[yt-users] h5py error in plot call

Jordan Thomas Mirocha Jordan.Mirocha at Colorado.EDU
Mon Feb 15 08:57:14 PST 2010


Matt,
Here's the output.  Density is in there.

jmirocha@ EnzoTest $ h5ls -r /Users/jmirocha/Research/sims/runs/ 
EnzoTest/RD0038/RD0038.cpu0001
/Grid00000002            Group
/Grid00000002/Dark_Matter_Density Dataset {32, 64, 64}
/Grid00000002/Density    Dataset {32, 64, 64}
/Grid00000002/GasEnergy  Dataset {32, 64, 64}
/Grid00000002/Temperature Dataset {32, 64, 64}
/Grid00000002/TotalEnergy Dataset {32, 64, 64}
/Grid00000002/particle_index Dataset {40479}
/Grid00000002/particle_mass Dataset {40479}
/Grid00000002/particle_position_x Dataset {40479}
/Grid00000002/particle_position_y Dataset {40479}
/Grid00000002/particle_position_z Dataset {40479}
/Grid00000002/particle_velocity_x Dataset {40479}
/Grid00000002/particle_velocity_y Dataset {40479}
/Grid00000002/particle_velocity_z Dataset {40479}
/Grid00000002/x-velocity Dataset {32, 64, 64}
/Grid00000002/y-velocity Dataset {32, 64, 64}
/Grid00000002/z-velocity Dataset {32, 64, 64}

Thanks for the help,
Jordan

On Feb 15, 2010, at 9:51 AM, Matthew Turk wrote:

> 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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>>>>>>
>>>>>>
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