RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations

Abstract

Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. Typically RE functionality is integrated into the molecular simulation software package. A primary motivation of the tight integration of RE functionality with simulation codes has been performance. This is limiting at multiple levels. First, advances in the RE methodology are tied to the molecular simulation code for which they were developed. Second, it is difficult to extend or experiment with novel RE algorithms, since expertise in the molecular simulation code is required. The tight integration results in difficulty to gracefully handle failures, and other runtime fragilities. We propose the RepEx framework which is addressing aforementioned shortcomings, while striking the balance between flexibility (any RE scheme) and scalability (several thousand replicas) over a diverse range of HPC platforms. The primary contributions of the RepEx framework are: (i) its ability to support different Replica Exchange schemes independent of molecular simulation codes, (ii) provide the ability to execute different exchange schemes and replica counts independent of the specific availability of resources, (iii) provide a runtime system that has first-class support for task-level parallelism, and (iv) provide a required scalability along multiple dimensions.