[yt-users] h5py Issues

Brian Crosby crosby.bd at gmail.com
Fri Jul 23 14:15:43 PDT 2010


Wonderful, thanks guys, and good spotting, Cameron!  I appreciate it.

-Brian

On Jul 23, 2010, at 5:10 PM, Matthew Turk wrote:

> Hi Cameron,
> 
> No, that's *exactly* the type of error you'd expect from that.  I did
> not notice the mismatch.  Good catch, thanks!
> 
> -Matt
> 
> On Fri, Jul 23, 2010 at 2:09 PM, Cameron Hummels
> <chummels at astro.columbia.edu> wrote:
>> 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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