NAMD

#!/bin/bash
#SBATCH -J namd
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=80
module purge 
module load namd/3.0.2
export PPN=$(($SLURM_CPUS_PER_TASK-1))
export PPNEND=$(($PPN-1))
 

# Devices reflect the number of gpu to use 
# This GPU 
srun -n 1 --mpi=pmi2 --distribution=block:block $NAMD +setcpuaffinity +idlepoll ++ppn $PPN +pemap 0-$PPNEND +commap $PPN +devices 0 wrapper.sh stmv_gpuoff_nve.namd > out.log
 

# should defien pemap based on nuber of gpu and number of threads 
srun --mpi=pmi2 --distribution=block:block $NAMD +setcpuaffinity ++ppn $PPN +pemap 0-38,40-78 +commap 39,79 +devices 0,1 stmv_gpuoff_nve.namd