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.     

MPI-HMMER-Boost: Distributed FPGA Acceleration

HMMER, based on the profile Hidden Markov Model (HMM) is one of the most widely used sequence database searching tools, allowing researchers to compare HMMs to sequence databases or sequences to HMM databases. Such searches often take many hours and consume a great number of CPU cycles on modern computers. We present a cluster-enabled hardware/software-accelerated implementation of the HMMER search tool hmmsearch. Our results show that combining the parallel efficiency of a cluster with one or more high-speed hardware accelerators (FPGAs) can significantly improve performance for even the most time consuming searches, often reducing search times from several hours to minutes.