[yt-users] h5py error in plot call
Britton Smith
brittonsmith at gmail.com
Mon Feb 15 10:01:06 PST 2010
Hi all,
The problem is now fixed. I had mistakenly had Jordan move his hdf5 install
to another location without remaking yt with an hdf5.cfg that reflected this
move. After doing an rm -rf build dist in the yt directory, changing the
hdf5.cfg file, and recompiling, the problem is solved.
Britton
On Mon, Feb 15, 2010 at 9:57 AM, Jordan Thomas Mirocha <
Jordan.Mirocha at colorado.edu> wrote:
> 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
>>>>>>>> _______________________________________________
>>>>>>>> yt-users mailing list
>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>
>>>>>>>
>>>>>>>
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