Benchmark of GENESIS 1.3 and 1.4 on PC clusters

  • MD conditions:
    • Force field: CHARMM
    • Integrator: VVER (PME every 2 steps)
    • Ensemble: NVE
    • Time step: 2 fs
  • Hardware and compilation options:
    • CPU: Intel Xeon Gold 6142 (2.6 GHz)
    • GPU: Geforce GTX 1080 Ti
    • Precision: Mixed precision

DHFR (23,558 atoms)

  • switch, cutoff, pairlist = 10, 12, 13.5 Å

STMV (1,066,628 atoms)

  • switch, cutoff, pairlist = 10, 12, 13.5 Å

Benchmark of GENESIS 1.0 and 1.1

  • MD conditions:
    • Integrator: VVER or RESPA (PME every 2 steps)
    • Ensemble: NVE
    • Time step: 2 fs
  • Hardware and compilation options:
    • Intel and GPU benchmarks (CPU, CPU+GPU)
      • CPU: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (2 CPU x 8 cores/node)
      • GPU: NVIDIA Tesla K20x (2 GPUs/node)
      • Compiler: openmpi 1.10.1 + intel (fortran/C) 15.0.5.223 + cuda 6.5
      • Precision : double precision (dp) or mixed precision (sp)
    • K computer benchmarks
      • CPU: SPARC64(TM) VIIIFx (8 cores/node)
      • Compiler: Fujitsu compiler
      • Precision: double precision

MSPA (216,726 atoms) on Intel

  • Force field: CHARMM c36
  • PME grid = 144, 144, 144
  • switch, cutoff, pairlist = 10, 12, 13.5 Å

STMV (1,066,628 atoms) on Intel

  • Force field: CHARMM
  • PME grid = 256, 256, 256
  • switch, cutoff, pairlist = 9, 10, 11.5 Å

STMV (1,066,628 atoms) on Intel

  • Force field: CHARMM
  • PME grid = 256, 256, 256
  • switch, cutoff, pairlist = 9, 10, 11.5 Å

27 × STMV (28,798,956 atoms) on K

  • Force field: CHARMM
  • PME grid = 512, 512, 512
  • switch, cutoff, pairlist = 9, 10, 11.5 Å

Updated: