Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code

Abstract

Parallel molecular dynamics programs employing shared memory or replicated data architectures encounter problems scaling to large numbers of pro- cessors. Spatial decomposition schemes offer better performance in theory, but of- ten suffer from complexity of implementation and difficulty in load balancing. In the program NAMD 2, we have addressed these issues with a hybrid decomposi- tion scheme in which atoms are distributed among processors in regularly sized patches while the work involved in computing interactions between patches is de- composed into independently assignable compute objects. When needed, patches are represented on remote processors by proxies. The execution of compute objects takes place in a prioritized message-driven manner, allowing maximum overlap of work and communication without significant programmer effort. In order to avoid obfuscation of the simulation algorithm by the parallel framework, the algorithm associated with a patch is encapsulated by a single function executing in a separate thread. Output and calculations requiring globally reduced quantities are similarly isolated in a single thread executing on the master node. This combination of fea- tures allows us to make efficient use of large parallel machines and clusters of mul- tiprocessor workstations while presenting minimal barriers to method development and implementation.