gromacs

About

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

An extensive selection of documentation and tutorials is available. Please refer to this documentation to learn how to achieve specific simulation outcomes, the necessary control parameters, and required formats for input/output files.

Versions and Availability

Module Names for gromacs on qb2
Machine Version Module Name
None Available N/A N/A
▶ **FIX-ME** FAQ?

Usage

A sample script to run GROMACS follows:

 #!/bin/bash
 #PBS -A your_allocation
 #PBS -q checkpt
 #PBS -l nodes=1:ppn=8
 #PBS -l walltime=12:00:00
 #PBS -V
 #PBS -j oe
 #PBS -N gromacs_test
 
 # mdrun_d is the MPI version of mdrun.  
 export EXEC=mdrun_d
 export WORKDIR=$PBS_O_WORKDIR
 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
   
 cd $WORKDIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -s fws_em.tpr \
        -o fws_em.trr -c fws_b4pr.pdb -e em.edr -g em.log

The script is then submitted using qsub:

$ qsub job_script

where job_script is the name you gave the script file.

▶ QSub FAQ?

Portable Batch System: qsub

qsub

All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.

Usage
$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.

Example Job Script
 #!/bin/bash
 #
 # Use "workq" as the job queue, and specify the allocation code.
 #
 #PBS -q workq
 #PBS -A your_allocation_code
 # 
 # Assuming you want to run 16 processes, and each node supports 4 processes, 
 # you need to ask for a total of 4 nodes. The number of processes per node 
 # will vary from machine to machine, so double-check that your have the right 
 # values before submitting the job.
 #
 #PBS -l nodes=4:ppn=4
 # 
 # Set the maximum wall-clock time. In this case, 10 minutes.
 #
 #PBS -l walltime=00:10:00
 # 
 # Specify the name of a file which will receive all standard output,
 # and merge standard error with standard output.
 #
 #PBS -o /scratch/myName/parallel/output
 #PBS -j oe
 # 
 # Give the job a name so it can be easily tracked with qstat.
 #
 #PBS -N MyParJob
 #
 # That is it for PBS instructions. The rest of the file is a shell script.
 # 
 # PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS:
 #
 #   1. Copy the necessary files from your home directory to your scratch directory.
 #   2. Execute in your scratch directory.
 #   3. Copy any necessary files back to your home directory.

 # Let's mark the time things get started.

 date

 # Set some handy environment variables.

 export HOME_DIR=/home/$USER/parallel
 export WORK_DIR=/scratch/myName/parallel
 
 # Set a variable that will be used to tell MPI how many processes will be run.
 # This makes sure MPI gets the same information provided to PBS above.

 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`

 # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".

 cp $HOME_DIR/hydro $WORK_DIR
 cd $WORK_DIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro

 # Mark the time processing ends.

 date
 
 # And we're out'a here!

 exit 0

Resources

Usefule links for running GROMACS with hybrid MPI and OpenMP.

Plesae refer to GROMACS 4.6.7 User Manual for running GROMACS with GPU.

Last modified: July 23 2015 10:56:47.