Characterization of Smith-Waterman sequence database search in X10
Y. Ji, Li Liu, Guangwen Yang · 2012
Productivity and performance are always viewed as two sides of parallel programming languages. X10 is a new object-oriented parallel language for both high-productivity and high-performance. To help the development of X10, we characterize the performance of X10 in bioinformatics using the fundamental application Smith-Waterman (SW) sequence database search. We implement the SW application in X10 on multi-core shared-memory architecture. Through comparing with three SW implementations in C++, we make following suggestions for X10 as well as its compiler.