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

[Barry Smith]

> On Jun 5, 2015, at 1:49 PM, Paul T. Bauman <ptbauman at gmail.com> wrote:
> 
> 
> 
> On Fri, Jun 5, 2015 at 2:42 PM, Harshad Sahasrabudhe <hsahasra at purdue.edu> wrote:
>   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. 
> 
> FYI, this information is contained in the libMesh::CouplingMatrix which you can get from the libMesh::DofMap.

   Thanks.  Maybe using this information could be "automated" within PETSc/libMesh so that one could "trivially" use the finite differencing to compute the Jacobian with coloring within PETSc/libMesh when the Jacobian cannot be provided directly by the user?  For example within PETSc if one provides the option -snes_fd_color then SNES does

  ierr = PetscOptionsBool("-snes_fd_color","Use finite differences with coloring to compute Jacobian","SNESComputeJacobianDefaultColor",flg,&flg,NULL);CHKERRQ(ierr);
  if (flg) {
    DM             dm;
    DMSNES         sdm;
    ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
    ierr = DMGetDMSNES(dm,&sdm);CHKERRQ(ierr);
    sdm->jacobianctx = NULL;
    ierr = SNESSetJacobian(snes,snes->jacobian,snes->jacobian_pre,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
    ierr = PetscInfo(snes,"Setting default finite difference coloring Jacobian matrix\n");CHKERRQ(ierr);
  }

with PETSc/libMesh it would have to stick the correct matrix nonzero structure (from? "libMesh::CouplingMatrix") into the ,snes->jacobian_pre  "Jacobian" "matrix" 

  Barry