shm acc #run #juicefs

amber.sh

#!/bin/bash
#SBATCH --gpus=1 
#SBATCH -p gpu_4090
#SBATCH

module load amber/amber22-mpi-cuda118

mkdir -p /dev/shm/${USER}
SUB_DIR=`pwd`
WORK_DIR=/dev/shm/${USER}/abmer_work_${SLURM_JOB_ID}
mkdir -p ${WORK_DIR}
mkdir -p /dev/shm/${USER}/tmp
export TMPDIR=/dev/shm/${USER}/tmp

# Synchronize the mdinfo file in the WORK_DIR with the SUB_DIR
# by copying mdinfo from WORK_DIR to SUB_DIR every 10 seconds.
# The function runs indefinitely until it is manually stopped.
sync_mdinfo() {
    while true; do
        if [ -f ${WORK_DIR}/mdinfo ]; then
            rsync -av ${WORK_DIR}/mdinfo ${SUB_DIR} 2>/dev/null
        fi
        sleep 10
    done
}
sync_mdinfo &
SYNC_PID=$!

# 任务结束后自动转储持久化目录并移除临时文件
trap "kill ${SYNC_PID}; cd ${SUB_DIR}; rsync -av ${WORK_DIR} ./ && rm -rf ${WORK_DIR}" EXIT

cp wat_md.in ${WORK_DIR}
cp 5K21_solv.prmtop ${WORK_DIR}
cp md.rst ${WORK_DIR}
cp equi_all_subrestrain-2.rst ${WORK_DIR}
cp md.nc ${WORK_DIR}

cd ${WORK_DIR}
pmemd.cuda -O \
    -i wat_md.in \
    -o md.log \
    -c equi_all_subrestrain-2.rst \
    -p 5K21_solv.prmtop \
    -r md.rst \
    -ref equi_all_subrestrain-2.rst \
    -x md.nc