[gmx-users] chaining jobs in queuing systems

[Mark Abraham]

Florian Haberl wrote:
> Hi,
> 
> has anyone written a chain job submit script for queing systems, perhaps for 
> pbs?
> I mean if a job has finished, another job will be started with the results of 
> the first one, till a certain runtime.

I have some elaborate perl scripts that control a PBS job by iteratively 
running a secondary script (which needn't be MD, of course), querying 
the PBS API about how progress of the time allocation is going, and 
keeping iterating that secondary script so long as there's enough time 
available from PBS for the next iterate to finish. You need something 
like the script Dallas Warren posted to actually do your MD sensibly, 
and you handle the final iterative job re-submission at the higher level 
of scripting in my approach. The advantages are that you should never 
waste time because your PBS allocation runs out before mdrun returns, 
and you get the chaining effect of never not being in the PBS queue.

My scripts require some installation of CPAN modules and require you to 
have some moderate knowledge of perl to adapt them to your needs, but 
they're available if you email me.

Mark