[yt-users] scipy broke yt? maybe python?

[Nathan Goldbaum]

On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> Hi Nathan,
>
> I am not sure how to get a core dump or how to make gdb give me useful
> things.  But maybe this will help...
>
> By running my code via a command line, I find that
> import h5py
> import scipy
> import yt
> from yt.analysis_modules.cosmological_observation.api import LightRay
>
> all are fine.  But,
>
> from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum
> from yt.analysis.modules.absorption_spectrum.api import generate_total_fit
>

And both of these succeed when scipy isn't installed?

What happens if you do:

import scipy.optimize

Also you're using the conda-based python that the latest version of the
install script builds, right? Maybe you should try the conda binary builds
instead:

$ pip uninstall scipy
$ conda install scipy


>
> both give me a Segmentation fault and kick me out of python
>
> I can keep trying to figure out how to have gdb give me something useful,
> but does this give any clues in the meantime?
>
> Thanks,
> Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Stephanie,
>>
>> It's very hard to say what's going wrong without more information.
>>
>> Can you get a core dump or run python under gdb to get a stack trace at
>> the place where the segmentation fault happens?
>>
>> Can you run this on your laptop? If so, do you get a segmentation fault
>> there?
>>
>> -Nathan
>>
>> On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <stonnes at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I have the yt-conda installation of yt.  I am trying to create an
>>> absorption spectrum, so need the command "generate_total_fit".
>>>
>>> yt told me I needed scipy for this to work.  yt does not have scipy.  So
>>> I typed:
>>> >pip install scipy
>>>
>>> scipy was installed.
>>>
>>> However, then my submission script no longer worked at all and I was
>>> given the error:
>>>
>>> /var/spool/torque/mom_priv/jobs/50052.mies.stanford.edu.SC: line 26:
>>> 3750 Segmentation fault      python HI_absorbers.py
>>>
>>> When I pip uninstall scipy, my code runs again!
>>> The only commands in my script are
>>> source /home/stonnes/yt-conda/bin/activate
>>> python HI_absorbers.py
>>>
>>> Can anyone help me out with this?
>>>
>>> Thanks!
>>> Stephanie
>>>
>>> --
>>> Dr. Stephanie Tonnesen
>>> Alvin E. Nashman Postdoctoral Fellow
>>> Carnegie Observatories, Pasadena, CA
>>> stonnes at gmail.com
>>>
>>> _______________________________________________
>>> yt-users mailing list
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>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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