GENESIS (GENeralized-Ensemble SImulation System) is an application for performing molecular dynamics simulations of biomolecular systems. OCTOPUS enables the use of GENESIS 2.1.5 via batch requests.
Basic Usage
This section explains how to run GENESIS using OCTOPUS. For more detailed usage instructions, please refer to the GENESIS Official Web Page.
GENESIS can only be executed through batch requests. Please connect to the front-end node, create the input data and job script required for the calculation, and then submit it as a batch job.
Input data and job scripts can be created on your local terminal or by connecting to the front-end node and using a text editor such as Vim, vi or emacs. For instructions on how to use the editor, please refer to the Editor Usage Page.
Environment Setup
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Module files are available.
The module file to load depends on the calculation precision. After loading BaseApp, please load a GENESIS module of your desired precision.
$ module load BaseApp
$ module load GENESIS/2.1.5.double # Double-precision
$ module load GENESIS/2.1.5.mixed # Mixed-precision
$ module load GENESIS/2.1.5.single # Single-precision
Creating a Job Script
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The following is an example of a job script for running GENESIS in mixed-precision with 16 MPI processes and 4 threads. There are no specific requirements for the filename, but it is named genesis.sh in this section.
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#!/bin/bash #PBS -q OCT #PBS --group=[group name] #PBS -l elapstim_req=01:00:00 #PBS -l cpunum_job=64 #PBS -v OMP_NUM_THREADS=4 #PBS -T intmpi #PBS -b 1 module load BaseApp module load GENESIS/2.1.5.mixed cd $PBS_O_WORKDIR mpirun ${NQSV_MPIOPTS} -np 16 spdyn p16.inp > p16.out |
For other lines in the job script, please refer to here.
Submitting a Job Script
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Once the input file and job script are complete, submit the job.
$ qsub genesis.sh
If the execution is successful, the calculation results will be saved in the result file.
