[petsc-users] Generating xdmf from h5 file.

[subramanya sadasiva]

Hi Matt, 
That did not help. Is there any other way to output the 
mesh to something that paraview can view?  I tried outputting the file 
to a vtk file using 
ex12 -dm_view vtk:my.vtk:ascii_vtk 

which, I saw in another post on the forums, but that did not give me any output. 

(Sorry for sending this twice. but I noticed my reply did not go into the users forum)

Subramanya


Date: Wed, 24 Sep 2014 17:19:51 -0500
Subject: Re: [petsc-users] Generating xdmf from h5 file.
From: knepley at gmail.com
To: potaman at outlook.com
CC: petsc-users at mcs.anl.gov

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



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 yourHDF5 file, there is no 'time' since you are not running a TS. This access to h5['time'] should just be protected, andan empty array should be put in if its not there.
  Matt 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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