Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures

Parallel Molecular Dynamics: Implications for Massively Parallel Machines

Molecular dynamics simulation is a class of applications that require reducing the execution time of xed-size problems. This reduction in execution time is important to drug design and protein interaction studies. Many implementations of parallel molecular dynamics have been developed, but very little work has addressed issues related to the use of machines with 50,000 processors for modest-siz...

Parallel Molecular Dynamics: Communication Requirements for Massively Parallel Machines

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of maten'als to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of fu iun massively parallel processing systems for modest-sized problems in ihe range of 50,000 a t o m and th...

Parallel Molecular Dynamics: Communication Requirements for Massively Parallel Machine

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. Many implementations of parallel molecular dynamics have been developed , but few groups have addressed issues related to the use of massively parallel machines with 100K to 1M processors for small to modes...

High Performance Networks for Massively Parallel Architectures

The past few years have seen a rise in popularity of massively parallel architectures that use fat-trees as their interconnection networks. In this paper we study the communication performance of a parametric family of fat-trees, the k-ary n-trees, built with constant arity switches interconnected in a regular topology. Through simulation on a 4-ary 4-tree with 256 nodes, we analyze some varian...

Compiling FORTRAN for Massively Parallel Architectures