[yt-users] error in submitting script to cluster

[Britton Smith]

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 at 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 at 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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> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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