I think you can also fix this by adding #PBS -V to your job script, which should allow your job to inherit your environment.

Britton

On Tue, May 4, 2010 at 2:47 PM, Matthew Turk <matthewturk@gmail.com> wrote:
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
>
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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