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Linux-Cluster with SLURM

gromacs/2018

SuperMUC NG with SLURM

gromacs/2018

#!/bin/bash
#SBATCH -o /home/cluster/<group>/<user>/mydir/gromacs.%j.out
#SBATCH -D /home/cluster/<group>/<user>/mydir
#SBATCH -J <job_name>
#SBATCH --get-user-env
#SBATCH --clusters=cm2_tiny
#SBATCH --ntasks=28
#SBATCH --mail-type=end
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --export=NONE
#SBATCH --time=24:00:00

module load slurm_setup
module load gromacs
module list
#generate .tpr file
gmx grompp -v -f full -o full -c after_pr -p speptide
# start mdrun
mpiexec gmx mdrun -s full -e full -o full -c after_full -g flog

#!/bin/bash
#SBATCH -o ./%x.%j.out
#SBATCH -e ./%x.%j.err
#SBATCH -D ./
#SBATCH --mail-type=END
#SBATCH --time=00:15:00
#SBATCH --partition=test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=48
#SBATCH --export=NONE
#SBATCH --get-user-env
#SBATCH --mail-user=<email_address>@<domain>
#SBATCH --account=<project id>
#SBATCH -J <job name>

module load slurm_setup
module load gromacs
module list
mpiexec gmx mdrun -v -deffnm <input filenames>

Scaling on LRZ Systems

SNGcm2cm3

Image Added

Image Added


Documentation

After loading the environment module, the $GROMACS_DOC variable points to a directory containing documentation and tutorials.

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