[petsc-users] Crash when trying to use FD Jacobian

[Harshad Sahasrabudhe]

>
>   It is not the coloring you need to generate, just the nonzero structure.
> (From that PETSc computes the coloring) so do as I suggest in my other
> email.


Thanks, I'll try that out.

On Fri, Jun 5, 2015 at 2:36 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> > On Jun 5, 2015, at 1:30 PM, Harshad Sahasrabudhe <hsahasra at purdue.edu>
> wrote:
> >
> > Hi Matt,
> >
> > Thanks for helping me out with this.
> >
> > Ah, this is going to be somewhat harder. Unless PETSc know the
> connectivity of your Jacobian, which means the influence between
> > unknowns, it can only do one vector at a time
> >
> > Yes, I'm discretizing the  equation on a FEM mesh, so I know the
> connectivity between different DOFs.
> >
> > Do you have a simplified Jacobian matrix you could use for
> preconditioner construction?
> >
> >  I have an approximate diagonal Jacobian matrix, which doesn't give good
> results.
> >
> > It is trying to use get coloring for the Jacobian
> >
> > Is there some documentation on coloring which I can read up so that I
> can generate the coloring for the Jacobian myself?
>
>   It is not the coloring you need to generate, just the nonzero structure.
> (From that PETSc computes the coloring) so do as I suggest in my other
> email.
>
>    Barry
>
>
> >
> > Thanks,
> > Harshad
> >
> > On Fri, Jun 5, 2015 at 1:59 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Fri, Jun 5, 2015 at 12:32 PM, Harshad Sahasrabudhe <
> hsahasra at purdue.edu> wrote:
> > Hi,
> >
> > I'm solving a non-linear equation using NEWTONLS. The SNES is called
> from a wrapper in the LibMesh library. I'm trying to use the default FD
> Jacobian by not setting any Mat or callback function for the Jacobian.
> >
> > When doing this I get the following error. I'm not able to figure out
> why I get this error. Can I get some pointers to what I might be doing
> wrong?
> >
> > Ah, this is going to be somewhat harder. Unless PETSc know the
> connectivity of your Jacobian, which means the influence between
> > unknowns, it can only do one vector at a time:
> >
> >   -snes_fd
> >
> > which is really slow. It is trying to use get coloring for the Jacobian
> so that it can do many vectors
> > at once. Do you have a simplified Jacobian matrix you could use for
> preconditioner construction?
> > Then it could use that.
> >
> >   Thanks,
> >
> >      Matt
> >
> > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > [0]PETSC ERROR: Object is in wrong state!
> > [0]PETSC ERROR: Not for unassembled matrix!
> > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > [0]PETSC ERROR: ./nemo on a linux named conte-fe02.rcac.purdue.edu by
> hsahasra Fri Jun  5 13:25:27 2015
> > [0]PETSC ERROR: Libraries linked from
> /home/hsahasra/NEMO5/libs/petsc/build-real/linux/lib
> > [0]PETSC ERROR: Configure run at Fri Mar 20 15:18:25 2015
> > [0]PETSC ERROR: Configure options --with-x=0 --download-hdf5=1
> --with-scalar-type=real --with-single-library=0 --with-shared-libraries=0
> --with-clanguage=C++ --with-fortran=1 --with-cc=mpiicc --with-fc=mpiifort
> --with-cxx=mpiicpc COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> --download-metis=1 --download-parmetis=1
> --with-valgrind-dir=/apps/rhel6/valgrind/3.8.1/ --download-mumps=1
> --with-fortran-kernels=0
> --with-blas-lapack-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl
> --download-superlu_dist=1
> --with-blas-lapack-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl
> --with-blacs-lib=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so
> --with-blacs-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include
> --with-scalapack-lib="-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64
> -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" i
> --with-scalapack-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include
> --with-pic=1 --with-debugging=1
> > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > [0]PETSC ERROR: MatGetColoring() line 481 in
> /home/hsahasra/NEMO5/libs/petsc/build-real/src/mat/color/color.c
> > [0]PETSC ERROR: SNESComputeJacobianDefaultColor() line 64 in
> /home/hsahasra/NEMO5/libs/petsc/build-real/src/snes/interface/snesj2.c
> > [0]PETSC ERROR: SNESComputeJacobian() line 2152 in
> /home/hsahasra/NEMO5/libs/petsc/build-real/src/snes/interface/snes.c
> > [0]PETSC ERROR: SNESSolve_NEWTONLS() line 218 in
> /home/hsahasra/NEMO5/libs/petsc/build-real/src/snes/impls/ls/ls.c
> > [0]PETSC ERROR: SNESSolve() line 3636 in
> /home/hsahasra/NEMO5/libs/petsc/build-real/src/snes/interface/snes.c
> > [0]PETSC ERROR: solve() line 538 in
> "unknowndirectory/"src/solvers/petsc_nonlinear_solver.C
> > application called MPI_Abort(comm=0x84000000, 73) - process 0
> >
> > Thanks,
> > Harshad
> >
> >
> >
> > --
> > 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
> >
>
>
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