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gromacs_tmpi_stream.sh
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gromacs_tmpi_stream.sh
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#!/bin/bash
OUT_DIR=$1
if [ -z "${OUT_DIR}" ]; then
OUT_DIR=".."
fi
OUT_FILE=${OUT_DIR}/gromacs_tmpi_stream.txt
# Support execution from outside root dir
_CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd)"
cd $_CWD
cd adh_dodec/
tar zxf adh_dodec.tar.gz
# 1GPU
echo "benchmark,adh_dodec,gpus_1,rank_1,thread_48" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 1 -ntomp 48 -noconfout -nb gpu -bonded cpu -pme gpu -v -gpu_id 0 -nstlist 100 -dlb yes -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 2GPUs
echo "benchmark,adh_dodec,gpus_2,rank_2,thread_16" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 2 -ntomp 16 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 01 -nstlist 200 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 4GPUs
echo "benchmark,adh_dodec,gpus_4,rank_4,thread_16" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 4 -ntomp 16 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 0123 -nstlist 400 -dlb yes -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 8GPUs
echo "benchmark,adh_dodec,gpus_8,rank_4,thread_4" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 8 -ntomp 4 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 01234567 -nstlist 400 -dlb yes -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
cd ..
cd stmv/
tar zxf stmv.tar.gz
# 1GPU
echo "benchmark,stmv,gpus_1,rank_1,thread_48" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 1 -ntomp 48 -noconfout -nb gpu -bonded cpu -pme gpu -v -gpu_id 0 -nstlist 200 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 2GPUs
echo "benchmark,stmv,gpus_2,rank_3,thread_16" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 3 -ntomp 16 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gputasks 011 -nstlist 200 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 4GPUs
echo "benchmark,stmv,gpus_4,rank_8,thread_8" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 8 -ntomp 8 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 0123 -nstlist 400 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 8GPUs
echo "benchmark,stmv,gpus_8,rank_8,thread_8" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 8 -ntomp 8 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 01234567 -nstlist 400 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
cd ..
cd cellulose_nve/
tar zxf cellulose_nve.tar.gz
# 1GPU
echo "benchmark,cellulose,gpus_1,rank_1,thread_48" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 1 -ntomp 48 -noconfout -nb gpu -bonded cpu -pme gpu -v -gpu_id 0 -nstlist 200 -dlb yes -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 2GPUs
echo "benchmark,cellulose,gpus_2,rank_4,thread_16" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 4 -ntomp 16 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 01 -nstlist 200 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 4GPUs
echo "benchmark,cellulose,gpus_4,rank_4,thread_16" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 4 -ntomp 16 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 0123 -nstlist 400 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}
# 8GPUs
echo "benchmark,cellulose,gpus_8,rank_8,thread_8" | tee -a ${OUT_FILE}
gmx mdrun -pin on -nsteps 100000 -resetstep 90000 -ntmpi 8 -ntomp 8 -noconfout -nb gpu -bonded gpu -pme gpu -npme 1 -v -gpu_id 01234567 -nstlist 400 -s topol.tpr 2>&1 | tee -a ${OUT_FILE}