MODYLAS is an Open Source Software (license permission required) package for general-purpose classical molecular dynamics. The software supports various methods required for the molecular dynamics computation in nano-molecules and biomolecules including the Fast Multiple Method (FMM) of treating long-range electrostatic interactions. For the official website, please visit here.
MODYLAS execution is only allowed to process by batch request. An example job script and the job execution method are explained below.
Writting a Job Script
The following example is a job script for running MODYLAS with 8 MPI processes x 24 threads (using 8 nodes). Although a file name is not specified, we named "modylas.sh" in this section.
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#!/bin/bash #PBS -q SQUID #PBS -l cpunum_job=76 #PBS --group=[group name] #PBS -l elapstim_req=01:00:00 #PBS -b 8 #PBS -T intmpi #PBS -v OMP_NUM_THREADS=24 #PBS -v PARALLEL=24 module load BaseApp module load MODYLAS/1.0.4 cd $PBS_O_WORKDIR mpirun ${NQSV_MPIOPTS} -np 8 modylas pyp111 |
For other lines of the job script, see here.
How to execute
Submit the job script you created.
% qsub modylas.sh
How to check the status of the submitted job is here. When the execution is finished, the calculation result is output to the result file.
