Beowulf Cluster Computing

1. Beowulf Cluster Computing PROJECT: We constructed a parallel processing computer system using the Beowulf cluster computing design created at NASA in an attempt to build a powerful computer that could assist in Bioinformatics research and data analysis. BEOWULF CLUSTERS:A Beowulf Cluster is a computer design that uses parallel processing across multiple computers to create cheap and powerful supercomputers. A Beowulf Cluster in practice is usually a collection of generic computers, either stock systems or wholesale parts purchased independently and assembled, connected through an internal network. A cluster has two types of computers, a master computer, and node computers. When a large problem or set of data is given to a Beowulf cluster, the master computer first runs a program that breaks the problem into small discrete pieces; it then sends a piece to each node to compute. As nodes finish their tasks, the master computer continually sends more pieces to them until the entire problem has been computed. MPICH2:In order for the master and node computers to communicate, some sort message passing control structure is required. MPI,(Message Passing Interface) is the most commonly used such control, and the one that we've incorporated into our project. MPICH2 is a implementation of MPI that was specifically designed for use with cluster computing systems and parallel processing. It is an open source set of libraries for various high level programming languages that give programmers tools to easily control how large problems are broken apart and distributed to the various computers in a cluster. OUR CLUSTER: Using funding from the Biology department, the cluster we constructed contains eight computers with one master and seven node computers. Each computer in the cluster contains a dual core processor, giving us a total of 16 processors to utilize. Each runs on the Fedora Core 6 version of Linux and uses the MPICH2 libraries for message passing. They are all connected on a internal network through a high speed gigabyte switch. Each Computer in the cluster is equipped with: • Intel Core 2 Duo 6400 Processor(Master: Core 2 Duo 6700) • 2 Gigabytes of DDR RAM in Dual Channel • D-Link Gigabyte Network Interface Card(Master: 2x Cards) • 60 Gigabyte Hard Drive(Master: 1000 Gigabyte RAID 5) CLUSTER USES: Clusters have a variety of different applications in the world. They are used in bioinformatics to run DNA string matching algorithms or to run protein folding applications. Geologists also use clusters to emulate and predict earthquakes and model the interior of the Earth and sea floor Clusters are even used to render and manipulate high-resolution graphics in engineering. Our completed Beowulf cluster will use a computer algorithm known as BLAST,(Basic Local Alignment Search Tool), to analyze massive sets of DNA sequences for research into Bioinformatics. RESULTS: The total processing power of our cluster has yet to be determined. Once the cluster has been completely streamlined and stabilized, we will run benchmark tests to calculate its average and peak performances CLUSTER LAYOUT AND DESIGN: Researcher: Ben Case Researcher: Stephen Ciesla Advisor: Ed Harcout Biology Consultant: Lorraine Olendzenski Sample Cluster Computer SATA Hard Drives 2 GB RAM Intel Core 2 Processor D-Link Network Card