[petsc-users] Writing solution data to file when using DMDA.

[Åsmund Ervik]

Hi Barry,

Thanks for the hints. I couldn't find any "DMDACreateNatural", but after some grepping of the manual, I ended up with this:

[... in init]
DMDACreateNaturalVector()
VecScatterCreateToZero()

[... inside a loop, e.g. over time steps]
DMDAGlobalToNaturalBegin/End()
VecScatterBegin/End()
VecGetArray()
[... write to file]
VecRestoreArray()

Is this what you meant, or have I misunderstood anything? 

It seems to work fine both in sequential and parallel, the resulting plots look OK, but it has uncovered some race condition that I need to fix now.

Regards,
Åsmund

________________________________________
Fra: Barry Smith [bsmith at mcs.anl.gov]
Sendt: 19. mars 2014 00:27
Til: Åsmund Ervik
Kopi: petsc-users at mcs.anl.gov
Emne: Re: [petsc-users] Writing solution data to file when using DMDA.

On Mar 18, 2014, at 5:19 PM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:

> Dear PETSc users,
>
> I'm trying to wrap my head around parallel I/O. If I understand correctly, a decent way of doing this is having one rank (say 0) writing to disk, and the other ranks communicating their part of the solution to rank 0. Please correct me if I'm wrong here.
>
> I'm using DMDA to manage my domain decomposition. As a first step, I've been trying to create an array on rank 0 holding the entire global solution and then writing this to file by re-using some routines from our serial codes (the format is Tecplot ASCII). (I realize that neither this approach nor an ASCII format are good solutions in the end, but I have to start somewhere.) However, I haven't been able to find any DMDA routines that give me an array holding the entire global solution on rank 0. Are there any, or is this too much of a "dirty trick"? (For just 1 process there is no problem, the output files generated look good.)

    DMDACreateNatural()
    DMDAGlobalToNaturalBegin/End()
    VecScatterCreateToZero
    VecGetArray()  on process 0

    the final array is in the natural ordering, x direction first, y direction second, z direction third.
>
> I'm also willing to try the VTK way of doing things, but I hit a problem when I tried that: even though I include "petscviewer.h" (also tried adding "petscviewerdef.h"), when I do
>    call PetscViewerSetType(viewer,PETSCVIEWERVTK,ierr)
> my compiler complains that PETSCVIEWERVTK is undefined (has no implicit type). This is from Fortran90 using preprocessing macros to #include the files. I tried PETSCVIEWERASCII as well, same problem. This is with 3.4.3. Any hints on this?

   Hmm, they are in petscviewerdef.h in 3.4.4 but anyways you can pass ‘vtk’   or  ‘ascii’  as the type
>
> Also, there are many different examples and mailing list threads about VTK output. What is the currently recommended way of doing things? I need to output at least (u,v,w) as vector components of one field, together with a scalar field (p). These currently have separate DM's, since I only use PETSc to solve for p (the pressure).
>
> Best regards,
> Åsmund