Porting a molecular dynamics application on a low-cost cluster of personal computers running GAMMA

The Genoa Active Message Machine (GAMMA) is a low-cost cluster of Personal Computers (PCs) networked by commodity fast LAN (100base-T Ethernet) and running a Linux operating system kernel enhanced with low-latency, high throughput support to inter-process communication based on the Active Messages paradigm. The target of our work is the porting on GAMMA of a Molecular Dynamics (MD) code used to study polarizable fluids and written in FORTRAN with calls to PVM communication routines. Such porting required to extend the GAMMA programming library with FORTRAN stubs to GAMMA communication functions. Then the communication policy in the original PVM version of MD has been changed to fit the GAMMA Active Message-like communication style. As a third step, the performance of the obtained GAMMA version of MD has been measured and compared to the performance of the PVM version on the same hardware platform as well as to the performance obtained by the PVM version on a Memory Channel cluster of DEC SMP workstations of higher class of costs and on a eight-nodes IBM SP2. The results show the appealing cost/performance figure of GAMMA and the significant performance improvement exhibited by MD after being ported from PVM to GAMMA.