[yt-users] data_source SlicePlot Error

[Andrew James Emerick]

Nathan,

I can do "import h5py" without issue in a python script, and checked the
"from h5py import _errors" statement that seems to cause the breakage.
Updating via conda didn't fix the issue. I have hdf5 and h5py installed via
conda.

Doing some more checking it looks like (for whatever reason) when running
"yt update" it is looking for a version of the hdf5 library that I don't
have anywhere. When I did the soft linking of the libhdf5.so that I do have
to the libhdf5.so.6 that it is looking for, it yelled at me saying it is
trying to use the HDF5 version 1.8.4 headers, but can't find the
corresponding libraries. (the most up to date version I have installed is
1.8.14).

I guess a workaround would be to get the HDF5 1.8.4 library somewhere, but
I'm still bothered by this...

Thanks again.



Andrew E.


On Fri, Mar 27, 2015 at 5:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Fri, Mar 27, 2015 at 2:15 PM, Andrew James Emerick <
> aje2123 at columbia.edu> wrote:
>
>> Nathan,
>>
>> Thanks for the response. I have been delinquent in updating yt.
>>
>> Running "yt update", however gives me this error:
>> http://paste.yt-project.org/show/5492/
>>
>> Looks like an issue with finding the libhdf5.so.6 library that I
>> couldn't figure out on my own. I had installed yt from source as to not
>> disturb the python, numpy, hdf5, etc. installations I already had (managed
>> by anaconda). I have libhdf5.so.9 in my LD_LIBRARY_PATH (I already tried
>> soft linking .so.9 as .so.6 .. understandably it threw an error).
>>
>>
> The error is happening when python tries to import h5py.  Can you import
> h5py in a script that doesn't use yt?  How did you install h5py?
>
> $ conda update -f h5py
>
> might fix this.
>
>
>> Have you run across this before?
>>
>>
>>
>> Andrew E.
>>
>> On Fri, Mar 27, 2015 at 1:04 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Fri, Mar 27, 2015 at 10:00 AM, Andrew James Emerick <
>>> aje2123 at columbia.edu> wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> I just ran into an error in using "data_source" kwarg with the
>>>> SlicePlot function (error message copied below):
>>>>
>>>> slice = yt.SlicePlot(ds, axis, field, data_source=region)
>>>> File
>>>> "/home/emerick/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py",
>>>> line 1816, in SlicePlot
>>>>     return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
>>>> TypeError: __init__() got an unexpected keyword argument 'data_source'
>>>>
>>>> I have no problem doing the above with ProjectionPlot. If anyone knows
>>>> what could be causing this I'd appreciate the help. Otherwise I can do some
>>>> digging into the code myself.
>>>>
>>>>
>>> Hi Andrew,
>>>
>>> This should work, but might not if you haven't updated yt in a while.
>>> Can you update to the latest development version and try again?
>>>
>>> -Nathan
>>>
>>>
>>>>
>>>>
>>>> Thanks,
>>>> Andrew E.
>>>> --
>>>> Graduate Student
>>>> Columbia University
>>>> Department of Astronomy
>>>>
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>>>>
>>>
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>>
>>
>> --
>> Graduate Student
>> Columbia University
>> Department of Astronomy
>>
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>>
>
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-- 
Graduate Student
Columbia University
Department of Astronomy
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