[yt-users] data_source SlicePlot Error

Andrew James Emerick aje2123 at columbia.edu
Fri Mar 27 22:41:09 PDT 2015 

I feel like I may have just tied myself into a package installation knot...

I decided to try and preempt future headaches by just installing via conda
($conda install yt). This ran fine, and I can now run "yt update" without
getting the error message. So now, for the commands you asked for:

which yt   ->         /home/emerick/anaconda/bin/yt
which python >     /home/emerick/anaconda/bin/python
import yt; yt.__file__ -> /home/emerick/code/yt/yt/__init__.pyc

Now, that is somewhat baffling. The final path is the path to the original
yt installation (installed from source, managed by mercurial) I was using.
The weird part is that that path is not located in any environment
variables that I could think of (e.g. $PATH, $PYTHONPATH, $LD_LIBRARY_PATH,
etc.).

I figured there was a chance it would work now, even given the above, but
when running the same code as before I get a new error (though I guess
maybe I shouldn't be surprised): http://paste.yt-project.org/show/5494/



Andrew E.


On Sat, Mar 28, 2015 at 12:40 AM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Fri, Mar 27, 2015 at 9:28 PM, Andrew James Emerick <
> aje2123 at columbia.edu> wrote:
>
>> 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...
>>
>
> I'm not sure what's going wrong here.  You shouldn't need to create a
> softlink and you shouldn't need to install an old version of the hdf5
> library. It sort of looks like you have the remnants of an old python
> installation conflicting with your current anaconda installation.
> Unfortunately it's really hard to debug this sort of thing remotely...
>
> Can you paste the output of:
>
> $ which yt
> $ which python
> $ python -c 'import yt; yt.__file__'
>
> I'm looking for yt being installed in a strange place outside of your
> normal python installation.
>
> You could try the yt conda package, installable via "consta install yt",
> which is newer than the old pre-yt 3.1 development version you had
> installed.
>
> You could also try installing yt from a fresh clone of the yt mercurial
> repository.  See the instructions here:
>
>
> http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-from-source
>
> Finally, you could build a fresh conda package based on the yt mercurial
> repostiory.  That will require a small modification to the conda recipe to
> point it at the mercurial repository instead of the release tarball on pypi.
>
> Hope you're able to sort this out.
>
> -Nathan
>
> PS Python packaging is literally the worst.
>
>
>> 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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>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>
>>>>>>
>>>>>
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>>>>>
>>>>
>>>>
>>>> --
>>>> Graduate Student
>>>> Columbia University
>>>> Department of Astronomy
>>>>
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>>
>> --
>> Graduate Student
>> Columbia University
>> Department of Astronomy
>>
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-- 
Graduate Student
Columbia University
Department of Astronomy
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