Development of GENESIS for large scale MD simulations

Speaker: Jaewoon Jung (RIKEN)
Date: Wednesday, 2 December 2015, 15:00-16:45
Session: Molecular Dynamics I
Talk type: Extra talk (30 min)

Abstract: GENESIS (GENeralized Ensemble Simulation System) is a software package for molecular dynamics (MD) simulations of macromolecules. In GENESIS, we have developed a new method for hybrid parallelization (MPI+OpenMP) using the midpoint cell method combined with the three dimensional decomposition Fast Fourier Transform (FFT). We also developed an efficient parallelization scheme of MD on hybrid CPU+GPU clusters by minimizing the communicational cost. Based on these developments, we achieved very good parallel performance on massively parallel supercomputers. On K, it is scalable up to 65,536 cores and 262,144 cores for 1 million atoms and 10 million atoms systems, enabling 57 ns/day and 35 ns/day performances, respectively. On TSUBAME CPU+GPU clusters, the same systems are scalable up to 256 and 1,024 nodes, with 45 ns/day and 15 ns/day performances. GENESIS also has various REMD algorithms (T-REMD, REUS, multi-dimensional REMD under the NVT, NPT, NPAT, and NPγT) for generalized ensemble generations.