[yt-users] error when running on cluster nodes

[Tsz Ka Li]

Hi Matt,

I used the same python (~/yt-ppc64/bin/python) as I did in the command 
line. I think I tried python2.6 but I got the same error. (Actually how 
are they different?) The machine I am using is the Turing cluster in UI 
(http://www.cse.illinois.edu/turing/), which is an Apple Xserve cluster 
using G5 processors. You can find on the website some information about 
it. Sorry I am not that familiar with cluster issues. I suppose the 
nodes have full installation, though I don't know where to check. I am 
using the default compilers on Turing, which are gcc for C/C++ and xlf 
for Fortran.

Thank you very much for looking into this issue for me.

Cheers,
Tsz Ka


On 2/16/2011 10:22 PM, Matthew Turk wrote:
> Hi Tsz Ka,
>
> Usually these problems are seen when you're running the wrong version
> of Python, or you're using some combination of C++ compilers.  I think
> unless you're running on Compute Node Linux, following the suggestions
> on the XT5 Installation page may not be necessary, and I am afraid I
> don't recognize the machine (ppc64) you're running on.  Which machine
> is it -- can you tell me a little more about it?  And do you know if
> the compute nodes have a full installation stack?  And can you verify
> you're using the correct python executable?
>
> Best,
>
> Matt
>
> On Wed, Feb 16, 2011 at 6:54 PM, Tsz Ka Li<tszkali2 at illinois.edu>  wrote:
>> Hi all,
>> I run into an error which occurs when I submit a yt script to run on cluster
>> nodes. The script runs successfully from the command line though, and I am
>> NOT running MPI here. The error is as follows:
>>
>> Traceback (most recent call last):
>>    File "MergerTree.py", line 1, in<module>
>>      from yt.mods import *
>>    File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/mods.py", line 92, in
>> <module>
>>      from yt.visualization.api import \
>>    File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/api.py",
>> line 34, in<module>
>>      from plot_collection import \
>>    File
>> "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/plot_collection.py",
>> line 26, in<module>
>>      from matplotlib import figure
>>    File
>> "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/figure.py",
>> line 16, in<module>
>>      import artist
>>    File
>> "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/artist.py",
>> line 6, in<module>
>>      from transforms import Bbox, IdentityTransform, TransformedBbox,
>> TransformedPath
>>    File
>> "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/transforms.py",
>> line 34, in<module>
>>      from matplotlib._path import affine_transform
>> ImportError:
>> /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so:
>> undefined symbol:
>> _ZZN2Py15PythonExtensionINS_22ExtensionModuleBasePtrEE9behaviorsEvE1p
>>
>> Apparently it is related to matplotlib. I tried to do something similar to
>> the instructions on the wiki for CrayXT5 Installation
>> (http://yt.enzotools.org/wiki/CrayXT5Installation) in the section 'Running
>> on a compute node', but I still got the same error.
>>
>> Does anyone have ideas on what this means? I appreciate any help from you.
>>
>> Thanks,
>> Tsz Ka
>>
>> _______________________________________________
>> yt-users mailing list
>> 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
>