Aron already mentioned the negative values of ntwr, which is good advice
and will do what you want probably better than the 2-restart approach.
Other unsolicited advice based on my experience -- set nstlim to something
that will actually finish within the amount of time. Most queuing systems
will allow you to submit a stack of jobs that will execute one right after
the other (via dependencies). If you are using PBS/torque, see this page
as a quick intro to taking full(er) advantage of its capabilities:
http://jswails.wikidot.com/using-pbs
Also, I would suggest writing restart files infrequently -- maybe only 5
times the entire simulation. Restart files are by far the most expensive
things to write out, since they're written (typically) in ASCII at higher
precision, and with velocities as well as coordinates. This makes them well
over 2x larger than a single frame of a mdcrd file. By setting ntwr =
-nstlim / 5, you will get at most 5 restarts and will lose at most 1/5 of
the total amount of data you were expecting.
HTH,
Jason
P.S., if you use SGE instead of Torque/PBS, you can still set up
dependencies, but the usage is slightly different. Manual pages help here!
On Wed, Jan 23, 2013 at 5:17 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Dear AMBER users,
>
> Is it possible to save 2 restart (.rst) files instead of one every ntwr
> steps, namely the current one (e.g. trajectory.rst) and the previous one
> (e.g. trajectory.old.rst). For some reason the queueing system on the
> supercomputer I am using cannot resume the simulation from the previous one
> if the previous has finished in less that 24 hours. For instance AMBER runs
> 6 ns/day for my system so in the configuration file I put "nstlim=5000000,
> dt=0.002". This raises the problem that the queueing system may kill the
> job while AMBER writes the restart file, hence the next job cannot start.
> That results to a loss of 24 GPU hours.
>
>
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 23 2013 - 15:30:04 PST
