[yt-users] Error in Executing yt Commands
Kacper Kowalik
xarthisius.kk at gmail.com
Thu Jul 30 08:51:40 PDT 2015
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>> 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
>>>>>
>>>>> 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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