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Amber20 GPU Run on exx96 Template (Heat, Equilibration, Neutral Dynamics)

#!/bin/bash
#SBATCH --job-name="20exGPU"
#SBATCH --output=out_20exGPU
#SBATCH --error=err_20exGPU
#SBATCH -N 1
#SBATCH --partition=exx96
#SBATCH -B 1:1:1
#SBATCH --cpus-per-gpu=1
#SBATCH --mem-per-gpu=7168
#SBATCH --gres=gpu:geforce_rtx_2080_s:1

# env
export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
export CUDA_HOME=/usr/local/n37-cuda-9.2
export PATH=/usr/local/n37-cuda-9.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/n37-cuda-9.2/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH="/usr/local/n37-cuda-9.2/lib:${LD_LIBRARY_PATH}"
export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH

# Amber20
source /usr/local/amber20/amber.sh

### JOB-SPECIFIC COMMANDS ###

###########
# MD Runs #
###########

# 20ps Heating step
mkdir ../HEAT/HEAT_57
pmemd.cuda -O -i /home66/kscopino/BIN/N2_SCRIPTS/20ps_heat.in  -p ../TLEAP/5JUP_N2_GCU_wat.prmtop -c ../EMIN/5JUP_N2_GCU_emin11.rst -r ../HEAT/HEAT_57/5JUP_N2_GCU_heat_57.rst -ref ../EMIN/5JUP_N2_GCU_emin11.rst -o ../HEAT/HEAT_57/5JUP_N2_GCU_heat_57.out -x ../HEAT/HEAT_57/mdcrd_heat_57 -inf ../HEAT/HEAT_57/mdinfo_heat_57
if tail -2 ../HEAT/HEAT_57/5JUP_N2_GCU_heat_57.out | head -1 | grep -q random; then
	echo 'Your heat job 5JUP_N2_GCU_57to58 has lost its GPU. Please restart.' | mailx -s "5JUP_N2_GCU_57to58 LOST GPU" kscopino@wesleyan.edu
fi

# 3ns Equilibration step
mkdir ../EQUIL/EQUIL_57
pmemd.cuda -O -i /home66/kscopino/BIN/N2_SCRIPTS/3ns_equil.in -p ../TLEAP/5JUP_N2_GCU_wat.prmtop -c ../HEAT/HEAT_57/5JUP_N2_GCU_heat_57.rst -r ../EQUIL/EQUIL_57/5JUP_N2_GCU_equil_57.rst -ref ../HEAT/HEAT_57/5JUP_N2_GCU_heat_57.rst -o ../EQUIL/EQUIL_57/5JUP_N2_GCU_equil_57.out -x ../EQUIL/EQUIL_57/mdcrd_eq_57 -inf ../EQUIL/EQUIL_57/mdinfo_eq_57
if tail -2 ../EQUIL/EQUIL_57/5JUP_N2_GCU_equil_57.out | head -1 | grep -q random; then
	echo 'Your equilibration job 5JUP_N2_GCU_57to58 has lost its GPU. Please restart.' | mailx -s "5JUP_N2_GCU_57to58 LOST GPU" kscopino@wesleyan.edu
fi

# 100ns Neutral dynamics
mkdir ../NEUTRAL/NEUTRAL_57
mkdir ../NEUTRAL/NEUTRAL_57/DATA
pmemd.cuda -O -i /home66/kscopino/BIN/N2_SCRIPTS/100ns_nd.in -p ../TLEAP/5JUP_N2_GCU_wat.prmtop -c ../EQUIL/EQUIL_57/5JUP_N2_GCU_equil_57.rst -r ../NEUTRAL/NEUTRAL_57/5JUP_N2_GCU_nd_57.rst -ref ../EQUIL/EQUIL_57/5JUP_N2_GCU_equil_57.rst -o ../NEUTRAL/NEUTRAL_57/5JUP_N2_GCU_nd_57.out -x ../NEUTRAL/NEUTRAL_57/mdcrd_nd_57 -inf ../NEUTRAL/NEUTRAL_57/mdinfo_nd_57
if tail -2 ../NEUTRAL/NEUTRAL_57/5JUP_N2_GCU_nd_57.out | head -1 | grep -q random; then
	echo 'Your neutral dynamics job 5JUP_N2_GCU_57to58 has lost its GPU. Please restart.' | mailx -s "5JUP_N2_GCU_57to58 LOST GPU" kscopino@wesleyan.edu
fi

Path to Above Script

/home66/kscopino/AMBER20/BIN/SLURM_EXAMPLES/20exGPU.sh