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18exGPUAmber18 GPU Run on exx96 Template (Heat, Equilibration, Neutral Dynamics) #!/bin/bash #SBATCH --job-name="18exGPU" #SBATCH --output=out_18exGPU #SBATCH --error=err_18exGPU #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=/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 fiPath to Above Script /home66/kscopino/AMBER18/BIN/SLURM_EXAMPLES/18exGPU.sh |