[torqueusers] help with unwanted concurrency in a torque script

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Dec 7 18:25:55 MST 2009


Hi Josh,

I haven't run them in bash, but since all the pbs directives are
comments in csh, it can be run as a standard csh batch script. In this
case it performs exactly as expected.

As far as confusion between different runs goes, that's unlikely since
(there are parts of the script that I've left off for simplicity, but
don't affect this issue) the last command is a set of DELETE FROM
statements - there is nothing left in the database between runs.

The other interesting thing is that while the running it as a csh script
works from the command line, running it as a csh script from a torque
script breaks the same way as having the commands within the torque
script - I haven't tried using perl as the glue to see if somehow it can
be bound into a single glob.

My suspicion is that somehow postgresql's non-completion before the
completion of each command is ignored when run in the torque context,
but not in any other context. But I don't have any thing except my
limited observations to base this on.

I've had a look at the -W switch, and it's unfortunately not going to do
the job for me here.

cheers
Dan

On Mon, 2009-12-07 at 17:09 -0800, Joshua Bernstein wrote:
> Ah,
> 
>         I had another look at the script. It is interesting that CSH
> and BASH behave 
> differently. Perhaps those commands depend upon some envar that is
> being handled 
> differently between the two shells?
> 
>         My suggestion of job dependencies assumed the population and
> the analysis steps 
> were in separate scripts. Perhaps you're submitting this script more
> then once 
> and both are running at the same time?
> 
> -Josh
> 



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