[yt-users] h5py Issues

Matthew Turk matthewturk at gmail.com
Fri Jul 23 14:10:35 PDT 2010


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
>>> ________________________________(_)_\(_)_______________
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
> --
> 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
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>



More information about the yt-users mailing list