[yt-users] h5py error in plot call

Matthew Turk matthewturk at gmail.com
Sun Feb 14 17:33:37 PST 2010


Hi all,

So one thing that is interesting is that, like Britton said, h5py is
throwing the error even though HDF5LightReader (the yt module) is
having the problems.  What h5py does, to my understanding, is
intercept all the HDF5 error calls, thus making it a bit more
difficult for us to get a proper error stack back from
HDF5LightReader.  What I'd recommend trying, in order to tie down the
error a bit more, is to use h5py to access the data and see what
errors it reports.  You can do this with:

from yt.mods import *
import h5py
pf = load(path_to_your_data)
g = pf.h.grids[0]
h5_file = h5py.File(g.filename)
rho = h5_file["/Grid%08i/Density" % g.id][:]
print rho.shape, rho.min(), rho.max()

and then if it has problems, that could lead us to the problem.

Thanks,

Matt

On Sun, Feb 14, 2010 at 3:44 PM, Britton Smith <brittonsmith at gmail.com> wrote:
> 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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