I think you can also fix this by adding #PBS -V to your job script, which should allow your job to inherit your environment.<br><br>Britton<br><br><div class="gmail_quote">On Tue, May 4, 2010 at 2:47 PM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Christine,<br>
<br>
It looks like somehow the HOME variable doesn't get set. If you add<br>
that to your submission script -- either using setenv or export -- it<br>
should fix it. Depending on how the environment variables get set,<br>
you may also have to set PYTHONHOME and MPLCONFIGDIR, as per:<br>
<br>
<a href="http://yt.enzotools.org/wiki/CrayXT5Installation#BatchQueue" target="_blank">http://yt.enzotools.org/wiki/CrayXT5Installation#BatchQueue</a><br>
<br>
Let us know, if this works, though -- it might be worthwhile for me to<br>
go through and double-check all the places where yt tries to pull out<br>
environment variables and make sure there are fallbacks.<br>
<br>
Best,<br>
<br>
Matt<br>
<div><div></div><div class="h5"><br>
On Tue, May 4, 2010 at 1:28 PM, Christine Simpson<br>
<<a href="mailto:csimpson@astro.columbia.edu">csimpson@astro.columbia.edu</a>> wrote:<br>
> Hi,<br>
><br>
> I am trying to run yt scripts on a computing cluster that uses condor.<br>
> I have installed yt and successfully run scripts from the command line,<br>
> but I get an error when I try to submit scripts to the cluster. I think<br>
> the problem lies in how I submit the script through condor, however, I<br>
> am trying to get a better understanding of the python error to help me<br>
> figure it out. I was hoping you yt/python folks could give me some<br>
> insight.<br>
><br>
> The script I'm testing out is the one that does a simple radial profile,<br>
> I copied it from the wiki:<br>
><br>
> from yt.mods import * # set up our namespace<br>
> fn= "output_0064" # parameter file to load<br>
> pf = load(fn) # load data<br>
><br>
> pc = PlotCollection(pf) # defaults to center at most dense point<br>
> pc.add_profile_sphere(50.0, "kpc", # how many of which unit at pc.center<br>
> ["RadiusMpc", "Density"], weight="CellMassMsun", # x, y, weight<br>
> x_bounds = (1e-3, 10.0)) # cut out zero-radius and tiny-radius<br>
> cells<br>
> # But ... weight defaults to CellMassMsun, so we're being redundant<br>
> here!<br>
><br>
> pc.save(fn) # save all plots<br>
><br>
><br>
> I get this error:<br>
><br>
> Traceback (most recent call last):<br>
> File "simple_radial_profile.py", line 3, in <module><br>
> from yt.mods import * # set up our namespace<br>
> File<br>
> "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/mods.py",<br>
> line 32, in <module><br>
> import yt.lagos as lagos<br>
> File<br>
> "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/lagos/__init__.py", line 29, in <module><br>
> from yt.config import ytcfg<br>
> File<br>
> "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt/src/yt-1.5/yt/config.py", line 33, in <module><br>
> 'RunDir': os.path.join(os.getenv("HOME"),'.yt/EnzoRuns/'),<br>
> File<br>
> "/hmt/sardine/hpc/scratch/astro/users/cms2166/yt///lib/python2.6/posixpath.py", line 67, in join<br>
> elif path == '' or path.endswith('/'):<br>
> AttributeError: 'NoneType' object has no attribute 'endswith'<br>
><br>
> The problem is with the line that imports the yt module, but I'm not<br>
> sure exactly what the issue is. I thought that maybe it was an issue<br>
> with not finding PYTHONPATH, but I'm not sure.<br>
><br>
> If anyone has any ideas about this error, I'd appreciate them.<br>
><br>
> Thanks<br>
> Christine Simpson<br>
><br>
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</div></div></blockquote></div><br>