GROMACS

GROMACS

Gromacs

Contents

            1. Description

            2. Requirement

            3. How to run job Gromacs using HPC

            4. Contact Us

Description:

A molecular dynamics package primarily designed for biomolecular systems.
http://www.gromacs.org/

Requirement

Step 1: Please register to UTM HPC Account
Step 2: HPC admin (hpc@utm.my) will sent HPC account to your email.

How to run job Gromacs using HPC

Submit a Gromacs job

In the example below the input files curcumin8.tpr will be run after submit a job using PBS script, pbs-script. For example, create a submission script file called pbs-script that contains the lines below. This example requests one node and sixteen processor cores.

#!/bin/sh

#PBS -l nodes=1:ppn=16

TPR_FILE=curcumin8.tpr
EXEC=mdrun_mpi
PROGRAM="$VO_ACADEMICGRID_SW_DIR/gromacs/bin/$EXEC"

cd $PBS_O_WORKDIR

export PATH=$MPI_OPENMPI_PATH/bin:$PATH
export LD_LIBRARY_PATH=$MPI_OPENMPI_PATH/lib:$VO_ACADEMICGRID_SW_DIR/gromacs/lib:$LD_LIBRARY_PATH

mpiexec $PROGRAM -s $TPR_FILE -c -cpo

Transfering Files & Submitting Job

Then, upload the submission script above and your input file to the HPC using WinSCP tool. To submit a job, please using a Putty tool and run the command below. How to access the HPC server, please go to our New User Guide page.
 

Submit the Gromacs submission job to the queue:

Users can submit the job using two options as below. The pbs-script name below is the name of your submission script.

qsub -q bigmem pbs-script
OR
qsub -q hpc pbs-script
Please note that queue for hpc above have 8 core’s for each cluster/node so if you are using this cluster please make sure in the script, you state “ppn=8″ to make sure your job can run.

Contact Us

Any problem about HPC, please email to hpc@utm.my or our facebook (Gromacs)