ssa.py does not submit job to cluster

[Former user]

Hi,

I am trying to use the ssa.py-par_ana protocol to submit a parallellized job to the cluster.

I have made the needed changes in the ssa.py code and run par_ana. I got a number of input files that seem to correspond to the parallelization, but no results. I talked to the admin of my cluster and they say no job was submitted by ssa.py.

We would like to know how does ssa.py perform the submission. Also, if I have to generate a submit file with the PBS commands.

Thanks a lot.

[Charlie Xia]

What par_ana and ssa.py does is really an embarrasing parallelism, They divide the data matrix into N trunks and perform (X,Y) pair calculation of these trunks by submitting each of pair's computation to a node. The script is really simple python:

1. The following sets queue name and maximum queue capacity

core_max=63 mem_max=300 uname="lixia" qname="main"

2. then use qstat and qsub to query total jobs concurrent and to submit jobs.

qstat -u $uname | awk '{print $8}' qsub -q $qname $pbsFile

3. change the PBS part in par_ana for system-specific parameters and use the script to create those $pbsFile files.

PBS_PREAMBLE = """#!/bin/bash #PBS -N %s #PBS -S /bin/bash #PBS -j oe #PBS -o %s #PBS -l walltime=299:00:00 #PBS -l nodes=1:ppn=1,mem=%d000mb,vmem=%d000mb,pmem=%d000mb"""