umbrella_equil_pull.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

#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

module load cuda/11.8
export OPENMM_CUDA_COMPILER=/mnt/sw/nix/store/3xpm36w2kcri3j1m5j15hg025my1p4kx-cuda-11.8.0/bin/nvcc


conda deactivate &> /dev/null

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

n_steps=10
init="out"
equil_prefix="equil"
prod_prefix="umbrella_equil_pull"

input_param=" -ff amber -t toppar.str -p ${init}.parm7 -c $init.rst7  -irst $equil_prefix.rst --restart-timer "
python -u openmm_workflow.umbrella -i ${prod_prefix}.inp ${input_param} -orst $prod_prefix.rst -odcd $prod_prefix.dcd  --platform CUDA --restart-timer  | tee equil.log 

nbatch () {
    sbatch -J $( echo "$(pwd | awk -F/ '{print $(NF-2)$(NF-1)$NF}' | sed "s^_^^g" | sed "s^memb^^g" | sed "s^plumed^^g" | sed "s^CFTR^^g" | sed "s^simreadysystems^^" | sed "s^process_traj^^g"| sed "s^process_equil^^g")$(echo $1 | sed "s^\.pbs^^g"  | sed "s^\.slurm^^g" | sed "s^_^^g" | sed "s^memb^^g"  | sed "s^glob^^g" | sed "s^window^^g" | sed "s^long^^g" | sed "s^mart^^g" )" | tail -c 11 ) $1
    }


line=$(squeue -h -j $SLURM_JOBID -O timeused) # Leading '-' aids parsing.
line=$(echo -$line)

parts=( 0 0 0 0 )
index=3

while [ ${#line} -gt 0 ]; do
  parts[${index}]=${line##*[-:]}
    line=${line%[-:]*}
      ((index--))
      done

root=$(echo ${parts[*]})


used_d=$(echo $root | awk  '{print $1}')

used_h=$(echo $root | awk  '{print $2}')

total_h=$(( $used_d * 24 + $used_h))

if [  $total_h -gt 0 ] ;
then
    nbatch prod.slurm
fi