[yt-dev] seg fault on projections

[Eric Hallman]

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/plot_collection.py", line 758, in add_projection
    **field_parameters)
  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__
    self._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/data_containers.py", line 309, in _refresh_data
    self.get_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/data_containers.py", 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 <s at skory.us> 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
>> s at skory.us
>> http://stephenskory.com/
>> 510.621.3687 (google voice)
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