Obtaining Scalable Performance from Molecular Dynamics Codes on HPC Machines
Peter V. Coveney, Fabrizio Giordanetto, Neil Stringfellow · 2002
A large amount of computational time allocated on high performance computers is used for molecular dynamics simulations, and there is increasing demand for scalable codes particularly in the eld of large molecule simulations in disciplines such as biochemistry. This paper investigates the performance of the latest generation of molecular dynamics codes on high performance machines and discusses design strategies which have led to increased scalability. Examples are given which demonstrate the ability of these codes to solve problems which scale in size with the number of processors available, as well as their scalability in terms of decreasing execution time.