Hi Shankar, This is a classic error that shows up when your Python interpreter and your site-packages are compiled with different unicode on/off values. Usually it means that you're running wiht a different python interpreter than you mean to -- could you verify that the Python interpreter you're calling in the queue is the correct one? (It also looks like h5py is not being picked up, which I suspect is related to this issue.) One thing to do is to submit the queue script with an explicit path: /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/bin/python2.6 hop_yt.py Another would be to make sure you're using -V as an option in your qsub script. If you're not using this, the queue system might override your PATH and PYTHONPATH environment variables in an odd way. -Matt On Fri, Jan 28, 2011 at 10:41 AM, Agarwal, Shankar <sagarwal@ku.edu> wrote:
Hi,
I am having a strange problem on Ember. When I try to run my python scripts interactively, they run fine. But when I submit them to a queue, I get the following error:
set_SCR: using existing PBS job directory /scratch/batch/25508 set_SCR: using existing PBS job directory /scratch/batch/25508 yt.lagos WARNING 2011-01-28 09:18:12,423 No h5py. Data serialization disabled. Traceback (most recent call last): File "hop_yt.py", line 7, in <module> from yt.mods import * File "/gpfs1/u/ac/sagarwal/software/enzo/src/yt/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/gpfs1/u/ac/sagarwal/software/enzo/src/yt/yt/lagos/__init__.py", line 47, in <module> from yt.arraytypes import * File "/gpfs1/u/ac/sagarwal/software/enzo/src/yt/yt/arraytypes.py", line 30, in <module> import numpy as na File "/u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/__init__.py", line 130, in <module> import add_newdocs File "/u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/add_newdocs.py", line 9, in <module> from lib import add_newdoc File "/u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/__init__.py", line 5, in <module> import multiarray ImportError: /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_FromUnicode
My PATH is : /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/bin:/usr/apps/math/gsl/intel/1.14/bin:/blahblah.....
PYTHONPATH : /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib/python2.6/site-packages
LD_LIBRARY_PATH : /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/lib:/usr/apps/math/gsl/intel/1.14/lib:/usr/local/lib64:/lib:/lib64:/usr/lib64:/usr/lib:/usr/X11R6/lib64:/blahblah...
My script :
from yt.mods import * import yt.extensions.HaloProfiler as HP from yt.extensions.HaloMassFcn import *
fn = "RedshiftOutput0001" pf = load(fn) halos = HaloFinder(pf,160,padding=0.02) halos.write_out("HopAnalysis.out")
pc = PlotCollection(pf,center=[0.5,0.5,0.5]) for ax in range(3): p = pc.add_slice("Density", ax) pc.save()
Any suggestions. Shankar _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org