MASSIVELY PARALLEL PROCESSING ON THE INTEL PARAGON SYSTEM: ONE TOOL IN ACHIEVING THE GOALS OF THE HUMAN GENOME PROJECT

A massively parallel computing system is one tool that has been adopted by researchers in the Human Genome Project. This tool is one of many in a toolbox of theories, algorithms, and systems that are used to attack the many questions posed by the project. A good tool functions well when applied alone to the problem for which it was devised. A superior tool achieves its solitary goal, and supports and interacts with other tools to achieve goals beyond the scope of any individual tool. It is our thesis that Intel's massively parallel Paragon™ XP/S system is a superior tool. This paper presents specific requirements for a superior computing tool for the Human Genome Project (HGP) and shows how the Paragon system addresses these requirements.

Computing requirements for HGP are based on three factors:

1. computing requirements of algorithms currently used in sequence homology, protein folding, and database insertion/retrieval;

2. estimates of the computing requirements of new applications arising from evolving biological theories; and

3. the requirements for facilities that support collaboration among scientists in a project of this magnitude.

The Paragon system provides many hardware and software features that effectively address these requirements. These features include high-performance RISC processors for compute-intensive applications, a scalable architecture for increasing problem sizes, flexible resource management for ease-of-use and machine sharing, adherence to communication standards and remote access facilities for interactive and collaborative work with applications and researchers at remote facilities.

The power of these system features are exemplified by the results of applications in sequence alignment, sequence analysis, and molecular phylogeny, developed by computer scientists at Argonne National Laboratory and biologists at the University of Illinois, and executed on the massively parallel Intel Touchstone Delta system, a one-of-a-kind prototype of the Paragon XP/S system.