MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

SOFTWARE DETAILS

ID=28, NAMD2.cuda.ucx

  • Module/Version: namd-ucx-smp/2.14
  • Toolchain/Version: iccifortcuda/2020.1.114
  • CPU instruction set: avx2
  • Example job submission script:
    1. #!/bin/bash
    2. #SBATCH --ntasks=1 --nodes=1 -A def-svassili
    3. #SBATCH --cpus-per-task=12
    4. #SBATCH --gpus-per-node=1
    5. #SBATCH --mem-per-cpu=2000 --time=3:0:0
    6. echo numsteps $1 >> run_${SLURM_JOBID}.in
    7. ml StdEnv/2020 cuda/11.4 namd-ucx-smp/2.14
    8. (( NUM_PES=$SLURM_CPUS_PER_TASK - 1 ))
    9. srun --mpi=pmi2 namd2 ++ppn $NUM_PES +idlepoll ${RUN_IN} > ${TMPFILE}
  • Benchmark submission script:
    1. #!/bin/bash
    2. #SBATCH --ntasks=1 --nodes=1 -A def-svassili
    3. #SBATCH --cpus-per-task=12
    4. #SBATCH --gpus-per-node=1
    5. #SBATCH --mem-per-cpu=2000 --time=3:0:0
    6. # Usage: sbatch $0 number_of_steps
    7. INPFILE=namd.in
    8. STEPS=$1
    9. TMPFILE=tf_${SLURM_JOBID}
    10. RUN_IN=run_${SLURM_JOBID}.in
    11. cp ${INPFILE} ${RUN_IN}
    12. echo numsteps $1 >> run_${SLURM_JOBID}.in
    13. ml StdEnv/2020 cuda/11.4 namd-ucx-smp/2.14
    14. a
    15. echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
    16. cat /proc/cpuinfo | grep "model name" | uniq
    17. (( NUM_PES=$SLURM_CPUS_PER_TASK - 1 ))
    18. srun --mpi=pmi2 namd2 ++ppn $NUM_PES +idlepoll ${RUN_IN} > ${TMPFILE}