Re: [petsc-users] Problems about fd_coloring

[Smith, Barry F. via petsc-users]

> On Apr 26, 2019, at 7:24 AM, Yingjie Wu via petsc-users 
> <petsc-users@mcs.anl.gov> wrote:
> 
> Dear PETSc developers:            
> Hi,            
> I want to try some of the operations of matrix coloring. I have written a 
> model of a system of non-linear equations and solved it using - snes_fd, so 
> there is no Compute_Jacobian routine. Previous developers suggested that I 
> use:
>  -snes_fd_color -snes_fd_color_use_mat -mat_coloring_type greendy 
> to improve computational efficiency. I know little about coloring. It seems 
> to be a way to store the matrix structure, so that when the finite difference 
> routine is used, the difference can be calculated only at the position of 
> non-zero elements of Jacobian matrix, avoiding the difference calculation of 
> "0" elements. I don't know if I understand this correctly. 

   This is close enough understanding.
>           
> 
> My program is a two-dimensional problem, but it does not use the DM object to 
> allocate the solution vector X. Is there any problem with fd_coloring?   

  In order to use coloring you MUST provide the Jacobian matrix with its 
correct nonzero structure (you don't need to provide the numerical values). The 
fd coloring code then uses the nonzero structure and the SNES function you 
provide to compute the Jacobian efficiently. 

  Depending on your discretization it is either trivial or somewhat straight 
forward to provide the Jacobian nonzero structure. For example for finite 
differences on a 2d grid you can figure out which entires in the matrix are 
nonzero based on the finite difference stencil. For finite elements it is 
slightly more involved but essentially for each row of the matrix there are 
nonzero entries for all columns that that are connected by the finite element 
discretization (that is if you were to compute the Jacobian explicitly and get 
a nonzero value then you get one a nonzero location in the matrix). 

  Now in parallel one must be careful and insure you handle the nonzero 
structure correctly for vertices that are not on the same processor.

  Barry

>         
> 
> For users like me who don't know coloring, how should I get some usage 
> methods? It seems that the instructions on manual are somewhat brief.
> 
> In addition, because Matrix Free needs an efficient Preconditioner and 
> because some complex parameter variables make it impossible for me to 
> analytically construct Jacobian matrices, the finite difference approximation 
> of Jacobian matrices may be the most appropriate method at present.The reason 
> I want to know about fd_coloring is to improve computational efficiency.
> 
> I hope to get your advice.
> 
> Thanks,
> Yingjie