Archived: 25 November 1999
Published in the Internet Journal of Chemistry 3, number 4 (2000).
Access to High Performance Computing (HPC) power remains crucial for many computational chemistry problems. Unfortunately, traditional supercomputers or cluster computing solutions from commercial vendors remain very expensive, even for entry level configurations and are therefore often beyond the reach of many small to medium-sized research groups and universities. Clusters of networked commodity computers provide an alternative computing system that can offer substantially better price/performance than commercial supercomputers. For some applications they can offer a comparable absolute performance as well. We have constructed a prototype PC cluster (or Beowulf) dedicated to computational chemistry problems using the electronic structure applications GAUSSIAN and GAMESS.
This paper introduces the concept of Beowulf computing clusters and describes the system requirements for running the ab initio software packages used by computational chemists at the University of Adelaide. We discuss the economic and performance trade-offs and design choices made in constructing the Beowulf system, including the choice of processors, networking, storage systems, operating system and batch queuing software.
We present some benchmark results for the GAUSSIAN 98 and GAMESS-US programs across two platforms, the Beowulf cluster and an SGI PowerChallenge. In addition, we analyse the price/performance as well as other issues such as throughput, scalability, software support, maintenance, and future trends.
Keywords: Computational chemistry; Beowulf cluster; cluster computing; parallel computing; performance benchmarks; Linux.
Postscript version (gzip compressed)