[yt-users] h5py Issues

[Brian Crosby]

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 o__ Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
> ________________________________(_)_\(_)_______________
> 
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