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

[Matthew Knepley]

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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