GROMACS

To load the module for the default version of GROMACS, which initializes your environment for the GROMACS application, use module load gromacs.

To execute a serial GROMACS versions 5 program interactively, simply run it on the command line, e.g.:

gmx pdb2gmx

Parallel multinode GROMACS versions 5 programs should be run in a batch environment with srun, e.g.:

srun gmx_mpi_d mdrun

Note that '_mpi' indicates a parallel executable and '_d' indicates a program built with double precision ('_gpu' denotes a GPU executable built with CUDA).  See the module help output for specific versions for more details on executable naming conventions.

When you log into Pitzer you are actually connected to a login node. To  access the compute nodes, you must submit a job to the batch system for execution. Batch jobs can request multiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session on Pitzer, one can run the following command:

sinteractive -A <project-account> -N 1 -n 40 -t 1:00:00

which gives you one node and 40 cores (-N 1 -n 40) with 1 hour (-t 1:00:00). You may adjust the numbers per your need.

Non-interactive Batch Job (Parallel Run)

A batch script can be created and submitted for a serial, cuda (GPU), or parallel run. You can create the batch script using any text editor in a working directory on the system of your choice. Sample batch scripts and input files for all types of hardware resources are available here:

~srb/workshops/compchem/gromacs/

This simple batch script demonstrates some important points:

#!/bin/bash
# GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
# see fwspider_tutor.pdf
#SBATCH --job-name fwsinvacuo.pitzer
#SBATCH --nodes=2 --ntasks-per-node=28
#SBATCH --account=PZS0711
# turn off verbosity for noisy module commands
set +vx
module purge
module load intel/18.0.3
module load mvapich2/2.3
module load gromacs/2018.2
module list
set -vx

cd $SLURM_SUBMIT_DIR
echo $SLURM_SUBMIT_DIR
sbcast -p 1OMB.pdb $TMPDIR/1OMB.pdb
sbcast -p em.mdp $TMPDIR/em.mdp

cd $TMPDIR
mpiexec -ppn 1 gmx pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
mpiexec -ppn 1 gmx editconf -f fws.gro -d 0.7

mpiexec -ppn 1 gmx editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
mpiexec -ppn 1 gmx grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr -maxwarn 1
mpiexec -ppn 1 ls -l 
mpiexec gmx_mpi mdrun -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr

cp -p * $SLURM_SUBMIT_DIR/