Gromacs
This shows an example job submission file for running Gromacs on Anvil. The Gromacs versions can be changed depending on the available modules on Anvil (see module spider gromacs).
#!/bin/bash
# FILENAME: myjobsubmissionfile
#SBATCH -A myallocation # Allocation name (run 'mybalance' command to find)
#SBATCH -p shared #Queue (partition) name
#SBATCH --nodes=1 # Total # of nodes
#SBATCH --ntasks=16 # Total # of MPI tasks
#SBATCH --time=96:00:00 # Total run time limit (hh:mm:ss)
#SBATCH --job-name myjob # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
# Manage processing environment, load compilers and applications.
module --force purge
module load gcc/11.2.0
module load openmpi/4.0.6
module load gromacs/2021.2
module list
# Launch md jobs
#energy minimizations
mpirun -np 1 gmx_mpi grompp -f minim.mdp -c myjob.gro -p topol.top -o em.tpr
mpirun gmx_mpi mdrun -v -deffnm em
#nvt run
mpirun -np 1 gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
mpirun gmx_mpi mdrun -deffnm nvt
#npt run
mpirun -np 1 gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
mpirun gmx_mpi mdrun -deffnm npt
#md run
mpirun -np 1 gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr
mpirun gmx_mpi mdrun -deffnm md
The GPU version of Gromacs was available within ngc container on Anvil. Here is an example job script.
#!/bin/bash
# FILENAME: myjobsubmissionfile
#SBATCH -A myallocation-gpu # Allocation name (run 'mybalance' command to find)
#SBATCH -p gpu #Queue (partition) name
#SBATCH --nodes=1 # Total # of nodes
#SBATCH --ntasks=16 # Total # of MPI tasks
#SBATCH --gpus-per-node=1 #Total # of GPUs
#SBATCH --time=96:00:00 # Total run time limit (hh:mm:ss)
#SBATCH --job-name myjob # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
# Manage processing environment, load compilers and applications.
module --force purge
module load modtree/gpu
module load ngc
module load gromacs
module list
# Launch md jobs
#energy minimizations
gmx grompp -f minim.mdp -c myjob.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em -ntmpi 4 -ntomp 4
#nvt run
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt -ntmpi 4 -ntomp 4 -nb gpu -bonded gpu
#npt run
gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -deffnm npt -ntmpi 4 -ntomp 4 -nb gpu -bonded gpu
#md run
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr
gmx mdrun -deffnm md -ntmpi 4 -ntomp 4 -nb gpu -bonded gpu