Eric

On Mar 15, 2012, at 10:32 AM, Matthew Turk wrote:

Hi Eric,

This is intentional, but I think Dave's were something else.
RefineBy=2 allows you to use the (much, much faster) quadtree-based
projection; Enzo's default is RefineBy=4, so if you just run a unigrid
you're likely not going to override that. The overlap proj is what we
used up until about a year ago by default. The specific bug you saw
is puzzling to me, and I'm not sure without more detailed traceback
how to proceed. Could you run with --paste-detailed ?

On Thu, Mar 15, 2012 at 10:29 AM, Eric Hallman <hallman@txcorp.com> wrote:
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@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@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@skory.us
http://stephenskory.com/
510.621.3687 (google voice)
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Eric Hallman
Tech-X Corporation hallman@txcorp.com
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