Table des matières

Benchmark for NAMD on Jean Zay

JUBE 2.2.2 was used to benchmark NAMD.

A CPU scalibility test is performed by varying the number of nodes used . A GPU scalability test is performed on one node (due to limitations of the current installation).

Bench1

Complete page

Description

  • Type: Molecular dynamic
  • Number of atoms: 80814
  • Step size: 2fs
  • Number of steps: 1e5
  • Constraints:
    • Ensemble: NPT (Langevin temperature: 310K, Langevin pressure: 1 atm)
    • Rigid bonds (all)
  • Electrostatics: Particle-Mesh Ewald
  • Non bonded cutoff: 12 Angstroms