<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Matt,<div> I ran with paste-detailed, but I thought that would give a paste bin link? Anyway, with --detailed, here is the output manually put in the paste bin: </div><div><br></div><div><a href="http://paste.yt-project.org/show/2232/">http://paste.yt-project.org/show/2232/</a></div><div><br></div><div>Eric<br><div><div>On Mar 15, 2012, at 10:32 AM, Matthew Turk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Eric,<br><br>This is intentional, but I think Dave's were something else.<br>RefineBy=2 allows you to use the (much, much faster) quadtree-based<br>projection; Enzo's default is RefineBy=4, so if you just run a unigrid<br>you're likely not going to override that. The overlap proj is what we<br>used up until about a year ago by default. The specific bug you saw<br>is puzzling to me, and I'm not sure without more detailed traceback<br>how to proceed. Could you run with --paste-detailed ?<br><br>On Thu, Mar 15, 2012 at 10:29 AM, Eric Hallman <<a href="mailto:hallman@txcorp.com">hallman@txcorp.com</a>> wrote:<br><blockquote type="cite">Matt,<br></blockquote><blockquote type="cite"> my prior error below is not related to the previous problem. But it does<br></blockquote><blockquote type="cite">bring up a weird issue I thought you'd be interested in. I did not define<br></blockquote><blockquote type="cite">any refinement criteria, but Enzo is writing the parameter "RefineBy" as =4<br></blockquote><blockquote type="cite">by default in a unigrid run. This is causing yt to use something called<br></blockquote><blockquote type="cite">"overlap_proj"? Which is crashing the projection. If I go back and set<br></blockquote><blockquote type="cite">RefineBy=2, the problem vanishes. This is maybe more of a Enzo issue than<br></blockquote><blockquote type="cite">yt, but if one is using non-factor-of-two refinement, it could cause<br></blockquote><blockquote type="cite">problems. Could this be related to Dave Collins' problem with RefineBy=4?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Eric<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Mar 15, 2012, at 10:10 AM, Matthew Turk wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Okay, let's back out that changeset. I think it is okay to mandate an<br></blockquote><blockquote type="cite">instantiated hierarchy if you want to have detailed, output-specific field<br></blockquote><blockquote type="cite">information.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Mar 15, 2012 10:02 AM, "Eric Hallman" <<a href="mailto:e.hallman@me.com">e.hallman@me.com</a>> wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Matt and Stephen,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> I can confirm that the seg fault disappears on Mac OS X when updating to<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">h5py-2.0.1, though a simple projection is still giving an out of bounds<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">error on a simple unigrid data set. Not sure why that occurs. But I think<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Matt is definitely right about h5py:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">p = pc.add_projection('Density',0)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> File<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"/Users/hallman/work/yt-i386/lib/python2.7/site-packages/yt-2.4dev-py2.7-macosx-10.4-x86_64.egg/yt/visualization/plot_collection.py",<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">line 758, in add_projection<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> **field_parameters)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> File<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"/Users/hallman/work/yt-i386/lib/python2.7/site-packages/yt-2.4dev-py2.7-macosx-10.4-x86_64.egg/yt/data_objects/data_containers.py",<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">line 1930, in __init__<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> self._refresh_data()<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> File<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"/Users/hallman/work/yt-i386/lib/python2.7/site-packages/yt-2.4dev-py2.7-macosx-10.4-x86_64.egg/yt/data_objects/data_containers.py",<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">line 309, in _refresh_data<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> self.get_data()<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> File<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"/Users/hallman/work/yt-i386/lib/python2.7/site-packages/yt-2.4dev-py2.7-macosx-10.4-x86_64.egg/yt/data_objects/data_containers.py",<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">line 2127, in get_data<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> pdxs = na.concatenate(pdxs, axis=1)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">IndexError: axis 1 out of bounds [0, 1)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Mar 15, 2012, at 4:55 AM, Matthew Turk wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Stephen,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">A bunch of people have been reporting segfaults. I am starting to<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">think it may be an issue of an older h5py combined with this change,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">which may build up multiple copies of the hierarchy and keep multiple<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">copies of a file (in this case the data file) open.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I think we should consider backing this change out, and providing it<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">in a more subtle way -- for instance, making field info just always<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">create the hierarchy. Here it actually almost always creates it<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">twice. Remove the deletion, just leave the hierarchy in existence.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">-Matt<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Wed, Mar 14, 2012 at 10:46 PM, Stephen Skory <<a href="mailto:s@skory.us">s@skory.us</a>> wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Bah humbug.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I did a fresh install on my mac, and the problem went away. I wonder<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">what cruft I had left over was getting in the way? I deleted the .yt<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">file etc...<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Anyway, sorry for the noise, move along.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Stephen Skory<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:s@skory.us">s@skory.us</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://stephenskory.com/">http://stephenskory.com/</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">510.621.3687 (google voice)<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">yt-dev mailing 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href="http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">yt-dev mailing list<br></blockquote><blockquote type="cite"><a href="mailto:yt-dev@lists.spacepope.org">yt-dev@lists.spacepope.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Eric Hallman<br></blockquote><blockquote type="cite">Tech-X Corporation <a href="mailto:hallman@txcorp.com">hallman@txcorp.com</a><br></blockquote><blockquote type="cite">5621 Arapahoe Ave, Suite A Phone: (720) 254-5833<br></blockquote><blockquote type="cite">Boulder, CO 80303 Fax: (303) 448-7756<br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote>_______________________________________________<br>yt-dev mailing list<br><a href="mailto:yt-dev@lists.spacepope.org">yt-dev@lists.spacepope.org</a><br>http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org<br></div></blockquote></div><br></div><br><br><div apple-content-edited="true">
<div>-- <br>Eric Hallman<br>Tech-X Corporation hallman<a href="mailto:kruger@txcorp.com">@txcorp.com</a><br>5621 Arapahoe Ave, Suite A Phone: (720) 254-5833<br>Boulder, CO 80303 Fax: (303) 448-7756<br>--</div><div><br></div><br class="Apple-interchange-newline">
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