[Swift-devel] using cobalt-script mode on the bluegene/p

[Allan Espinosa]

it is interesting how I caught stdouts from the echo of my
hello_wrapper.sh scripts but not the stdout of the mpi program. It was
directed to a file in my ~/.globus directory as specified by the cqsub
command in the cobalt provider.  This is due to a known cobalt bug
(https://trac.mcs.anl.gov/projects/cobalt/ticket/310).

But the workflow finished successfully.  As of now, either we should
explicitly indicate output files in our mpi jobs or manually grab
stdout and stderr outputs in the depths of your ~/.globus directory.

my sites.xml:
<config>
<pool handle="INTREPID">
  <filesystem provider="local" />
  <execution provider="cobalt"/>
  <profile namespace="globus" key="hostCount">64</profile>
  <profile namespace="globus" key="project">HTCScienceApps</profile>
  <profile namespace="globus" key="maxtime">20</profile>
  <profile namespace="globus" key="mode">script</profile>
  <profile namespace="globus" key="queue">prod-devel</profile>
  <workdirectory >/intrepid-fs0/users/espinosa/scratch/mpi_runs</workdirectory>
</pool>
</config>

my hello_wrapper.sh for the app function hello():
#!/bin/bash
echo "Cobalt script job"
cobalt-mpirun -np 256 -mode vn -cwd `pwd` \
  /home/espinosa/experiments/mpitest/hello

echo "Finished script"

workflow:
type file;

app (file out) hello() {
    hello stdout=@filename(out);
}

file output<"stdout.file">;

output = hello();


-- 
Allan M. Espinosa <http://allan.88-mph.net/blog>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>