基因序列分析软件Hmmpfam的可扩展并行性能优化

基于MPI(message passing interface)平台实现了HMMER软件包核心程序之一Hmmpfam的大规模并行计算.该版本针对原PVM(parallel virtual machine)并行版本在并行规模扩大后,master易成为通信瓶颈的问题,对通信结构进行了优化,提出了一种新的三层通信结构,在序列和HMM模型的两个层次上实现了并行化,并分别提供了有效的负载平衡策略,同时优化了I/O性能,在700多台处理机上达到95%的效率.

Scalable Parallel Performance Optimization of the Gene Sequence Analyzing Software Hmmpfam

A scalable parallel MPI (message passing interface) version of the popular protein structure prediction tool Hmmpfam is presented, which is one of the kernel programs in the HMMER package. The master process in the previous PVM (parallel virtual machine) version is a communication bottleneck, and the speedup will decrease rapidly when running on large scale parallel systems. A novel three-level communication structure is presented, by which the parallel processing at sequence level and HMM model level is obtained in both. Meanwhile, the load-balance strategies to sequence level and HMM model level distribution are provided separately. Since disk access for getting HMM model costs very much, a so-called once load strategy is provided to reduce the cost. By all these optimization methods, 95% in parallel efficiency is achieved when running on a parallel computer containing more than 700 processors.