[yt-dev] seg fault on projections

[Eric Hallman]

Matt,
  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?

Eric


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" <e.hallman at me.com> 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/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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-- 
Eric Hallman
Tech-X Corporation               hallman at txcorp.com
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