Performance evaluation and optimization of the ls1-MarDyn Molecular Dynamics code on the Cray XE6

Today Molecular Dynamics (MD) Simulations are a key tool in many research and industry areas: Biochemistry, solid state physics, chemical engineering, to just mention some. While in the past MD was a playground for some very simple problems, the ever-increasing compute power of super computers lets handle more and more complex problems: It allows increasing number of particles and more sophisticated molecular models which were too compute intensive in the past. In this paper we will present performance studies and results obtained with the ls1-MarDyn MD code on the new Hermit System (Cray XE6) at HLRS. The code’s scalability up to the full system with 100.000 cores will be discussed as well as a comparison to other platforms. Furthermore we will present in detail code analysis using the Cray software environment. From the obtained results we will discuss further improvements which will be necessary for upcoming systems in the post petascale era. Keywords-performance, optimization, Cray, XE6, molecular dynamics