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@gmail.com

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

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

On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <nathan12343@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@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@gmail.com

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