[yt-users] h5py Issues
Cameron Hummels
chummels at astro.columbia.edu
Fri Jul 23 14:09:05 PDT 2010
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
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