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

[Harshad Sahasrabudhe]

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?

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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