[yt-users] h5py error in plot call

[David Collins]

Whenever I see odd hdf5 errors, checking the validity of the call I'm
making (filename, field name, data) usually sorts it out-- Can you use
h5py to directly check that your filename/fieldname/datavalues in the
file are reasonable?

d.

>> 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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>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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