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

[Barry Smith]

> On Jun 5, 2015, at 3:02 PM, Paul T. Bauman <ptbauman at gmail.com> wrote:
> 
> 
> 
> On Fri, Jun 5, 2015 at 3:37 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> 
> > 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? 
> 
> Thanks Barry, this is a good suggestion. To be honest, however, since MOOSE does its own finite differencing (I think...) and other libMesh-based infrastructure does as well,

   We should fix that :-) Have one common abstraction/API for "differencing" for Jacobians with multiple implementations instead of multiple APIs and multiple implementations :-)

  Barry


> this may not be a developer priority immediately. (Might be something good to hack on in a couple weeks at PETSc 20.) That said...
>  
> 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"
> 
> Looks easy enough. Looking at the SNESSetJacobian documentation, the ctx (in your example, 0) would need to be a pointer a MatFDColoring?
> 
> Best,
> 
> Paul