[yt-users] h5py error in plot call

[Britton Smith]

What's strange to me is that it's an h5py error coming from a call to the
hdf5 light reader, which I didn't think used h5py.  Matt, do you have any
ideas?

Britton

On Sun, Feb 14, 2010 at 4:38 PM, Jordan Thomas Mirocha <
Jordan.Mirocha at colorado.edu> wrote:

> Hello,
> The other day I updated to h5py 1.2, and am now getting the following error
> message when I try to make projections or slices.
>
> yt         INFO       2010-02-14 16:25:07,976 Created plot collection with
> default plot-center = [0.5, 0.5, 0.5]
> yt         INFO       2010-02-14 16:25:07,976 Adding plot for axis 2
> yt         INFO       2010-02-14 16:25:07,981 Storing the binary hierarchy
> yt         INFO       2010-02-14 16:25:07,985 Gathering a field list (this
> may take a moment.)
> Warning: divide by zero encountered in divide
> Warning: invalid value encountered in sqrt
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in divide
> Warning: invalid value encountered in sqrt
> Traceback (most recent call last):
>  File "/Library/Frameworks/Python.framework/Versions/Current/bin/yt", line
> 8, in <module>
>   load_entry_point('yt==1.6dev', 'console_scripts', 'yt')()
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
> line 523, in run_main
>   sys.exit(YT.main())
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
> line 257, in main
>   return self.cmd(args)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
> line 280, in cmd
>   retval = self.onecmd(argv)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
> line 412, in onecmd
>   return self._dispatch_cmd(handler, argv)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/cmdln.py",
> line 1100, in _dispatch_cmd
>   return handler(argv[0], opts, *args)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
> line 205, in arg_iterate
>   func(self, subcmd, opts, arg)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/commands.py",
> line 334, in do_plot
>   else: pc.add_slice(opts.field, ax, center=center)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/raven/PlotCollection.py",
> line 182, in add_slice
>   return self.__add_slice(PlotTypes.SlicePlot, *args, **kwargs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/raven/PlotCollection.py",
> line 206, in __add_slice
>   data_source = self.pf.hierarchy.slice(axis, coord, field, center=center,
> **kwargs)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/BaseDataTypes.py",
> line 700, in __init__
>   self._refresh_data()
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/BaseDataTypes.py",
> line 237, in _refresh_data
>   self.get_data()
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/BaseDataTypes.py",
> line 589, in get_data
>   for grid in self._get_grids()]
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/BaseDataTypes.py",
> line 43, in save_state
>   tr = func(self, grid, field)
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/BaseDataTypes.py",
> line 805, in _get_data_from_grid
>   dv = self.hierarchy.io._read_data_slice(grid, field, self.axis,
> wantedIndex) * conv_factor
>  File
> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-1.6dev-py2.5-macosx-10.3-i386.egg/yt/lagos/DataReadingFuncs.py",
> line 239, in _read_data_slice
>   (grid.id, field), axis, coord).transpose()
> h5py._stub.ValueError: Invalid group number (Function arguments: Out of
> range)
>
> Any ideas?
> Thanks,
> Jordan
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