Re: [AMBER] in PARALLEL does not finish

From: Jason Swails <>
Date: Mon, 12 Jul 2010 13:32:57 -0400

It may be that your machine does not have enough memory. For a modestly
sized system running a full nmode calculation, it may take about 2 GB of
memory per frame to run an nmode calculation, so your machine would have to
have at least 32 GB of memory to run 16 simultaneous calculations in this
case. Perhaps there is no error and it is just taking too much time...

You should try to run a small number of frames in serial first and see if
those finish. That way, you can diagnose whether the problem is related to
the parallel or not. If that works, perhaps try just using 2 threads, then
maybe 3, etc. You could also figure out how many threads your node can
support by looking at the memory requirements of each process. is also parallel, but uses MPI which can parallelize across
multiple nodes instead of being restricted to a single one.

Good luck!

On Mon, Jul 12, 2010 at 12:55 PM, Anselm Horn <> wrote:

> Dear all,
> I'm running an Nmode-Analysis of MM-PBSA from Amber11 (no patches) for a
> ligand-receptor-complex in parallel using the script. The
> input variable PARALLEL is set to 16, the number of cores on the local
> machine.
> However, the script does not finish properly:
> After analyzing the last computed snapshot of the complex (entry in the
> log file: "Ana entropy"), it does not proceed to compute the receptor or
> the ligand coordinate files. The computing machine still has 16
> processes running with 100%, but nothing happens, no further
> output is generated until the queuing system kills the job.
> I then tried the case with just the receptor marked for analysis in the
> file, but the same thing occurred: After computing all
> entropy contributions for the receptor snapshots the script hangs before
> doing the final statistics analysis and output. The last file generated
> is the <file>_rec.all.out.
> It seems to me that the child processes do not finish properly, but
> maybe I also have an error in some input settings?
> Has anybody experienced a similar behaviour - and found a remedy?
> I'm looking forward to your hints, because I very much appreciate the
> fact that has been made parallel.
> Regards,
> Anselm Horn
> Bioinformatik
> Institut für Biochemie
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jul 12 2010 - 11:00:03 PDT
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