Title :
Programming environment based on distributed shared arrays for high-performance scientific computing
Author :
Nomoto, Akira ; Kaneko, Wataru ; Terada, Tohru ; Nakamura, Shugo ; Shimizu, Kentaro
Author_Institution :
Dept. of Biotechnol., Tokyo Univ., Japan
Abstract :
This paper describes the design and implementation of a parallel programming environment called "distributed shared array" (DSA), which provides a shared global array abstract across different machines connected by a network. In DSA, users can define and use global arrays that can be accessed uniformly from any machines in the network. Explicit management of array area allocation, replication, and migration is achieved by explicit calls for array manipulation: defining array regions, reading and writing array regions, synchronization, and control of replication and migration. The DSA is integrated with Grid (Globus) services. This paper also describes the use of our model for gene cluster analysis and molecular dynamics simulation. In these applications, global arrays are used for storing the distance matrix and atom coordinates. Large array areas, which cannot be stored in the memory of individual machines, are made available by the DSA. Scalable performance of DSA was obtained compared to that of conventional parallel programs written in MPI.
Keywords :
message passing; parallel algorithms; parallel architectures; parallel programming; shared memory systems; MPI; array area allocation; array manipulation; conventional parallel programs; distributed shared arrays; explicit calls; gene cluster analysis; grid services; high-performance scientific computing; migration control; molecular dynamics simulation; parallel programming environment; replication control; shared global array abstract; synchronization; Application software; Computer networks; Concurrent computing; Distributed computing; Hardware; Memory management; Parallel programming; Programming environments; Programming profession; Scientific computing;
Conference_Titel :
Applications and the Internet Workshops, 2004. SAINT 2004 Workshops. 2004 International Symposium on
Print_ISBN :
0-7695-2050-2
DOI :
10.1109/SAINTW.2004.1268699