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| Authors: | Martin Gerber, Thomas Gössi |
| Group: | Computer Engineering |
| Type: | Inproceedings |
| Title: | Automatic Parallelization of Gromos Molecular Dynamics Simulation Package for Distributed Memory Environments |
| Year: | 1999 |
| Month: | April |
| Pub-Key: | GG99a |
| Book Titel: | High Performance Computing Symposium 99 |
| Keywords: | ham, md, molecular dynamics |
| Abstract: | In this paper, we present a control/data flow specification model for replicated data parallel algorithms. Combined with an architecture graph and a mapping function, our domain-specific,
semi-automatic approach takes on the job of generating source code of static data initialization and the schedule according to the specification graph, including all interprocessor
communications. The remaining manual work is composed of two tasks: firstly the parametrization of the functions (parallelization), secondly the specification of the algorithm. MPI (Message
Passing Interface) is used for interprocessor communication, appropriate function calls are inserted automatically. For the Molecular Dynamics application Gromos (GROningen MOlecular Simulation Software) we discuss load balancing issues as well as scalability and communication overhead problems. With the new environment it is still possible to generate sequential code with an overhead lower than 10% compared with the original hand-coded sequential program. Several platforms have been tested with the parallel code, e.g. a comparison of a workstation cluster interconnected with FastEthernet with an IBM RS/6000 SP distributed memory multiprocessor is presented. |
| Remarks: | High Performance Computing Symposium 99, April 11-15, San Diego, California |
| Location: | San Diego, California |
| Resources: | [BibTeX] [Paper as PDF] |
