[torqueusers] help with unwanted concurrency in a torque script

Gareth.Williams at csiro.au Gareth.Williams at csiro.au
Mon Dec 7 19:04:46 MST 2009

> -----Original Message-----
> From: Dan Kortschak [mailto:dan.kortschak at adelaide.edu.au]
> Sent: Tuesday, 8 December 2009 12:26 PM
> To: Joshua Bernstein
> Cc: torqueusers at supercluster.org
> Subject: Re: [torqueusers] help with unwanted concurrency in a torque
> script
> 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

We had someone with what seemed a similar problem with sqlite.  That turned out to be a programming/scripting error - there was no flush to the database in the script, but there was an implicit flush when one ran the same commands in an interactive session.  Strange but true.  Might be related to having a terminal (or not) in the environment



> 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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