Kurzak Jakub, Pettitt B Montgomery
Department of Computer Science, University of Houston, Houston, Tx 77204-5004.
J Algorithm Comput Technol. 2008;2(4):557-579. doi: 10.1260/174830108786231722.
Biomolecular simulations require increasingly efficient parallel codes. We present an efficient communication algorithm for irregular problems exhibiting an all-to-many communication pattern. The algorithm is developed using message passing on distributed memory machines and assumes explicit knowledge of the interconnection topology. The algorithm maximizes locality of interprocessor communication by adopting to an arbitrary interconnection topology and at the same time takes multiprocessor nodes into account. The solution is incorporated into our implementation of the fast multipole method with periodic boundary conditions used for molecular dynamics simulations, but we believe it generalizes to many algorithms demonstrating an all-to-many communication pattern. We show that an irregular algorithm can be forced to behave like a systolic algorithm.
生物分子模拟需要越来越高效的并行代码。我们提出了一种针对呈现全对多通信模式的不规则问题的高效通信算法。该算法是在分布式内存机器上使用消息传递开发的，并假设对互连拓扑有明确的了解。该算法通过采用任意互连拓扑来最大化处理器间通信的局部性，同时考虑了多处理器节点。该解决方案已被纳入我们用于分子动力学模拟的具有周期性边界条件的快速多极方法的实现中，但我们相信它可以推广到许多展示全对多通信模式的算法。我们表明，一种不规则算法可以被强制表现得像一种脉动算法。
