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<body class='hmmessage'><div dir='ltr'>Hi Matt, <br>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 <br>ex12 -dm_view vtk:my.vtk:ascii_vtk <br><br>which, I saw in another post on the forums, but that did not give me any output. <br><br>(Sorry for sending this twice. but I noticed my reply did not go into the users forum)<br><br>Subramanya<br><br><br><div><hr id="stopSpelling">Date: Wed, 24 Sep 2014 17:19:51 -0500<br>Subject: Re: [petsc-users] Generating xdmf from h5 file.<br>From: knepley@gmail.com<br>To: potaman@outlook.com<br>CC: petsc-users@mcs.anl.gov<br><br><div dir="ltr"><div class="ecxgmail_extra"><div class="ecxgmail_quote">On Wed, Sep 24, 2014 at 5:08 PM, subramanya sadasiva <span dir="ltr"><<a href="mailto:potaman@outlook.com" target="_blank">potaman@outlook.com</a>></span> wrote:<br><blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Hi, <br>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, <br><br>ex12 -dm_view hdf5:my.h5 <br><br>When I do, <br>petsc_gen_xdmf.py my.h5 <br><br>I get the following error, <br><br> File "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line 220, in <module><br> generateXdmf(sys.argv[1])<br> File "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line 208, in generateXdmf<br> time = np.array(h5['time']).flatten()<br> File "/usr/lib/python2.7/dist-packages/h5py/_hl/group.py", line 153, in __getitem__<br> oid = h5o.open(<a href="http://self.id" target="_blank">self.id</a>, self._e(name), lapl=self._lapl)<br> File "h5o.pyx", line 173, in h5py.h5o.open (h5py/h5o.c:3403)<br>KeyError: "unable to open object (Symbol table: Can't open object)"<br><br>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? <br></div></div></blockquote><div><br></div><div>That code is alpha, and mainly built for me to experiment with an application here, so it is not user-friendly. In your</div><div>HDF5 file, there is no 'time' since you are not running a TS. This access to h5['time'] should just be protected, and</div><div>an empty array should be put in if its not there.</div><div><br></div><div> Matt</div><div> </div><blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;"><div><div dir="ltr">Thanks<span class="ecxHOEnZb"><font color="#888888"><br>Subramanya <br> </font></span></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener
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