[yt-users] running volume_render.py in a batch script

Cameron Hummels chummels at astro.columbia.edu
Thu Apr 14 08:39:46 PDT 2011


Hi Shankar,

I've never used Ember, but on Kraken I experienced problems such as you
describe.  The issue on Kraken was that the login nodes could see much
more of the file system than the compute nodes could.  The compute nodes
on Kraken can only see the scratch space, so unless my install of yt and
my data sat on the scratch space, my script would fail.  Perhaps Ember
has a similar filesystem lay out.  You could always test this with a
submission script that mpiruns a simple yt script to output some basic
like the extrema of a PF.  If it can do this, then you don't suffer from
the same problems that I did.

Just an idea.

Cameron


On 4/14/11 11:06 AM, Agarwal, Shankar wrote:
> Hi,
>
> I have a volume_render.py script that runs fine on the login node on NCSA-EMBER. But the same script crashes with the following error when run through qsub.
>
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: aborting job
> MPI: Received signal 11
>
>
> My batch script is...
>
> #!/bin/sh -x
> #PBS -l walltime=00:10:00
> #PBS -l mem=32000mb
> #PBS -l ncpus=1
> #PBS -q debug
> #PBS -V
> #PBS -A TG-AST080030N
> #PBS -N movie
> #PBS -m be
> #export MPI_MEMMAP_OFF=1
> cd /gpfs1/u/ac/sagarwal/junk
> mpirun -np 1 /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/bin/python2.6 volume_render.py
>
>
>
> Here are the first few lines of the volume_render.py...
>
> import matplotlib;matplotlib.use("Agg");import pylab
> import numpy as na
> import time
> from yt.config import ytcfg; ytcfg["yt","loglevel"] = '50' ; ytcfg["lagos","serialize"] = "False"
>
> from yt.mods import *
> from yt.extensions.volume_rendering import *
> from yt.funcs import *
> mh = na.log10(1.67e-24)
> from mpi4py import MPI
>
>
> Please let me know if it may have something to do with mpi4py.
> Shankar
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>



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