[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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