Optimizing COOP languages: study of a protein dynamics program

Fine-grained concurrent object-oriented programming (COOP) models can simplify the programming of irregular parallel applications but are often perceived as inefficient. In this paper, we study implementation techniques to obtain efficient parallel execution of fine-grained COOP languages using a medium-sized protein dynamics program. We found that even with high data locality and good sequential code efficiency, an implementation using only thread-oriented optimizations and software multithreading fails to achieve parallel efficiency. The two major sources of overhead are the lack of processor-level data reuse and fine-grained threads for remote object accesses. Two processor-oriented optimizations, processor-level caching and communication grouping, overcome these inefficiencies and achieve performance comparable to a highly-tuned SPMD program