Gromacs Job Scripts
(Redirected from Gromacs SBATCH)
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- Note
- Use 'module spider gromacs' to find available gromacs versions. The module loads below may be outdated.
Parallel (MPI)
#!/bin/bash #SBATCH --job-name=gromacs #SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --output=gmx-%j.out #SBATCH --ntasks=2 #SBATCH --cpus-per-task=4 #SBATCH --ntasks-per-socket=1 #SBATCH --distribution=cyclic:block #SBATCH --time=24:00:00 #SBATCH --mem-per-cpu=1gb module purge ml gcc/8.2.0 openmpi/4.0.1 gromacs/2019.2 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr
GPU Acceleration (MPI + multiple GPUs)
#!/bin/bash #SBATCH --job-name=multi-gpu #SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --output=gromacs_%j.log #SBATCH --nodes=1 #SBATCH --ntasks=2 #SBATCH --tasks-per-node=2 #SBATCH --cpus-per-task=7 #SBATCH --ntasks-per-socket=1 #SBATCH --distribution=cyclic:block #SBATCH --time=2:00:00 #SBATCH --mem-per-cpu=1gb #SBATCH --partition=hpg2-gpu #SBATCH --gres=gpu:tesla:2 module load gcc/5.2.0 openmpi/1.10.2 gromacs/2016.3-CUDA export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK srun --mpi=pmi2 --accel-bind=g --ntasks=$SLURM_NTASKS gmx mdrun -v