unbiased_production.slurm

#!/bin/sh
#SBATCH -p gpu
#SBATCH -C h100
#SBATCH -n 1
#SBATCH --gpus-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --ntasks-per-node=1
#SBATCH --time=1-00:00:00

module purge
module load modules/2.1.1-20230405
source $HOME/.bashrc

activate_cluster_conda () {
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/mnt/home/mastore/cluster_conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/mnt/home/mastore/cluster_conda/etc/profile.d/conda.sh" ]; then
        . "/mnt/home/mastore/cluster_conda/etc/profile.d/conda.sh"
    else
        export PATH="/mnt/home/mastore/cluster_conda/bin:$PATH"
    fi
fi
unset __conda_setup

if [ -f "/mnt/home/mastore/cluster_conda/etc/profile.d/mamba.sh" ]; then
    . "/mnt/home/mastore/cluster_conda/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<
}

activate_cluster_conda


#you can use newer cuda if you like but be careful it needs to be the one you installed openmm with.
#export MODULEPATH=/mnt/home/gkrawezik/modules/rocky8:$MODULEPATH
#module load cuda/12.1
#export OPENMM_CUDA_COMPILER=/mnt/home/gkrawezik/local/rocky8/cuda/12.1/bin/nvcc

#load in cuda and tell openmm where to find the cuda compiler 
module load cuda/11.8
export OPENMM_CUDA_COMPILER=/mnt/sw/nix/store/3xpm36w2kcri3j1m5j15hg025my1p4kx-cuda-11.8.0/bin/nvcc


conda activate openmm_workflow

#number of steps to run
n_steps=4
init="solvate"
equil_prefix="equil"
prod_prefix="production"

if [ ! -e prod_1.rst ] ; 
then 

    input_param=" -ff charmm -t toppar.str -p ${init}.psf -c $init.crd  -irst $equil_prefix.rst --restart-timer "
    python -m openmm_workflow.unbiased -i ${prod_prefix}.inp ${input_param} -orst prod_1.rst -odcd prod_1.dcd  --platform CUDA --restart-timer 
    sbatch unbiased_production.slurm

else 
    prev_steps=$(ls prod_*\.rst  | wc -l)
    curr_step=$(($prev_steps + 1 ))
    if [ $curr_step -lt $n_steps ]; 
then

        prod_name=prod_$curr_step
        input_param=" -ff charmm -t toppar.str -p ${init}.psf -c ${init}.crd  -irst prod_${prev_steps}.rst "
        python -m openmm_workflow.unbiased -i ${prod_prefix}.inp ${input_param} -orst ${prod_name}.rst -odcd ${prod_name}.dcd  --platform CUDA 
        sbatch unbiased_production.slurm
fi

fi