[yt-users] h5py Issues

[Cameron Hummels]

I've only been sparsely following this thread, but I noticed that you're 
running Python 2.4.2 on Kraken, whereas you're using yt in a directory 
labeled python2.6.  Could a mismatch of python versions cause such a 
problem?  Isn't the default version of python on kraken 2.6.4?  You 
could type "which python" to find out which version of python you're 
using, but 2.6.4 is in:

/sw/xt/python/2.6.4/sles10.1_gnu4.1.2//bin/python

If you want to switch to using 2.6.4, you could type:

$ module load python/2.6.4

Matt or Esteban, could a mismatch of python versions cause this problem 
in yt?  Or am I totally off-base here?

Cameron

Brian Crosby wrote:
> Stephen,
>
> This was being run as a batch job, 2 cores/node on 256 cores total.
>
> I just tried loading up yt on the login node of Kraken, and hit some 
> problems.  Does any of this illuminate things?
>
> Python 2.4.2 (#1, Dec  2 2008, 00:09:07) 
> [GCC 4.1.2 20070115 (SUSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from yt.mods import *
> yt.lagos   WARNING    2010-07-23 16:32:56,037 No h5py. Data 
> serialization disabled.
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/mods.py", 
> line 32, in ?
>     import yt.lagos as lagos
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/__init__.py", 
> line 47, in ?
>     from yt.arraytypes import *
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/arraytypes.py", 
> line 30, in ?
>     import numpy as na
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/__init__.py", 
> line 132, in ?
>     import add_newdocs
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/add_newdocs.py", 
> line 9, in ?
>     from lib import add_newdoc
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/lib/__init__.py", 
> line 4, in ?
>     from type_check import *
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/lib/type_check.py", 
> line 8, in ?
>     import numpy.core.numeric as _nx
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/core/__init__.py", 
> line 8, in ?
>     import numerictypes as nt
>   File 
> "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/numpy/core/numerictypes.py", 
> line 87, in ?
>     from numpy.core.multiarray import typeinfo, ndarray, array, empty, 
> dtype
> ImportError: No module named multiarray
>
>
> -Brian
>
> On Jul 23, 2010, at 4:23 PM, Stephen Skory wrote:
>
>> Brian & Matt,
>>
>> Hello from Boulder! I'm probably not going to be able to follow this 
>> up very
>> quickly. Until tomorrow my internet access is limited to cafés and we 
>> have lots
>> of other things to get done!
>>
>>> I'd suggest  moving it out of the way for now and continuing on.
>>> Stephen, if you're  listening, is it possible that the .yt file has had
>>> a ridiculous number of  HDF5 groups made, which is confusing and
>>> overflowing  h5py?
>>
>>
>> Nothing that I've added to yt makes use of the .yt file, so the 
>> various tools I
>> wrote Brian mentioned shouldn't affect it. One thought is I wonder if 
>> there are
>> memory limits on the login nodes on Kraken, and if this is being hit? 
>> Brian,
>> where you trying this on the login node, and if so, can you try it in an
>> interactive session (one node will suffice).
>>
>> _______________________________________________________
>> sskory at physics.ucsd.edu <mailto:sskory at physics.ucsd.edu> o__ Stephen 
>> Skory
>> http://physics.ucsd.edu/~sskory/ <http://physics.ucsd.edu/%7Esskory/> 
>> _.>/ _Graduate Student
>> ________________________________(_)_\(_)_______________
>>
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-- 
Cameron Hummels
PhD Candidate, Astronomy Department of Columbia University
Public Outreach Director, Astronomy Department of Columbia University
NASA IYA New York State Student Ambassador
http://outreach.astro.columbia.edu