Re: NAMD hangs with replica option

From: Josh Vermaas (
Date: Mon Jan 10 2022 - 08:35:49 CST

There is definitely a bug in the 2.14 MPI version. One of my students
has noticed that anything that calls NAMD die isn't taking down all the
replicas, and so the jobs will continue to burn resources until they
reach their wallclock limit.

However, the key is figuring out *why* you are getting an error. I'm
less familiar with metadynamics, but at least for umbrella sampling, it
is pretty typical for each replica to write out its own set of files.
This is usually done with something like:

outputname somename.[myReplica]

Where [myReplica] is a Tcl function that evaluates to the replica ID for
each semi-independent simulation. For debugging purposes, it can be very
helpful for each replica to spit out its own log file. This is usually
done by setting the +stdout option on the command line.

mpirun -np 28 namd2 +replicas 2 namd_metadynamics.inp +stdout


On 1/9/22 2:34 PM, jing liang wrote:
> Hi,
> I am running a metadynamics simulation with NAMD 2.14 MPI version.
> SLURM is being used for job scheduling, the way to run it by using 2
> replica on a 14 cores node is as follows:
> mpirun -np 28 namd2 +replicas 2 namd_metadynamics.inp
> In fact, I have tried upto 8 replicas and the resulting pmf looks very
> similar
> to what I obtain with other methods such as ABF. The problem is that
> by using
> the replicas option, the simulation hangs right at the end. I have
> looked at the
> output files and it seems that right at the end NAMD wants to access
> some files
> (for example, *.xsc, *hills*, ...) that already exist and NAMD throws
> an error.
> My guess is that this could be either a misunderstanding from my side
> in running NAMD with replicas or a bug in the MPI version.
> Have you observed that issue previously? Any comment is welcome. Thanks

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!qxoAM7sAMD7OOX4XekBXNyDSDwyL5GBEa1rt9qiV-ok0frmrn27DsCUvWPCFTfWyyQ$ 

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