Hi Christine, It looks like somehow the HOME variable doesn't get set. If you add that to your submission script -- either using setenv or export -- it should fix it. Depending on how the environment variables get set, you may also have to set PYTHONHOME and MPLCONFIGDIR, as per: http://yt.enzotools.org/wiki/CrayXT5Installation#BatchQueue Let us know, if this works, though -- it might be worthwhile for me to go through and double-check all the places where yt tries to pull out environment variables and make sure there are fallbacks. Best, Matt On Tue, May 4, 2010 at 1:28 PM, Christine Simpson <csimpson@astro.columbia.edu> wrote:
Hi,
I am trying to run yt scripts on a computing cluster that uses condor. I have installed yt and successfully run scripts from the command line, but I get an error when I try to submit scripts to the cluster. I think the problem lies in how I submit the script through condor, however, I am trying to get a better understanding of the python error to help me figure it out. I was hoping you yt/python folks could give me some insight.
The script I'm testing out is the one that does a simple radial profile, I copied it from the wiki:
from yt.mods import * # set up our namespace fn= "output_0064" # parameter file to load pf = load(fn) # load data
pc = PlotCollection(pf) # defaults to center at most dense point pc.add_profile_sphere(50.0, "kpc", # how many of which unit at pc.center ["RadiusMpc", "Density"], weight="CellMassMsun", # x, y, weight x_bounds = (1e-3, 10.0)) # cut out zero-radius and tiny-radius cells # But ... weight defaults to CellMassMsun, so we're being redundant here!
pc.save(fn) # save all plots
I get this error:
Traceback (most recent call last): File "simple_radial_profile.py", line 3, in <module> from yt.mods import * # set up our namespace File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/lagos/__init__.py", line 29, in <module> from yt.config import ytcfg File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/config.py", line 33, in <module> 'RunDir': os.path.join(os.getenv("HOME"),'.yt/EnzoRuns/'), File "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt///lib/python2.6/posixpath.py", line 67, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith'
The problem is with the line that imports the yt module, but I'm not sure exactly what the issue is. I thought that maybe it was an issue with not finding PYTHONPATH, but I'm not sure.
If anyone has any ideas about this error, I'd appreciate them.
Thanks Christine Simpson
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