[yt-users] data_source SlicePlot Error

Andrew James Emerick aje2123 at columbia.edu
Fri Mar 27 23:01:09 PDT 2015


Nathan,

You're definitely right! Everything seems to be working now.

Thanks for walking me through this.



Andrew E.

On Sat, Mar 28, 2015 at 1:56 AM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Fri, Mar 27, 2015 at 10:41 PM, Andrew James Emerick <
> aje2123 at columbia.edu> wrote:
>
>> 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/
>>
>
> This is actually due to a very recent change by Cameron Hummels, who
> totally revamped the plot callbacks recently. The annoate_line callback
> should take two coordinates and draw a straight line between them.  Take a
> look at the dev docs:
>
>
> http://yt-project.org/docs/dev/visualizing/callbacks.html#overplot-a-straight-line
>
> And the docstring for the callback:
>
>
> http://yt-project.org/docs/dev/reference/api/generated/yt.visualization.plot_modifications.LinePlotCallback.html#yt.visualization.plot_modifications.LinePlotCallback
>
>
>>
>>
>>
>> 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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>>>>>>>>
>>>>>>>>
>>>>>>>
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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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>>
>> --
>> Graduate Student
>> Columbia University
>> Department of Astronomy
>>
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-- 
Graduate Student
Columbia University
Department of Astronomy
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