[yt-users] h5py problem

[Sam Skillman]

Hi John,

So I think the issue might be that the default mode of h5py.File is
read/write if it exists, and create if it doesn't.  In this case, I'm
guessing that it is trying to open it in read/write, then when it tries to
access it again it freaks out.  If you want to try changing line 73 of
yt/frontends/flash/data_structures.py
from:
        self._handle = h5py.File(self.hierarchy_filename)
to:
        self._handle = h5py.File(self.hierarchy_filename, 'r')

it.....might work.  No promises. Let us know if that works.  If not, then
seeing a pastebin of your script would be helpful.

Best,
Sam

On Tue, Jul 5, 2011 at 6:03 PM, Cameron Hummels <chummels at astro.columbia.edu
> wrote:

> Are you actively trying to create hdf5 files?  I know hdf5 won't
> overwrite an existing file by default, so perhaps if you've already
> created files in your loop, then try to run it again with those files
> still present, it will bail like this.
>
> If that isn't the case, I'm not sure.  If you could send your script, or
> pastebin it, that might provide more insight.
>
> Cameron
>
> On 07/05/2011 05:34 PM, John ZuHone wrote:
> > Hi all,
> >
> > I  have a loop that goes over a list of filenames I've generated, loads
> parameter files for them, passes each pf object to a procedure which grabs
> data from the file, and then loops back over. After the first iteration, I
> get this crash:
> >
> > Traceback (most recent call last):
> >   File
> "/local/data/duce2/zuhone/src/ctools/filter_particle_velocities.py", line
> 91, in <module>
> >     main()
> >   File
> "/local/data/duce2/zuhone/src/ctools/filter_particle_velocities.py", line
> 68, in main
> >     compute_turb_vels(pf, numVelCells, xp, yp, zp, vxp, vyp, vzp)
> >   File "/local/data/duce2/zuhone/src/ctools/compute_turb_vels.py", line
> 15, in compute_turb_vels
> >     leaf_grids = [g for g in pf.h.grids if len(g.Children) == 0]
> >   File
> "/local/data/duce2/zuhone/opt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
> line 163, in hierarchy
> >     self, data_style=self.data_style)
> >   File
> "/local/data/duce2/zuhone/opt/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py",
> line 73, in __init__
> >     self._handle = h5py.File(self.hierarchy_filename)
> >   File
> "/local/data/duce2/zuhone/opt/yt-x86_64/lib/python2.7/site-packages/h5py-1.3.1-py2.7-linux-x86_64.egg/h5py/highlevel.py",
> line 797, in __init__
> >     self.fid = self._generate_fid(name, mode, plist)
> >   File
> "/local/data/duce2/zuhone/opt/yt-x86_64/lib/python2.7/site-packages/h5py-1.3.1-py2.7-linux-x86_64.egg/h5py/highlevel.py",
> line 842, in _generate_fid
> >     fid = h5f.create(name, h5f.ACC_EXCL, fapl=plist)
> >   File "h5f.pyx", line 87, in h5py.h5f.create (h5py/h5f.c:1378)
> > h5py._stub.IOError: File exists (File accessability: Unable to open file)
> >
> > It does not matter where in the list of files I start, so it's not due to
> a single bad file. It's like it doesn't detect the file it's trying to read
> somehow, so it tries to create it, but then it finds out it already exists,
> and then aborts. Very odd.
> >
> > Best,
> >
> > John ZuHone
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
> --
> Cameron Hummels
> PhD Candidate, Astronomy Department of Columbia University
> Public Outreach Director, Astronomy Department of Columbia University
> NASA IYA New York State Student Ambassador
> http://outreach.astro.columbia.edu
> PGP: 0x06F886E3
>
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