MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

SOFTWARE DETAILS

ID=17, NAMD2.cuda

  • Module/Version: namd-multicore/2.14
  • Toolchain/Version: iccifortcuda/2020.1.114
  • CPU instruction set: avx2
  • Example job submission script:
    1. #!/bin/bash
    2. #SBATCH -c8 --gpus=1
    3. #SBATCH --mem-per-cpu=2000 --time=1:0:0
    4. module load StdEnv/2020 intel/2020.1.217 cuda/11.4 namd-multicore/2.14
    5. namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in
  • Benchmark submission script:
    1. #!/bin/bash
    2. #SBATCH -c8 --gpus=1
    3. #SBATCH --mem-per-cpu=2000 --time=1:0:0
    4. # Usage: sbatch submit.cuda.sh [number_of_steps]
    5. INPFILE=namd.in
    6. #------- End of user input ------
    7. STEPS=$1
    8. TMPFILE=tf_${SLURM_CPUS_PER_TASK}
    9. cp $INPFILE run.in
    10. echo numsteps $1 >> run.in
    11. module load StdEnv/2020 intel/2020.1.217 cuda/11.4 namd-multicore/2.14
    12. echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
    13. cat /proc/cpuinfo | grep "model name" | uniq
    14. # Run simulation three times
    15. namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in > $TMPFILE
    16. namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in >> $TMPFILE
    17. namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in >> $TMPFILE
    18. # Print average of three runs.
    19. echo -n "ns/day:"
    20. grep CPUTime $TMPFILE | cut -f5 -d " " | awk -v steps=$STEPS '{ total += $1; count++ } END { print count*3.6*2.4*steps*0.01/total}'
    21. #rm -f tf_* *.restart.* *.old *.BAK run.in