[yt-users] h5py error in plot call

Jordan Thomas Mirocha Jordan.Mirocha at Colorado.EDU
Mon Feb 15 08:49:14 PST 2010 

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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>>>>
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