[torqueusers] help with unwanted concurrency in a torque script

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Dec 7 17:40:52 MST 2009


Hi,

I am having problems with unexpected concurrency (at least unexpected
from my perspective) with a torque script. I am using pbs to manage a
batch queue on my workstation and at the moment am using it to run a set
of perl scripts that perform postgresql control.

The first script populates (eg populate below) the database and then
subsequent scripts (eg report and extract below) query to perform an
analysis of the data. The problem is that the report and extract scripts
appear to start before postgresql has completed the transactions, so the
reports are erroneous. This does not happen if the torque script is run
as a csh script.

Can any one suggest how to avoid this (without hooking in postgresql
process status communication)? And also where I should look to find out
more about this?

thanks


#!/bin/csh

### Job name
#PBS -N test

### Join queuing system output and error files into a single output file
#PBS -j oe

#PBS -q sequential

#PBS -l ncpus=1
#PBS -l mem=5gb,vmem=2gb
#PBS -l walltime=70:00:00

# Run the executables
populate --infile data
report
extract




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