[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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