[yt-users] Error in Executing yt Commands
Madison Fitzgerald
fitzg152 at msu.edu
Thu Jul 30 09:20:37 PDT 2015
Omgiod thank you! I don’t know why it was returning an undefined error, which was the source of my confusion, but I’m glad it was such a simple fix!
Thank you so much!
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 11:51 AM, Kacper Kowalik <xarthisius.kk at gmail.com> wrote:
>
> On 07/30/2015 10:38 AM, Madison Fitzgerald wrote:
>> 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/
>> Error: http://paste.yt-project.org/show/5760/
>>
>> Any thoughts?
>
> Hi Madison,
> use np.abs or np.absolute instead of np.fabs for yt arrays.
> Since you also know that all values are negative, I think it'd be faster
> to just add '-' instead of abs.
> Cheers,
> Kacper
>
>> 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
>>> <mailto:nathan12343 at gmail.com <mailto: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>
>>> <mailto: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
>>>>>>
>>>>>> 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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