Thanks to everyone who has answered this. The short answer is that
torque is not behaving the way I expected and not the way I have ever
seen it behave in the past. The I/O binding of these jobs may have
something to do with this, but I will look into it further.
cheers
On Mon, 2009-12-07 at 13:26 -0800, John R Pierce wrote:
> I'm totally unfamiliar with torque., but you probably need to tell
> torque to run the first script and wait for it to return before
> running
> the rest, its probably launching a bunch concurrently.
>
That *shouldn't* be the case as the contents of a torque script should
be run sequentially (many jobs depend on this and I've never seen job
parts run out of order), just as a sh script is (they are actually just
csh scripts in my case). My understanding is that the parallelisation
occurs either through using MPI or other parallel compilers or running a
number of torque jobs, BUT I've just tested the hypothesis by running it
as a straight csh script - and it works perfectly, so there must be
something like that going on. I'll ask some of our more experience
torque admins about it. Thanks.