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?


On Mar 15, 2012, at 10:10 AM, Matthew Turk wrote:

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.

On Mar 15, 2012 10:02 AM, "Eric Hallman" <> wrote:
Matt and Stephen,
 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:

p = pc.add_projection('Density',0)
 File "/Users/hallman/work/yt-i386/lib/python2.7/site-packages/yt-2.4dev-py2.7-macosx-10.4-x86_64.egg/yt/visualization/", line 758, in add_projection
 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/", line 1930, in __init__
 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/", line 309, in _refresh_data
 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/", line 2127, in get_data
   pdxs = na.concatenate(pdxs, axis=1)
IndexError: axis 1 out of bounds [0, 1)

On Mar 15, 2012, at 4:55 AM, Matthew Turk wrote:

> Hi Stephen,
> A bunch of people have been reporting segfaults.  I am starting to
> think it may be an issue of an older h5py combined with this change,
> which may build up multiple copies of the hierarchy and keep multiple
> copies of a file (in this case the data file) open.
> I think we should consider backing this change out, and providing it
> in a more subtle way -- for instance, making field info just always
> create the hierarchy.  Here it actually almost always creates it
> twice.  Remove the deletion, just leave the hierarchy in existence.
> -Matt
> On Wed, Mar 14, 2012 at 10:46 PM, Stephen Skory <> wrote:
>> Bah humbug.
>> I did a fresh install on my mac, and the problem went away. I wonder
>> what cruft I had left over was getting in the way? I deleted the .yt
>> file etc...
>> Anyway, sorry for the noise, move along.
>> --
>> Stephen Skory
>> 510.621.3687 (google voice)
>> _______________________________________________
>> yt-dev mailing list
> _______________________________________________
> yt-dev mailing list

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