High Performance Technical Computing Tutorial

PSB 2001


  1. Introduction to High Performance Technical Computing
  2. In this section, we’ll discuss the basic elements of high performance computing. The following topics will be discussed and reviewed:

    1. Sequential vs. parallel computing
    2. Overview of MPP, SMP, cc-NUMA, distributed systems, and cluster architectures
    3. A quick look at the components of modern day systems
      1. Hardware: microprocessors, memory, cache, disk and I/O, and interconnects microprocessors, memory, cache, disk and I/O, and interconnects
      2. Software: operating systems, programming environments and tools such as programming languages, debuggers, profilers and performance analysis tools

    The target audience would be students, faculty, researchers and the general public that are new to the High Performance Computing, Biocomputing and parallel processing. The audience should have a general background in computer technology, biology, chemistry, genetics, and/or biochemistry in order to obtain the maximum benefit from this section.

  3. High Performance Technical Computing for the Bioscience
  4. This section is targeted at students, faculty and researchers who are working in biosciences or related fields. The readers should have a good understanding of basic computer technology from experience or other sources such the first section. The following topics will be discussed:

    1. Beowulf vs. large SMP vs. MPP vs. vector systems for bioinformatics, bio-computing, and related fields
    2. Current applications and benchmarks
    3. Optimizations techniques
    4. Advances in parallel programming
    5. Application Service Providers (ASP)
  5. Future directions in High Performance Technical Computing
  6. The final section will talk about where the field of High Performance Computing is headed in the future. The following topics will be reviewed:

    1. Hardware and software trends
    2. Cluster Technology trends and future Cluster Technologies
    3. Graphics for Biocomputing
    4. Other forms of computing


For the past 15 years Compaq/Digital has been a key player the high performance technical computing market. With the introduction of the latest Alpha 21264a microprocessor (the EV67 chipset), and a 25-year roadmap for the Alpha microprocessor, Compaq will continue to be a driving force in High Performance Technical Computing market.

Compaq offers a complete range of HPTC solutions for the bioscience community. Compaq solutions range from single CPU Alpha system such as the new 1U DS10L through the soon-to-be announced 32 processor Wildfire system. Compaq also offer a complete line of AlphaServer clusters connected together with a wide range of System Area Interconnects (SyAN), including 10/100 Ethernet, Myrinet, ServerNet, and the high performance Quadrics Interconnect. With each system, Compaq offers a wide range of services and support, tailored to meet the customer’s needs. Compaq can put together a bioscience solution that fits the customers need and budget.

With major wins at private and public genome centers, pharmaceutical, and chemical companies, Compaq is the #1 supplier of computing solutions to the bioscience market.


Bruce Foster is the Compaq's High Performance Technical Computing marketing manager. Bruce is a 19-year employee of Compaq/Digital. He is currently responsible for the technical marketing in the biosciences and chemistry market segment. Bruce recently provided technical and base produce marketing support for the successful launch of Compaq's new SC supercomputer system and other high performance AlphaServers such as the ES40/EV67 and Wildfire. Prior to joining the High Performance Technical group, he held a number of positions at Compaq/Digital including: Advanced Development manager for compilers and tools, LISP developer, and Researcher for automatic manufacturing technology. Bruce holds a Ph.D. in Physical Chemistry from the University of Iowa. Prior to joining Compaq/Digital, he was a postdoctoral fellow at Yale University (Hal Wyckoff and Fred Richards' lab) and Harvard University (Don Wiley and Stephen Harrison's lab) in Molecular Biochemistry and Biophysics. Bruce has recently completed his Executive MBA from Boston University.

Susan Kennedy is Compaq’s BioScience market segment manager. Sue is a 15-year employee of Compaq/Digital. She currently manages all aspects of Compaq’s BioScience market solutions. Sue has a BS degree in Biology from the University of New Hampshire and has taken numerous classes on topics such as genetics and bioinformatics.