Mark Abraham wrote:
I can't. I run simulations on a cluster through a queue, and
sometimes the jobs are longer than the max time of the queue.
Yes you can. Do a pilot run and look at the last few lines of the
logfile - or better one of the crashed runs - you want reasonable
length so your setup time is amortized over all of the timesteps. That
will tell you how much simulation time you can do per unit wall clock
time. Now adjust the number of simulation steps accordingly.
I think you are right. I guess this is the best solution, after all.
The drawback is that I need to do a pilot run for each system I need to
simulate. And the number of processors I choose, too. O, no! It smells
like a benchmark!!!! :P
That's a reasonable start, but the nature of buffered output is such
that you can't guarantee that ener.edr and traj.trr are at the same
point. What you need to do is get gromacs to exit gracefully having
flushed its buffers. My PBS setup sends a SIGHUP that GROMACS 3.3.1
reads and does an appropriate end-of-last-step flush and a pirouette
to finish :-) I suggest passing the SIGHUP, delaying as long as you
can afford and only then copying the files back. This will work better
on average. It's probably overkill if you implement the first solution.
I don't know how to do that... Can you help me? (At least, I can learn
something new about scripting...)
If I'm right, trap is executed after its command finishes. So I cannot
send a SIGHUP signal from the trap.
On the other side, I have no rights on the signals from the queue. From
the FAQ of the cluster:
"To give the application a chance to exit gracefully, LSF first sends a
“friendly” signal (SIGUSR2) to
all processes of a job when its time limit is about to expire. If the
job is still running after a short
grace period, LSF sends increasingly “unfriendly” signals (SIGINT,
SIGTERM and SIGKILL). The last
one effectively kills the job."
Any ideas?
Thanks,
Gianluca
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