<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 1, 2016 at 4:37 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>Hi Nathan,<br><br></div><div>Yahoo! doing the conda install instead of pip has fixed it! </div></div></div></div></div></div></div></blockquote><div><br></div><div>The 4th of July weekend is saved!</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>For completion, though, here are the answers to the other two questions:<br><br></div>Yes, it all runs nicely (until scipy is needed) if I don't have scipy installed. <br><br></div>If I start python and type<br><br></div>import scipy.optimize<br><br></div>I get a Segmentation fault --when I used the pip install version. with conda install, import scipy.optimize seems to work fine.<br></div></div></div></blockquote><div><br></div><div>This must be a bug in scipy then, triggered by pip installing in whatever environment you have set up on this cluster. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div></div>Thanks!!!<span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">Stephanie<br><br></font></span></div><div class="gmail_extra"><span class=""><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Fri, Jul 1, 2016 at 2:15 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote"><span>On Fri, Jul 1, 2016 at 4:00 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Nathan,<br><br></div>I am not sure how to get a core dump or how to make gdb give me useful things. But maybe this will help...<br><br></div>By running my code via a command line, I find that <br></div>import h5py<br></div><div>import scipy<br></div><div>import yt<br></div><div>from yt.analysis_modules.cosmological_observation.api import LightRay<br><br></div><div>all are fine. But,<br><br></div><div>from yt.analysis.modules.absorption_spectrum.api import AbsorptionSpectrum<br></div><div>from yt.analysis.modules.absorption_spectrum.api import generate_total_fit<br></div></div></blockquote><div><br></div></span><div>And both of these succeed when scipy isn't installed?</div><div><br></div><div>What happens if you do:</div><div><br></div><div>import scipy.optimize</div><div><br></div><div>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:</div><div><br></div><div>$ pip uninstall scipy</div><div>$ conda install scipy</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div>both give me a Segmentation fault and kick me out of python<br><br></div><div>I can keep trying to figure out how to have gdb give me something useful, but does this give any clues in the meantime?<br><br></div><div>Thanks,<br></div><div>Stephanie<br></div></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Fri, Jul 1, 2016 at 12:28 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Stephanie,<div><br></div><div>It's very hard to say what's going wrong without more information.</div><div><br></div><div>Can you get a core dump or run python under gdb to get a stack trace at the place where the segmentation fault happens?</div><div><br></div><div>Can you run this on your laptop? If so, do you get a segmentation fault there?</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Fri, Jul 1, 2016 at 2:25 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div><div><div>Hi all,<br><br></div>I have the yt-conda installation of yt. I am trying to create an absorption spectrum, so need the command "generate_total_fit".<br><br></div>yt told me I needed scipy for this to work. yt does not have scipy. So I typed:<br></div>>pip install scipy<br><br></div>scipy was installed.<br><br></div>However, then my submission script no longer worked at all and I was given the error:<br><br>/var/spool/torque/mom_priv/jobs/<a href="http://50052.mies.stanford.edu.SC" target="_blank">50052.mies.stanford.edu.SC</a>: line 26: 3750 Segmentation fault python HI_absorbers.py<br><br></div><div>When I pip uninstall scipy, my code runs again! <br></div><div>The only commands in my script are<br></div><div>source /home/stonnes/yt-conda/bin/activate<br></div><div>python HI_absorbers.py<br><br></div><div>Can anyone help me out with this?<br><br></div><div>Thanks!<br></div><div>Stephanie<br><br clear="all"></div><div><div><div><div><div><div><div><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
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