Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
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Gemini, the network for the new Cray XE/XK systems, features low latency, high bandwidth and strong scalability. Its hardware support for remote direct memory access enables efficient implementation of the global address space programming languages. Although the user Generic Network Interface (uGNI) provides a low-level interface for Gemini with support to the message-passing programming model (MPI), it remains challenging to port alternative programming models with scalable performance. CHARM++ is an object-oriented message-driven programming model. Its applications have been shown to scale up to the full Jaguar Cray XT machine. In this paper, we present an implementation of this programming model on uGNIfor the Cray XE/XK systems. Several techniques are presented to exploit the uGNI capabilites by reducing memory copy and registration overhead, taking advantage of the persistent communication, and improving intra-node communication. Our micro-benchmark results demonstrate that the uGNI-based runtime system outperforms the MPI-based implementation by up to $50\%$ in terms of message latency. For communication intensive applications such as N-Queens, this implementation scales up to 15,360 cores of a Cray XE6 machine and is 70%faster than the MPI-based implementation. In molecular dynamics application NAMD, the performance is also considerably improved by as much as 18%.