[yt-users] h5py error in plot call
Jordan Thomas Mirocha
Jordan.Mirocha at Colorado.EDU
Sun Feb 14 18:25:28 PST 2010
Hi again,
I tried Matt's snippet of code and hit an error here:
g = pf.h.grids[0]
yt INFO 2010-02-14 19:20:47,399 Getting the binary
hierarchy
yt INFO 2010-02-14 19:20:47,403 Finished with binary
hierarchy reading
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
The remaining steps still worked, ending with
print rho.shape, rho.min(), rho.max()
(32, 64, 64) 0.001 196.019
Thanks for the help,
Jordan
On Feb 14, 2010, at 6:33 PM, Matthew Turk wrote:
> 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
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
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