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Description

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulations of large biomolecular systems. The code was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

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During run time only few files are involved in NAMD's I/O activities. As long as standard MD runs are carried out, this is unlikely to impose stress on the Lustre file system ($WORK) as long as one condition is met. Namely, file metadata operations (file stat, create, open, close, rename) should not occur at too short time intervals. First and foremost, this applies to the management of NAMD restart files. Instead of having a new set of restart files created several times per second, the NAMD input parameter restartfreq should be chosen such that they are written only every 5 minutes or in even longer intervals. For the case of NAMD replica-exchange runs the situation can be more severe. Here we already observed jobs where heavy metadata file I/O on the individual "colvars.state" files located in every replica's subdirectory has overloaded our Lustre metadata servers resulting in a severe slowdown of the entire Lustre file system. Users are advised to set corresponding NAMD input parameters such that each replica performs metadata I/O on these files in intervals not shorter than really needed, or, where affordable, that these files are written only at the end of the run.

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Job Script Examples

#!/bin/bash
#SBATCH --time 12:00:00
#SBATCH --nodes 5
#SBATCH --tasks-per-node 40

export SLURM_CPU_BIND=none

module load impi/2019.5
module load namd/2.13

mpirun namd2 inputfile > outputfile

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