[yt-users] h5py error in plot call

Jordan Thomas Mirocha Jordan.Mirocha at Colorado.EDU
Sun Feb 14 15:38:42 PST 2010


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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