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

[Stephanie Tonnesen]

Hi Nathan,

Yahoo!  doing the conda install instead of pip has fixed it!  For
completion, though, here are the answers to the other two questions:

Yes, it all runs nicely (until scipy is needed) if I don't have scipy
installed.

If I start python and type

import scipy.optimize

I get a Segmentation fault --when I used the pip install version.  with
conda install, import scipy.optimize seems to work fine.

Thanks!!!
Stephanie


--
Dr. Stephanie Tonnesen
Alvin E. Nashman Postdoctoral Fellow
Carnegie Observatories, Pasadena, CA
stonnes at gmail.com

On Fri, Jul 1, 2016 at 2:15 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
> 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
>>>>
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>>>>
>>>
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