[yt-users] Error in Executing yt Commands

Madison Fitzgerald fitzg152 at msu.edu
Thu Jul 30 08:38:08 PDT 2015


Oh! Well, that certainly simplifies things! Thank you! And it does fix my matplotlib error!

However, I still am seeing an error when I try to run my script (which was what happened to lead me down this insane road with updating yt and breaking matplotlib at the beginning). I’m getting an “Operation not defined” error, but when I create a scratch script to narrow down which part of line 14 is actually the undefined operation, they all work individually.

Script: http://paste.yt-project.org/show/5761/ <http://paste.yt-project.org/show/5761/>
Error: http://paste.yt-project.org/show/5760/ <http://paste.yt-project.org/show/5760/>

Any thoughts?

Again, thank you, I really appreciate all of your help.

Best,
Madison



Madison Fitzgerald

Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Undergraduate Research Assistant
Department of Physics and Astronomy
Honors College
Michigan State University

> On Jul 30, 2015, at 11:18 AM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> 
> "yt update" won't work with the miniconda-based installation. Instead, when we do a new release you'll be able to get the updated yt package by doing "conda update yt".
> 
> You don't need to run an activate script if you're using miniconda's Python, just start Python, import yt, and load your data :)
> 
> Nathan
> 
> On Thursday, July 30, 2015, Madison Fitzgerald <fitzg152 at msu.edu <mailto:fitzg152 at msu.edu>> wrote:
> I figured out that miniconda was having an issue with another version of python, installed when I took a python-based programming class, and I was able to redirect my path to point to miniconda’s version instead, which solved that problem. However, I think my problem now is figuring out how to activate yt with miniconda. By that, I mean, I receive this output after installation and trying to take the first step:
> 
> "Hermione:~ madisonfitzgerald$ yt update
> 
> yt module located at:
>     /Users/madisonfitzgerald/miniconda/lib/python2.7/site-packages
> 
> YT site-packages not in path, so you must
> update this installation manually by committing and
> merging your modifications to the code before
> updating to the newest changeset.”
> 
> 
> And I’m not sure what they mean by this.
> 
> Thank you so much for you help and your patience.
> 
> Madison Fitzgerald
> 
> Astrophysics | Lyman Briggs College
> Women’s & Gender Studies | College of Arts & Letters
> LGBTQ and Sexuality Studies Specialization
> Women in Science, President
> Undergraduate Teaching Assistant
> Undergraduate Research Assistant
> Department of Physics and Astronomy
> Honors College
> Michigan State University
> 
>> On Jul 30, 2015, at 2:10 AM, Nathan Goldbaum <nathan12343 at gmail.com <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>> 
>> Can you explain a little bit more what's going wrong with the miniconda-based installation?
>> 
>> Unfortunately none of us have been able to reproduce the issue you're having with the install script and since it has something to do with matplotlib, I don't think any of us would know off-hand how to fix it in-place.
>> 
>> Debugging issues like this over a mailing list is always potentially a frustrating experience, I'm sorry we haven't been able to come up with a suitable solution so far.
>> 
>> On Wednesday, July 29, 2015, Madison Fitzgerald <fitzg152 at msu.edu <javascript:_e(%7B%7D,'cvml','fitzg152 at msu.edu');>> wrote:
>> Hi everyone,
>> 
>> Kacper: Sorry, my bad, but no, it didn’t work, unfortunately.
>> 
>> John and Nathan: Thank you, but I haven’t gotten anything to work, which is especially frustrating because I had a functioning yt just a few days ago. Installing yt with miniconda has only made yt less willing to function, not solve my matplotlib issue.
>> 
>> Truthfully, I’m really not sure where to go from here. Any thoughts?
>> 
>> Thank you,
>> Madison
>> 
>> 
>> Madison Fitzgerald
>> 
>> Astrophysics | Lyman Briggs College
>> Women’s & Gender Studies | College of Arts & Letters
>> LGBTQ and Sexuality Studies Specialization
>> Women in Science, President
>> Undergraduate Teaching Assistant
>> Undergraduate Research Assistant
>> Department of Physics and Astronomy
>> Honors College
>> Michigan State University
>> 
>>> On Jul 29, 2015, at 11:01 PM, John ZuHone <jzuhone at gmail.com <>> wrote:
>>> 
>>> A bit late, but I can confirm that I was able to install from the install script on Mac OS 10.10 without any issue.
>>> 
>>>> On Jul 29, 2015, at 7:06 PM, Kacper Kowalik <xarthisius.kk at gmail.com <>> wrote:
>>>> 
>>>> Hi again,
>>>> did setting backend to 'agg' also fail?
>>>> Cheers,
>>>> Kacper
>>>> 
>>>> On Jul 29, 2015 5:32 PM, "Nathan Goldbaum" <nathan12343 at gmail.com <>> wrote:
>>>> 
>>>> 
>>>> On Wed, Jul 29, 2015 at 5:30 PM, Madison Fitzgerald <fitzg152 at msu.edu <>> wrote:
>>>> Hi Nathan,
>>>> 
>>>> I’m still getting the same error when I uninstall and then reinstall matplotlib. How would I be able to use miniconda as a workaround?
>>>> 
>>>> Following these instructions:
>>>> 
>>>> http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda <http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda>
>>>> 
>>>> By the way, did you completely erase the old yt installation before rerunning the install script? Not doing so might be the cause of your issue.
>>>>  
>>>> 
>>>> Thank you,
>>>> Madison
>>>> 
>>>> 
>>>> Madison Fitzgerald
>>>> 
>>>> Astrophysics | Lyman Briggs College
>>>> Women’s & Gender Studies | College of Arts & Letters
>>>> LGBTQ and Sexuality Studies Specialization
>>>> Women in Science, President
>>>> Undergraduate Teaching Assistant
>>>> Undergraduate Research Assistant
>>>> Department of Physics and Astronomy
>>>> Honors College
>>>> Michigan State University
>>>> 
>>>>> On Jul 29, 2015, at 5:30 PM, Nathan Goldbaum <nathan12343 at gmail.com <>> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>> On Wed, Jul 29, 2015 at 4:19 PM, Madison Fitzgerald <fitzg152 at msu.edu <>> wrote:
>>>>> Hi everyone,
>>>>> 
>>>>> I’ve run into an error whenever I try to execute any yt command (see yt_run_error.txt, attached because I can’t use “yt pastebin”). I’ve tried following the steps on the help page, including re-installing yt, and I still get this same error. I just installed the latest stable yt version (I can’t execute the command to give you specific numbers) on Mac OS X 10.10.4.
>>>>> 
>>>>> Does anyone know where I should start to fix this?
>>>>> 
>>>>> This is happening inside of matplotlib. 
>>>>> 
>>>>> Can you try reinstalling the matplotlib that's in the yt environment? You should be able to do that with:
>>>>> 
>>>>> $ pip uninstall matplotlib
>>>>> $ pip install matplotlib
>>>>> 
>>>>> And see if that works?
>>>>> 
>>>>> Failing that, a workaround would be to use a miniconda-based install.  
>>>>> 
>>>>> I'm currently running the install script on my mac laptop to see if I can reproduce your issue.
>>>>> 
>>>>> -Nathan
>>>>>  
>>>>> 
>>>>> Thank you,
>>>>> Madison
>>>>> 
>>>>> 
>>>>> Madison Fitzgerald
>>>>> 
>>>>> Astrophysics | Lyman Briggs College
>>>>> Women’s & Gender Studies | College of Arts & Letters
>>>>> LGBTQ and Sexuality Studies Specialization
>>>>> Women in Science, President
>>>>> Undergraduate Teaching Assistant
>>>>> Undergraduate Research Assistant
>>>>> Department of Physics and Astronomy
>>>>> Honors College
>>>>> Michigan State University
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
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