[yt-users] h5py error in plot call

Matthew Turk matthewturk at gmail.com
Mon Feb 15 08:51:44 PST 2010


Hi Jordan,

So can you try running this?

h5ls -r /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001

and seeing if /Grid00000002/Density is listed?  If so, could you copy
here the entire entry for /Grid00000002 ?

Best,

Matt

On Mon, Feb 15, 2010 at 8:49 AM, Jordan Thomas Mirocha
<Jordan.Mirocha at colorado.edu> wrote:
> Hi Matt,
> I was also just trying to make a density plot.  I ran your script, and
> here's what I get:
>
> Testing existence of datasets.
> yt         INFO       2010-02-15 09:44:54,574 Storing the binary hierarchy
> yt         INFO       2010-02-15 09:44:54,578 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
> Testing slices through the center of the domain.
> Slicing through EnzoGrid_0002, getting 2:0 from a [64 64 32]-shaped grid
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "mturk.py", line 34, in <module>
>    dv = pf.hierarchy.io._read_data_slice(g, field, axis, ind)
>  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()
> HDF5LightReader.ReadingError: ReadHDF5DataSetSlice: Unable to open
> /Users/jmirocha/Research/sims/runs/EnzoTest/RD0038/RD0038.cpu0001
>
> -Jordan
>
> On Feb 15, 2010, at 9:16 AM, Matthew Turk wrote:
>
>> Hi Jordan,
>>
>> I have a couple followup questions; which field are you taking a slice
>> of?  Is it a field that is defined everywhere in the simulation, or
>> only in a few grids?
>>
>> I've created a diagnostic script for you; if you could, could you run
>> this and tell me what it outputs?  You'll need to modify the location
>> of the data, on line 3.  If it runs successfully, without any
>> exceptions, then on line 20 you'll notice that I define the field to
>> slice as "Density."  Could you change that to the field you are
>> slicing through, and let me know if it runs to completion then?
>>
>> You can get the script by either downloading it from
>> http://paste.enzotools.org/show/321 or executing this command:
>>
>> yt_lodgeit.py --download=321
>>
>> Thanks!
>>
>> -Matt
>>
>> On Sun, Feb 14, 2010 at 6:25 PM, Jordan Thomas Mirocha
>> <Jordan.Mirocha at colorado.edu> wrote:
>>>
>>> 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
>>>>>> _______________________________________________
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>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
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