<div dir="ltr">Hey Brian,<div><br></div><div>I'm unfortunately not able to reproduce this locally. I'm using yt changeset fffa77d2fdc2 and have made two minor changes to your script to get it to run in my test environment: <a href="http://paste.yt-project.org/show/5776/">http://paste.yt-project.org/show/5776/</a></div><div><br></div><div>I'll also note that I needed to make a directory named "DD_zoom_images" in the same directory as DD0013 to get the script to run.</div><div><br></div><div>Are you able to reproduce this issue on another system besides the cluster using DD0013? Is this cluster blue waters?</div><div><br></div><div>Unfortunately I don't really understand how an issue with the unit system would lead to a seg fault - if there really is an AttributeError being raised, even in cython code or code called by cython code, the error should be raised to the user level and there shouldn't be a seg fault... Very strange.</div><div><br></div><div>Hopefully we can iterate on this and figure out what's going wrong.</div><div><br></div><div>-Nathan</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Aug 4, 2015 at 7:47 AM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@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">Absolutely. The dataset that it's crashing on is here:<div><br></div><div><a href="http://galactica.pa.msu.edu/~bwoshea/data/datasets/DD0013.tar" target="_blank">http://galactica.pa.msu.edu/~bwoshea/data/datasets/DD0013.tar</a><br></div><div><br></div><div>This particular script crashes immediately upon trying to generate the first image on this dataset.</div><div><br></div><div>--Brian</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Tue, Aug 4, 2015 at 8:23 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@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 class="h5">Any chance you can trigger this crash <span></span>using a script that relies on a public dataset? I'm happy to debug, but need to be able to reproduce this locally to see what's going wrong.<span><font color="#888888"><div><br></div></font></span><div><span><font color="#888888">Nathan</font></span><div><div><br><br>On Tuesday, August 4, 2015, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi folks,<div><br></div><div>I have been trying to make some dark matter density movies using the "all_cic" field, and have discovered that using "all_cic" can reliably cause yt to seg fault on the supercomputer I'm using (x86_64 linux cluster with kernel 2.6.32-504.8.1.el6.x86_64) using the tip of yt-dev (changeset fa08e386d0da). The script that causes the crash is here:</div><div><br></div><div><a href="http://paste.yt-project.org/show/5774/" target="_blank">http://paste.yt-project.org/show/5774/</a><br></div><div><br></div><div>After I turned up the log level and started using pdb to debug, I discovered that the line in the script that causes the seg fault is line 88:</div><div><br></div><div>dm_dens_x = my_reg[("deposit", "all_cic")].value<br></div><div><br></div><div>where my_reg is defined as (on line 82):</div><div><br></div><div>my_reg = ds.arbitrary_grid(left, right, dims=[1,800, 800])<br></div><div><br></div><div>After stepping through with pdb, it seems that the code dies in this function:</div><div><br></div><div>/mnt/home/oshea/yt-3/lib/python2.7/site-packages/sympy/core/basic.py(83)__new__()<br></div><div><br></div><div>with the traceback shown here:</div><div><br></div><div><a href="http://paste.yt-project.org/show/5775/" target="_blank">http://paste.yt-project.org/show/5775/</a><br></div><div><br></div><div>Based on this traceback, it seems that there are problems with the unit system. </div><div><br></div><div>Interestingly enough, though, this does not happen on every dataset - it seems to happen occasionally, but predictably. For example, I can generate two images using this script, but it will seg fault on the third. On a different dataset in the time series, it will produce one image and then seg fault on the second. If I run the script over and over, it will eventually produce quite a few images, until it runs into a situation where it seg faults on the first image I produce (at which point I went to the debugger).</div><div><br></div><div>I don't have enough experience with the guts of yt - and the units section of yt in particular - to have a sense of what might be happening here based on the traceback. Does anybody have any suggestions?</div><div><br></div><div>Thank you!</div><div><br></div><div>--Brian</div><div><br></div><div><br></div></div>
</blockquote></div></div></div>
<br></div></div>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>