Gromacs

Running Gromacs on CPU Node

1. Clone the demos repository:

   git clone git@github.com:CamberCloud-Inc/demos.git
   git fetch origin gromacs
   git checkout gromacs
   cd ~/demos/30-applications/03-molecular_dynamics/gromacs

2. Create the SLURM script:

   cat > run_sim.slurm << 'EOF'
   #!/bin/bash
   #SBATCH --job-name=sim_run
   #SBATCH --partition=cpu-queue
   #SBATCH --nodes=1
   #SBATCH --time=01:00:00
   #SBATCH --nodelist=cpu-queue-dy-c5x4-[1-20]
   #SBATCH --output=sim_run_%j.out
   #SBATCH --error=sim_run_%j.err
   
   spack load gromacs@2022.6
   
   srun bash sim.sh
   EOF

3. From sim.sh remove all occurrences of -nb gpu because we run on CPU only.

4. Submit the job:

   sbatch ./run_sim.slurm