> > 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 <[email protected]> wrote: > > > On Jun 5, 2015, at 1:30 PM, Harshad Sahasrabudhe <[email protected]> > 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 <[email protected]> > wrote: > > On Fri, Jun 5, 2015 at 12:32 PM, Harshad Sahasrabudhe < > [email protected]> 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 > > > >
