix ordering: nd
     factor fill ratio given 5, needed 2.59172
       Factored matrix follows:
         Mat Object:         1 MPI processes
           type: seqsbaij
           rows=693, cols=693
           package used to perform factorization: petsc
           total: nonzeros=10328, allocated nonzeros=10328
           total number of mallocs used during MatSetValues calls =0
               block size is 1
   linear system matrix = precond matrix:
   Mat Object:  (o_slin)   1 MPI processes
     type: seqaij
     rows=693, cols=693
     total: nonzeros=7277, allocated nonzeros=7345
     total number of mallocs used during MatSetValues calls =0
       not using I-node routines

with a "mat_type aij" for the assembled matrix and 
"pc_factor_mat_ordering_type nd".  The PC creates an "sbaij".

When/where is the "matrix ordering: nd" used since it is documented to 
not works on sbaij matrix?

Compare the number of non-zeros for the factored matrix obtained with a 
"natural ordering":

KSP Object:(o_slin) 1 MPI processes
   type: preonly
   maximum iterations=4000, initial guess is zero
   tolerances:  relative=1e-12, absolute=1e-20, divergence=1e+30
   left preconditioning
   using NONE norm type for convergence test
PC Object:(o_slin) 1 MPI processes
   type: cholesky
     Cholesky: out-of-place factorization
     tolerance for zero pivot 2.22045e-14
     matrix ordering: natural
     factor fill ratio given 5, needed 44.1099
       Factored matrix follows:
         Mat Object:         1 MPI processes
           type: seqsbaij
           rows=693, cols=693
           package used to perform factorization: petsc
           total: nonzeros=175778, allocated nonzeros=175778
           total number of mallocs used during MatSetValues calls =0
               block size is 1
   linear system matrix = precond matrix:
   Mat Object:  (o_slin)   1 MPI processes
     type: seqaij
     rows=693, cols=693
     total: nonzeros=7277, allocated nonzeros=7345
     total number of mallocs used during MatSetValues calls =0
       not using I-node routines

there is really something happening with "nd"...

------------------------
Question #2:
------------------------
Using petsc 3.5.2 compiled with "--with-debugging=no", if a try to use 
"mat_type sbaij", I get this friendly error:

[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Matrix reordering is not supported for sbaij matrix. Use 
aij format
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
[0]PETSC ERROR: 
/home/mefpp_ericc/depots_prepush/GIREF/bin/probDiffusion.dev on a 
arch-linux2-c-opt named melkor by eric Thu Nov 27 13:35:01 2014
[0]PETSC ERROR: Configure options --with-mpi-compilers=1 
--with-make-np=12 --prefix=/opt/petsc-3.5.2_opt_openmpi-1.6.5_mkl_mt 
--with-mpi-dir=/opt/openmpi-1.6.5 --with-debugging=no --download-ml=yes 
--with-mkl_pardiso=1 --with-mkl_pardiso-dir=/opt/intel/composerxe/mkl 
--download-mumps=yes --download-superlu=yes --download-superlu_dist=yes 
--download-parmetis=yes --download-metis=yes --download-hypre=yes 
--with-shared-libraries=1 --with-scalapack=1 
--with-scalapack-include=/opt/intel/composerxe/mkl/include 
--with-scalapack-lib="-L/opt/intel/composerxe/mkl/lib/intel64 
-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" 
--with-blas-lapack-dir=/opt/intel/composerxe/mkl/lib/intel64
[0]PETSC ERROR: #1 MatCholeskyFactorSymbolic_SeqSBAIJ() line 245 in 
/home/mefpp_ericc/petsc-3.5.2/src/mat/impls/sbaij/seq/sbaijfact.c
[0]PETSC ERROR: #2 MatCholeskyFactorSymbolic() line 3012 in 
/home/mefpp_ericc/petsc-3.5.2/src/mat/interface/matrix.c
[0]PETSC ERROR: #3 PCSetUp_Cholesky() line 124 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/pc/impls/factor/cholesky/cholesky.c
[0]PETSC ERROR: #4 PCSetUp() line 902 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #5 KSPSetUp() line 305 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c

But if i use petsc compiled with "--with-debugging=yes", I got this one:

[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: Index set is not a permutation
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
[0]PETSC ERROR: probDiffusion.dev on a arch-linux2-c-debug named melkor 
by eric Thu Nov 27 13:45:04 2014
[0]PETSC ERROR: Configure options --with-mpi-compilers=1 
--with-make-np=12 --prefix=/opt/petsc-3.5.2_debug_openmpi-1.6.5_mkl_mt 
--with-mpi-dir=/opt/openmpi-1.6.5 --with-debugging=yes --download-ml=yes 
--with-mkl_pardiso=1 --with-mkl_pardiso-dir=/opt/intel/composerxe/mkl 
--download-mumps=yes --download-superlu=yes --download-superlu_dist=yes 
--download-parmetis=yes --download-metis=yes --download-hypre=yes 
--with-shared-libraries=1 --with-scalapack=1 
--with-scalapack-include=/opt/intel/composerxe/mkl/include 
--with-scalapack-lib="-L/opt/intel/composerxe/mkl/lib/intel64 
-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" 
--with-blas-lapack-dir=/opt/intel/composerxe/mkl/lib/intel64
[0]PETSC ERROR: #1 ISSetPermutation() line 183 in 
/home/mefpp_ericc/petsc-3.5.2/src/vec/is/is/interface/index.c
[0]PETSC ERROR: #2 MatGetOrdering() line 261 in 
/home/mefpp_ericc/petsc-3.5.2/src/mat/order/sorder.c
[0]PETSC ERROR: #3 PCSetUp_Cholesky() line 107 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/pc/impls/factor/cholesky/cholesky.c
[0]PETSC ERROR: #4 PCSetUp() line 902 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #5 KSPSetUp() line 305 in 
/home/mefpp_ericc/petsc-3.5.2/src/ksp/ksp/interface/itfunc.c

Is this the expected behavior?

Thanks,

Eric

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