<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Matt,<div> my prior error below is not related to the previous problem. But it does bring up a weird issue I thought you'd be interested in. I did not define any refinement criteria, but Enzo is writing the parameter "RefineBy" as =4 by default in a unigrid run. This is causing yt to use something called "overlap_proj"? Which is crashing the projection. If I go back and set RefineBy=2, the problem vanishes. This is maybe more of a Enzo issue than yt, but if one is using non-factor-of-two refinement, it could cause problems. Could this be related to Dave Collins' problem with RefineBy=4?</div><div><br></div><div>Eric</div><div><br></div><div><br><div><div>On Mar 15, 2012, at 10:10 AM, Matthew Turk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><p>Okay, let's back out that changeset. I think it is okay to mandate an instantiated hierarchy if you want to have detailed, output-specific field information. </p>
<div class="gmail_quote">On Mar 15, 2012 10:02 AM, "Eric Hallman" <<a href="mailto:e.hallman@me.com">e.hallman@me.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Matt and Stephen,<br>
I can confirm that the seg fault disappears on Mac OS X when updating to h5py-2.0.1, though a simple projection is still giving an out of bounds error on a simple unigrid data set. Not sure why that occurs. But I think Matt is definitely right about h5py:<br>
<br>
p = pc.add_projection('Density',0)<br>
File "/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", line 758, in add_projection<br>
**field_parameters)<br>
File "/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", line 1930, in __init__<br>
self._refresh_data()<br>
File "/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", line 309, in _refresh_data<br>
self.get_data()<br>
File "/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", line 2127, in get_data<br>
pdxs = na.concatenate(pdxs, axis=1)<br>
IndexError: axis 1 out of bounds [0, 1)<br>
<br>
<br>
On Mar 15, 2012, at 4:55 AM, Matthew Turk wrote:<br>
<br>
> Hi Stephen,<br>
><br>
> A bunch of people have been reporting segfaults. I am starting to<br>
> think it may be an issue of an older h5py combined with this change,<br>
> which may build up multiple copies of the hierarchy and keep multiple<br>
> copies of a file (in this case the data file) open.<br>
><br>
> I think we should consider backing this change out, and providing it<br>
> in a more subtle way -- for instance, making field info just always<br>
> create the hierarchy. Here it actually almost always creates it<br>
> twice. Remove the deletion, just leave the hierarchy in existence.<br>
><br>
> -Matt<br>
><br>
> On Wed, Mar 14, 2012 at 10:46 PM, Stephen Skory <<a href="mailto:s@skory.us">s@skory.us</a>> wrote:<br>
>> Bah humbug.<br>
>><br>
>> I did a fresh install on my mac, and the problem went away. I wonder<br>
>> what cruft I had left over was getting in the way? I deleted the .yt<br>
>> file etc...<br>
>><br>
>> Anyway, sorry for the noise, move along.<br>
>><br>
>> --<br>
>> Stephen Skory<br>
>> <a href="mailto:s@skory.us">s@skory.us</a><br>
>> <a href="http://stephenskory.com/" target="_blank">http://stephenskory.com/</a><br>
>> <a href="tel:510.621.3687" value="+15106213687">510.621.3687</a> (google voice)<br>
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