[yt-users] Error in Executing yt Commands
Nathan Goldbaum
nathan12343 at gmail.com
Thu Jul 30 10:48:29 PDT 2015
To close this discussion, I've opened a pull request to add support for the
fabs ufunc to YTArray. I've also made the error message a bit nicer and
less mysterious.
https://bitbucket.org/yt_analysis/yt/pull-requests/1663/bugfix-add-support-for-the-fabs-ufunc-to/diff
On Thu, Jul 30, 2015 at 11:20 AM, Madison Fitzgerald <fitzg152 at msu.edu>
wrote:
> 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 <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 <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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