gianluca santarossa wrote:
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
Well in the real world, your simulations are likely to be sufficiently
similar that you can keep a spreadsheet of calculation rates as a
function of the number of particles and interpolate readily...
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.
I was theorizing that sending a SIGHUP would be possible... you need to
catch the signal to send your output back, but you need to send one to
the child process to get the buffers flushed. Actually man mdrun
suggests that gromacs doesn't listen for SIGHUP at all, so ignore me.
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."
man mdrun suggests that unless you were able to copy output back after
the SIGTERM, you'd struggle.
A plan B would be to intercept the SIGUSR2 with your script and send a
SIGTERM to the simulation... if that's possible.
Mark
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