Paper Citing NAMD - Abstract
Nomoto, A.; Kaneko, W.; Terada, T.; Nakamura, S.; Shimizu, K.
Programming environment based on distributed shared arrays for high-performance scientific computing
2004 INTERNATIONAL SYMPOSIUM ON APPLICATIONS AND THE INTERNET WORKSHOPS, PROCEEDINGS, 630-636, 2004
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.
