Amber18 GPU Run on mwgpu Template (Heat, Equilibration, Neutral Dynamics)
#!/bin/bash
#SBATCH --job-name="18mwGPU"
#SBATCH --output=out_18mwGPU
#SBATCH --error=err_18mwGPU
#SBATCH -N 1
#SBATCH --partition=mwgpu
#SBATCH -B 1:1:1
#SBATCH --cpus-per-gpu=1
# env
export PATH=/home/apps/CENTOS7/amber/amber18/bin:$PATH
export LD_LIBRARY_PATH=/home/apps/CENTOS7/amber/amber18/lib:/home/apps/CENTOS7/amber/amber18/lib64:$LD_LIBRARY_PATH
export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$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}"
### AMBER18 ###
source /share/apps/CENTOS7/amber/amber18/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/BIN/SLURM_EXAMPLES/18mwGPU.sh
