MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=15, PMEMD.cuda

  • Module/Version: amber/20.12-20.15
  • Toolchain/Version: gofbc/2020.1.403.114
  • CPU instruction set: avx512
  • Example job submission script:
    1. #!/bin/bash
    2. #SBATCH -c1 --gpus-per-node=1 --mem-per-cpu=2000 --time=1:0:0
    3. module --force purge
    4. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 amber/20.12-20.15
    5. pmemd.cuda -O -i pmemd.in -o production.log -p prmtop.parm7 -c restart.rst7
  • Benchmark submission script:
    1. #!/bin/bash
    2. #SBATCH -c1 --gpus-per-node=1
    3. #SBATCH --mem-per-cpu=2000 --time=1:0:0
    4. # Usage: sbatch submit.cuda.sh]
    5. INPFILE=pmemd_prod.in
    6. STEPS=20000
    7. # End of user input
    8. TMPFILE=tf_${SLURM_CPUS_PER_TASK}
    9. LOGFILE=production_${SLURM_CPUS_PER_TASK}.log
    10. module --force purge
    11. ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 amber/20.12-20.15
    12. # Print resource info
    13. echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
    14. cat /proc/cpuinfo | grep "model name" | uniq
    15. # Run simulation three times
    16. pmemd.cuda -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    17. grep "NonSetup CPU time" $LOGFILE > $TMPFILE
    18. pmemd.cuda -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    19. grep "NonSetup CPU time" $LOGFILE >> $TMPFILE
    20. pmemd.cuda -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    21. grep "NonSetup CPU time" $LOGFILE >> $TMPFILE
    22. # Print average of three runs.
    23. echo -n "ns/day:"
    24. awk -v steps=$STEPS '{total += $5; count++ } END { print count*3.6*2.4*steps*0.01/total}' $TMPFILE
    25. #rm $TMPFILE $LOGFILE mdinfo mdcrd restrt