Chao Mei

TL;DR: NAMD as mentioned in this paper is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems, which can scale to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.

TL;DR: New scalability challenges in biomolecular simulations: using much larger machines and simulating molecular systems with millions of atoms are described, and new techniques developed to overcome these challenges are described.

TL;DR: NucoLB is introduced, a topology-aware load balancer that focuses on redistributing work while reducing communication costs among and within compute nodes and takes the asymmetric memory access costs present on NUMA multi-core compute nodes, the interconnection network overheads, and the application communication patterns into account in its balancing decisions.

TL;DR: This paper studies several multicore performance issues on clusters using Intel, AMD and IBM processors in the context of the Charm++ runtime system, and presents the optimization techniques that overcome these performance issues.