[petsc-users] Matrix is missing diagonal entry

[Barry Smith]

   You could also fork off of master and find all the places where the code depends on diagonal entries existing and modify the code in each of these places to handle the missing diagonal. Then run all the test suite and add some new tests that explicitly test this functionality and then make a pull request.

    Barry

> On Oct 18, 2016, at 11:24 AM, Kong, Fande <fande.kong at inl.gov> wrote:
> 
> Thanks, Hong and Jed.
> 
> I am going to explicitly add a few zeros into the matrix.
> 
> 
> Regards,
> 
> Fande, 
> 
> On Tue, Oct 18, 2016 at 9:46 AM, Hong <hzhang at mcs.anl.gov> wrote:
> You need set 0.0 to the diagonals.
> Diagonal storage is used in PETSc library.
> 
> Hong
> 
> 
> On Tue, Oct 18, 2016 at 10:11 AM, Kong, Fande <fande.kong at inl.gov> wrote:
> Hi Developers,
> 
> Any reason to force users provide a matrix which does not miss any diagonal entries when using a LU-type solver? 
> 
> Sometime, it is impossible to have all diagonal entries in a matrix, that is, the matrix has to miss some diagonal entries. For example, there is a saddle-point matrix from the discretization of incomprehensible equations, and the lower part of the matrix is a zero block. The matrix usually looks like:
> 
> | A   B^T  |
> | B    0     |
> 
> 
> 
> 
> 
> [56]PETSC ERROR: Object is in wrong state
> [56]PETSC ERROR: Matrix is missing diagonal entry 33
> [56]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [56]PETSC ERROR: Petsc Release Version 3.6.2, unknown 
> [56]PETSC ERROR: ./fluid on a arch-linux2-cxx-opt named ys0755 by fandek Mon Oct 17 17:06:08 2016
> [56]PETSC ERROR: Configure options --with-clanguage=cxx --with-shared-libraries=1 --download-fblaslapack=1 --with-mpi=1 --download-parmetis=1 --download-metis=1 --with-netcdf=1 --download-exodusii=1 --with-hdf5=1 --with-debugging=no --with-c2html=0 --with-64-bit-indices=1 --download-hypre=1 --download-superlu_dist=1
> [56]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1729 in /petsc_installed/petsc/src/mat/impls/aij/seq/aijfact.c
> [56]PETSC ERROR: #2 MatILUFactorSymbolic() line 6457 in /petsc_installed/petsc/src/mat/interface/matrix.c
> [56]PETSC ERROR: #3 PCSetUp_ILU() line 204 in /petsc_installed/petsc/src/ksp/pc/impls/factor/ilu/ilu.c
> [56]PETSC ERROR: #4 PCSetUp() line 983 in /petsc_installed/petsc/src/ksp/pc/interface/precon.c
> [56]PETSC ERROR: #5 KSPSetUp() line 332 in /petsc_installed/petsc/src/ksp/ksp/interface/itfunc.c
> [56]PETSC ERROR: #6 PCSetUpOnBlocks_ASM() line 405 in /petsc_installed/petsc/src/ksp/pc/impls/asm/asm.c
> [56]PETSC ERROR: #7 PCSetUpOnBlocks() line 1016 in /petsc_installed/petsc/src/ksp/pc/interface/precon.c
> [56]PETSC ERROR: #8 KSPSetUpOnBlocks() line 167 in /petsc_installed/petsc/src/ksp/ksp/interface/itfunc.c
> [56]PETSC ERROR: #9 KSPSolve() line 552 in /petsc_installed/petsc/src/ksp/ksp/interface/itfunc.c
> [56]PETSC ERROR: #10 PCApply_LSC() line 83 in /petsc_installed/petsc/src/ksp/pc/impls/lsc/lsc.c
> [56]PETSC ERROR: #11 PCApply() line 483 in /petsc_installed/petsc/src/ksp/pc/interface/precon.c
> [56]PETSC ERROR: #12 KSP_PCApply() line 242 in /petsc_installed/petsc/include/petsc/private/kspimpl.h
> [56]PETSC ERROR: #13 KSPSolve_PREONLY() line 26 in /petsc_installed/petsc/src/ksp/ksp/impls/preonly/preonly.c
> [56]PETSC ERROR: #14 KSPSolve() line 604 in /petsc_installed/petsc/src/ksp/ksp/interface/itfunc.c
> [56]PETSC ERROR: #15 PCApply_FieldSplit_Schur() line 904 in /petsc_installed/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c
> [56]PETSC ERROR: #16 PCApply() line 483 in /petsc_installed/petsc/src/ksp/pc/interface/precon.c
> [56]PETSC ERROR: #17 KSP_PCApply() line 242 in /petsc_installed/petsc/include/petsc/private/kspimpl.h
> [56]PETSC ERROR: #18 KSPInitialResidual() line 63 in /petsc_installed/petsc/src/ksp/ksp/interface/itres.c
> [56]PETSC ERROR: #19 KSPSolve_GMRES() line 235 in /petsc_installed/petsc/src/ksp/ksp/impls/gmres/gmres.c
> [56]PETSC ERROR: #20 KSPSolve() line 604 in /petsc_installed/petsc/src/ksp/ksp/interface/itfunc.c
> [56]PETSC ERROR: #21 SNESSolve_NEWTONLS() line 233 in /petsc_installed/petsc/src/snes/impls/ls/ls.c
> [56]PETSC ERROR: #22 SNESSolve() line 3906 in /petsc_installed/petsc/src/snes/interface/snes.c
> 
> 
> Thanks,
> 
> Fande Kong,
> 
>