Bede Scripts

All molecular simulation software on Bede is compiled and looked after by the HECBioSim consortia support, if you have problems with any of the consortium compiled codes on Bede then please contact This email address is being protected from spambots. You need JavaScript enabled to view it. 

AMBER 18

An example of using AMBER 18 on a single node and single GPU.

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
#SBATCH -J jobname

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load amber/18

srun pmemd.cuda -O -i benchmark.in -c benchmark.rst -p benchmark.top -o benchmark.out

Gromacs 2020.3

An example using a single GPU on a single node.

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
#SBATCH -J jobname
#SBATCH -p gpu

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load gromacs/2020.3

gmx mdrun -deffnm benchmark -pin on -ntmpi 1 -ntomp 32 -nb gpu -bonded gpu -pme gpu


An example using a single GPU on a single node using the NVidia performance upgrades. A nice write up can be found here

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
#SBATCH -J jobname
#SBATCH -p gpu

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load gromacs/2020.3

# Single GPU NVidia optimisations on
export GMX_FORCE_UPDATE_DEFAULT_GPU=true

gmx mdrun -deffnm benchmark -pin on -ntmpi 1 -ntomp 32 -nb gpu -bonded gpu -pme gpu -nstlist 400

An example using a four GPUs on a single node using the NVidia performance upgrades. This is using thread MPI and not the external MPI library. Also note, this is only really worth it if you have a very large system 2-3M+ atoms, if time to solution is not an issue, then you are better off running 4 single GPU simulations and having the statistics. A nice write up can be found here

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --gres=gpu:4
#SBATCH --time=01:00:00
#SBATCH -J jobname
#SBATCH -p gpu

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load gromacs/2020.3

# Single GPU NVidia optimisations on
export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true
export GMX_FORCE_UPDATE_DEFAULT_GPU=true

gmx mdrun -deffnm benchmark -pin on -ntmpi 4 -ntomp 32 -nb gpu -bonded gpu -pme gpu -nstlist 400

NAMD 2.14

Here is an example of how to submit a single node single GPU simulation on Bede.

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=5
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
#SBATCH -J jobname
#SBATCH -p gpu

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load namd/2.14

namd2 +p $SLURM_NTASKS_PER_NODE +setcpuaffinity +devices $CUDA_VISIBLE_DEVICES ./benchmark.in &> bench.out

NAMD 3.0

The version of NAMD 3.0 currently installed on Bede is the alpha build 7, do note this is an alpha version currently but if you wish to test it with your work then here is an example script for a single node with a single GPU.

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:1
#SBATCH --time=01:00:00
#SBATCH -J jobname
#SBATCH -p gpu

# Replace "account-code" with your Bede project account code.
#SBATCH --account=account-code

module load hecbiosim
module load namd/3.0-alpha7-singlenode

namd3 benchmark.in > benchmark.out