[petsc-users] Generating xdmf from h5 file.

Matthew Knepley knepley at gmail.com
Wed Sep 24 17:19:51 CDT 2014

On Wed, Sep 24, 2014 at 5:08 PM, subramanya sadasiva <potaman at outlook.com>

> Hi,
> i was trying to use petsc_gen_xdmf.py to convert a h5 file to a xdmf file.
> The h5 file was generated by snes/ex12 which was run as,
> ex12 -dm_view hdf5:my.h5
> When I do,
> petsc_gen_xdmf.py my.h5
> I get the following error,
>  File "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py",
> line 220, in <module>
>     generateXdmf(sys.argv[1])
>   File
> "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 208, in generateXdmf
>     time        = np.array(h5['time']).flatten()
>   File "/usr/lib/python2.7/dist-packages/h5py/_hl/group.py", line 153, in
> __getitem__
>     oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
>   File "h5o.pyx", line 173, in h5py.h5o.open (h5py/h5o.c:3403)
> KeyError: "unable to open object (Symbol table: Can't open object)"
> I am not sure if the error is on my end. This is on Ubuntu 14.04 with the
> serial version of hdf5. I built petsc with --download-hdf5, is it necessary
> to use the same version of hdf5 to generate the xdmf file?

That code is alpha, and mainly built for me to experiment with an
application here, so it is not user-friendly. In your
HDF5 file, there is no 'time' since you are not running a TS. This access
to h5['time'] should just be protected, and
an empty array should be put in if its not there.


> Thanks
> Subramanya

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
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