[petsc-users] PETSc recommended visualization packages

[Blaise Bourdin]

Hi,

Let me add to Barry's frustration. I have spent most the last week trying to render animations of reasonably large computations (about 25M 3d unstructured elements divided in up to 25,000 exodusII files).

- Paraview is simple to get started with in the GUI. In theory, it is scriptable in python, but there is pretty much no documentation on the python API, which seems to be a mismatched combination of vtk calls, and several levels / revisions / versions of paraview interfaces. It is possible to generate a python trace of gui interactions, but for some reasons, some actions (image format and sizes, movies framnerates, for instance) are not recorded.
- visit's gui take a little more time to master, it is also scriptable in python. The python capture is more readable, and is somewhat documented (the doc is for 1.4.0, the current version 2.3.0). Movie generation is a pain and as far as I understand not feasible inside a python script. Instead, one has to save a session, and reopen it with the -movie CL interface. 
- Unless you are willing to rebuild visit or paraview from source (which is highly non-trivial and poorly documented), all these package install their own python, so that you don't have access to all other packages you may have on your system. I was not able to figure out how to import paraview or visit from my own python using the binary distributions
- EnSight is a good alternate choice if you can afford it. It is not open and not cheap but is quite good, reads most major format and has a pretty responsive support team. Their python scripting is well documented, but as far as I understand, it is not possible to import ensight from a python script. Instead, Ensight runs python scripts.

- About data formats: hdf5 / xdmf seems very well supported, but again, human-readable documentation on xdmf is lacking. It would be really nice if one could generate the proper xdmf description and geometry from a dm of a dmmesh. Would it be also possible to interface with moab and gain access to all the file formats they support?

Finally, I am skeptical about the benefit of implementing yet another file format that is incompatible with existing analysis, post processing, and mesh generation tools. 

Blaise


> Jed Brown wrote:
>> On Mon, Jul 4, 2011 at 21:44, Barry Smith <bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>> wrote:
>> 
>>    What are the recommended visualization packages for use with PETSc
>>    (for example making movies of contour plots and isosurfaces) and
>>    what are the recommended data formats to use to save Vecs for
>>    visualization?
>> 
>> 
>> VisIt
> Any links to VisIt? Goggle produced nothing.
> Thanks,
> Stephen
> 
>> and ParaView are the primary choices. In my experience, VisIt is a more complete system, but ParaView is easier to install and probably easier to get started with.
>> 
>> The VTK XML or binary formats are the easiest to get started with. See src/ts/examples/tutorials/ex14.c for an example of writing an XML file containing two fields on different grids (2D and 3D, structured, but deformed) in parallel. All file formats are horrible non-extensible crud, usually grown out of a particular application with structured grids of low-order/non-exotic basis functions on unstructured grids. They tend not to retain enough semantic information to reconstruct a state for further computations and also work for visualization without needing additional application-provided information.
> 
> 
> -- 
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-- 
Department of Mathematics and Center for Computation & Technology
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