MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=162

  • Dataset: 4cg1
  • Software: SANDER.QUICK.cuda.MPI (ambertools/21-gofbc-2020.1.403.114-avx2)
  • Resource: 12 tasks, 1 cores, nodes, 12 GPUs, with NVLink
  • CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
  • GPU: Tesla-V100-SXM2-32GB, 8 cores/GPU
  • Simulation speed: 0.0106064 ns/day
  • Efficiency: 39.3 %
  • Site: Cedar
  • Date: Feb. 9, 2022, 11:13 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH -A def-svassili
    #SBATCH --ntasks=12 --cpus-per-task=1 --nodes=3
    #SBATCH --gpus-per-task=v100l:1
    #SBATCH --mem-per-cpu=4000 --time=02:00:00

    module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21
    source $EBROOTAMBERTOOLS/amber.sh

    srun sander.quick.cuda.MPI -O -i B3LYP.in -p complex_solv_PNP.prmtop -c mini-QMMM_4.rst -ref mini-QMMM_4.rst -o stdout

  • Notes:

  • Simulation input file:

    Applying constraints on specific distances of the substrate specially Ser-substrate, substrate-W185, Meth
    &cntrl
    nstlim=40, dt=0.001,
    ntpr=2, ntwr=1000, ntwx=1000,
    ntt=3, temp0=310.0, gamma_ln=1.0, ig=-1,
    taup=2.0,
    ntc=2, ntf=2, iwrap=1,
    cut = 12.0,
    ntr=0,
    nmropt=0,
    ifqnt=1
    /
    &qmmm
    iqmatoms=840,841,842,843,844,845,846,847,848,1914,1915,1916,1917,1918,1919,1920,1921,1922,1905,1906,1907,1908,1909,1910,1911,1912,1913,3943,3944,3946,3948,3947,3942,3945,3949,3950,3951,3952,3953,3954,3955,3956,3957,3958,3959,3960,3961,
    qmcharge=0,
    spin=1
    qm_theory="quick",
    qmmm_int=5,
    qm_ewald=0,
    /
    &quick
    method = "B3LYP",
    basis = "6-31G*",
    /