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

[Matthew Knepley]

On Fri, 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?
>

Yes, section 5.6 of the manual.

  Thanks,

     Matt


> 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
>>
>
>


-- 
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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