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

[Stephanie Tonnesen]

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

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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