Computational Biology and Bioinformatics
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Overview:
The Beowulf Linux cluster is a 24 node distributed memory multi-processor system. It contains a head node and 23 computation nodes, each containing two 2.8 GHz Intel Xeon processors with 533 MHz system bus, 512KB of cache (per cpu) and 2 GB of RAM (per node). The nodes are interconected with Gigabit Ethernet. A public network connects the head node with the internet. The cluster uses Red Hat Linux version 8.0 as its operating system. It uses the Portable Batch System (PBS) and the Maui Scheduler to distribute the computational workload across the nodes. The system is optimized for running parallel computations using MPI (message passing interface), but can also be used for standard serial programs.
Installed Software:
  • System software: Intel C++ compiler 7.0, Intel Fortran Compiler 7.0, GNU Compiler Collection (GCC 3.2-7), Java (J2SDK 1.4.1_02), Perl 5.8.0, Bioperl 1.4, R-2.0, modeller-7v7-1, MPICH 1.2.5, Sift 2.1, Joy-5.10, ATLAS 3.4.1, GSL (GNU Scientific Library) 1.6-1, Standalone BLAST, MySQL-connector-java 2.0.14, MySQL-connector-C++ 1.7.9_3, QTL Cartographer V.1.16,
  • Database System: MySQL 3.23.55
    • Running Jobs:
    Jobs are submitted from the head node by creating a PBS job command file which specifies certain attributes of the job such as how long the job is expected to run and how many nodes of the cluster are needed (e.g. for parallel programs). MAUI then schedules when the job is to start running on the cluster (based in part on those attributes), runs and monitors the job at the scheduled time, and returns any ouput to the user once the job completes.
    Job Submission Tutorial
    Contact system administrator

    Yan Cui's Lab at University of Tennessee Health Science Center