[petsc-users] accessing sequential data (e.g. image) at (i, j, k) in DM in parallel

[Matthew Knepley]

On Fri, Oct 4, 2013 at 6:11 AM, Bishesh Khanal <bisheshkh at gmail.com> wrote:

> Dear all,
>
> I have a part of a code that does NOT use Petsc, and contains an image K
> of dimensions mXnXr.
> It also provides me with a function to access any value at (i,j,k), e.g.
> using K.getVoxelAt(i,j,k).
>
>
> Now in my petsc code I create a DMDA of size mXnXr to solve a pde. The
> coefficients of the pde at each grid point should physically correspond to
> the one in the image K.
> The usual code I would use to create a matrix from DM is:
>
> DMDALocalInfo info;
> ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
>
> for (PetscInt k = info.zs; k<info.zs+info.zm; ++k) {
>         for (PetscInt j = info.ys; j < info.ys+info.ym; ++j) {
>             for (PetscInt i = info.xs; i < info.xs+info.xm; ++i) {
>
> //Here (i,j,k) refers to the indexing/ordering that is internally
> organized/distributed to different processors.
>
>             }
>         }
>  }
>
> Now, the problem is that I cannot use getVoxel(i,j,k) within the above
> loop because the ordering and distribution of the image K and the function
> getVoxel(i,j,k) knows nothing about the "da" I create in my part of the
> code. K might have been stored by each processor locally. So I believe if I
> want to use the coefficients from the image K in my code within the above
> loop, first I need to either:
> 1) create global vectors from the DMDA and copy all the values of image K
> to this global vector. Then access the values from this global vector.
> or
> 2) find a way to transform (i,j,k) within the above loop to a valid
> (i,j,k) for the function getVoxel(i,j,k)
>
> What should I do to resolve the problem ?
>

This explanation is confused. I do not think you mean "global vector", but
rather you mean the K would be completely held by every process. There
is only one question here:

   Is your image K distributed across processes?

If so, just match your DA to that distribution. If not, its replicated on
every process and getVoxel() will work fine.

   Matt


> Thanks,
> Bishesh
>
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20131004/0b6af0ab/attachment.html>