[petsc-users] PETSc recommended visualization packages

[Ethan Coon]

Hmm, I've been tricked apparently.  What I thought was PETSc writing out
VTK was actually PFLOTRAN writing out VTK from PETSc data structures.  

On a day-to-day basis I tend to use HDF5, and I've checked that that
does, in fact, work with only PETSc, and only a few lines of PETSc.
Follow/run example:

http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/src/dm/da/examples/tutorials/ex9.c.html

Then load that in python with h5py and view with matplotlib:

In [1]: import h5py

In [2]: ex9 = h5py.File('hdf5output')

In [3]: ex9
Out[3]: <HDF5 file "hdf5output" (mode r+, 142.7k)>

In [4]: ex9.keys()
Out[4]: ['Vec_0x84000000_0']

In [5]: vec = ex9[ex9.keys()[0]]

In [6]: vec
Out[6]: <HDF5 dataset "Vec_0x84000000_0": shape (90, 100, 2), type
"<f8">

In [7]: vec.shape  # vec was created from a 2D DA, size (90,100), with 2 dofs
Out[7]: (90, 100, 2)

In [8]: from matplotlib import pyplot as plt

In [9]: plt.imshow(vec[:,:,0].transpose(), origin='lower')
Out[9]: <matplotlib.image.AxesImage object at 0x2310850>

In [10]: plt.colorbar()
Out[10]: <matplotlib.colorbar.Colorbar instance at 0x2313320>

In [11]: plt.show()


The downside of this option is that, in order for hdf5 files to work in
anything but python (which is smart enough to use introspection on the
file itself) you need a special viewer (the VisIt people call this a
"flavor" of HDF5), see

http://visitusers.org/index.php?title=VisIt_and_HDF5

These work on both VisIt and Paraview, but I've never tried to write one
myself, so I don't know how ugly they are.  They basically specify the
layout of the hdf5 file.  

Note that if you go with the HDF5 option, you'll likely want to move to
petsc-dev, which includes more HDF5 functionality, such as groups.

Ethan


On Thu, 2011-07-07 at 08:21 -0600, Andrew T Barker wrote:
> > Should PETSc ship some Python code to
> > read IS's, Vec's, Mat's in binary format? 
> 
> Yes.  Please.
> 
> I have played with matplotlib some to view Petsc output (vtk), with mixed results.  I wonder if Ethan would be willing to share an example or two?
> 
> Best,
> 
> Andrew

-- 
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289

http://www.ldeo.columbia.edu/~ecoon/
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