This is an archived page of the 2001 conference


Linux Clusters: the HPC Revolution

Last updated: 20 April 2001

Title   Cluster-In-A-Box
Presenter Jeremy Enos
Presenter Inst NCSA
Time 8:00am - 12:00pm
Description OSCAR (Open Source Cluster Application Resource) is a cluster-in-a-box package developed to lower the entry barriers into the cluster computing world and to eliminate the need for a cluster expert. OSCAR provides a single CD with a wizard-driven interface to building a cluster. It is designed to provide the most popular and universal cluster software available in open source. At the end of the wizard process, the cluster will be ready to run MPI or PVM jobs using the Portable Batch System (PBS). C3 tools are included for management and ssh for secure transactions. The build process and future plans for the cluster-in-a-box tecnologies will be covered in the tutorial.
Title Using the TotalView Debugger
Presenter Roy Heimbach
Presenter Inst NCSA
Time 8:00am - 12:00pm
Description This half-day tutorial will demonstrate the interactive features of the Totalview debugger from Etnus. Common MPI programming errors will be reviewed. A series of short example programs will be used to demonstrate diagnosis of MPI programming errors with the help of Totalview.
Title Performance Tuning Techniques for IA32- and IA64-Based Clusters
Presenter Troy Baer
Presenter Inst Ohio Supercomputing Center
Time 1:00pm - 5:00pm
Description This half-day tutorial will demonstrate several techniques for improving the single-processor performance of applications on clusters of IA32- and IA64-based systems, such as those in service at OSC, NCSA, and AHPCC. These techniques involve taking advantage of features common to most modern microprocessors, including multi-level caches and multiple pipelined functional units. The tutorial will concentrate primarily on techniques for IA32 based systems using the GNU and Portland Group compilers, but will also discuss some techniques applicable to IA64 based systems using the Intel and SGI compilers.

Topics covered in this tutorial include basics of microprocessor architectures, loop unrolling, hierarchical memory systems, avoiding cache thrashing, prefetching, inlining, high-performance numerical libraries, and performance analysis tools.
Title Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD
Presenter Jim Phillips
Presenter Inst University of Illinois at Urbana-Champaign
Time 1:00pm - 5:00pm
Description This tutorial will familiarize the participant with the design, assembly, and use of a small Linux cluster for a specific biomolecular application. We will begin with a discussion of currently available technology, the design of a cluster for a small research group, and cost-benefit tradeoffs. The group will be broken into groups of mixed experience, each of which will assemble and install a small cluster using the Scyld Beowulf cluster operating system (

Our motivating application will be molecular dynamics simulations of large biomolecular systems using the program NAMD, distributed free of charge with source code ( After an introduction to molecular dynamics and NAMD, we will experiment with NAMD performance on the just-built small clusters, a 32-processor cluster, and the large clusters at NCSA.

We will conclude with a demonstration of interactive molecular dynamics, connecting the visualization program VMD, a haptic interface device, and a NAMD simulation running on a Linux cluster. We will encourage open discussion of any questions on cluster design and use during the tutorial.