Gromacs-Sapelo2old

Category

Chemistry

Program On

Sapelo2

Version

2016.4, 2018.1

Author / Distributor

First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE) Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE)

Description

GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.[

Running Program

Also refer to Running Jobs on Sapelo2.

For more information on Environment Modules on Sapelo2 please see the Lmod page.

Version 2016.4

This version was compiled with GCC 5.4.0 and it uses CUDA 8.0.61. It was not patched with PLUMED. It is installed in /usr/local/apps/eb/GROMACS/2016.4-foss-2016b-GPU-enabled. To use this version of Gromacs, please first load its module with

module load GROMACS/2016.4-foss-2016b-GPU-enabled

Version 2018.1

This version was compiled with GCC 5.4.0 and it uses CUDA 8.0.61. It was patched with PLUMED 2.4.2. It is installed in /usr/local/apps/eb/GROMACS/2018.1-foss-2016b-PLUMED-2.4.2-cuda-8.0.61-intel. To use this version of Gromacs, please first load its module with

module load GROMACS/2018.1-foss-2016b-PLUMED-2.4.2-cuda-8.0.61-intel

Note that this version of Gromacs does not run on the nodes with K20Xm GPU cards. Even though the name of the module has the suffix "intel" to indicated that it was compiled on an Intel processor, the binaries should also work on the AMD nodes in the batch queue.

Sample job submission script sub.sh to run v. 2018.1 and use 10 CPU cores and 1 GPU K40 card:

#PBS -S /bin/bash
#PBS -q gpu_q
#PBS -N testjob
#PBS -l nodes=1:ppn=10:gpus=1:K40
#PBS -l walltime=4:00:00:00
#PBS -l mem=20gb

cd $PBS_O_WORKDIR

module load GROMACS/2018.1-foss-2016b-PLUMED-2.4.2-cuda-8.0.61-intel

source $EBROOTGROMACS/bin/GMXRC

gmx mdrun -nt $PBS_NP [options]

where [options] need to be replaced by the arguments you wish to use. The job name testjob should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node (ppn), a suitable wall time (the example above specifies 4 days), and a suitable amount of memory.

Submit the job to the queue with

qsub sub.sh

Documentation

Please see http://www.gromacs.org/

Installation

• Version 2016.4 is installed in /usr/local/apps/eb/GROMACS/2016.4-foss-2016b-GPU-enabled
• Version 2018.1 (patched with PLUMED 2.4.2) is installed in /usr/local/apps/eb/GROMACS/2018.1-foss-2016b-PLUMED-2.4.2-cuda-8.0.61-intel

System

64-bit Linux