The Facility   CGRB Server room

The CGRB Biocomputing and Bioinformatics facility provides wide-ranging resources, expertise and support for computational needs of the molecular biosciences community at Oregon State University. The facility offers a robust computing environment for high-level computational biology and a versatile intellectual resource for interdisciplinary collaboration.

The first Genome cluster was a compute farm in the Beowulf tradition (2001); i.e., built with commodity hardware and freely available software. Growing to include more than 60 CPU's, Genome served both as a test bed for CGRB developers and system administrators and as an increasingly powerful tool for OSU faculty, staff and students. Learning from setbacks and capitalizing on successes, Genome has steadily grown to include more than 4000 processors. The new version of the Genome is currently has none of the original commodity hardware left. Space and BTU constraints motivated the migration to rack-mount multi-processor nodes and the need to address large amounts of RAM instigated the move to 64-bit hardware. Right now, about 90% of Genome is composed of rack-mount multi-processor nodes that contain 4, 8, 16, 24, 32, 40, 48, 64, 80, 120 and 160 core IBM, AMD or Intel based multi-core processors.

The Center for Genome Research and Biocomputing maintains an extensive and well-managed infrastructure consisting of a distributed service architecture, a greater than 4000-processor computer cluster and a secure private 1G/10G/40G network. Each machine has internal hard drive disk space, but is also connected over 3.5PB of NFS shared disk space. The CGRB encourages high-volume users to contribute to the computational infrastructure. Users are charged $32, $64, and $96 per/month for maintaining each processing machine, web/database server, and file server, respectively. The nodes are provided at the highest priority to the specific project and provided upon request at a lower priority to other CGRB researchers. Thus, subsets of cluster nodes are dedicated to specific research projects, but they function as part of a unified cluster when needed for intensive jobs. This priority-based scheduling has proven quite successful, both in terms of end-user satisfaction and in the execution of systems administration activities. Computational requirements are constantly re-evaluated and new hardware is integrated as needed. Researchers who do not own equipment and can not complete their work within the resources provided to general users can rent resources from the CGRB as needed to complete the work on time. Research rental hardware includes processing machines (including machines with 1TB of RAM), web/database servers and file space to store data. Please see Biocomputing Service Fees for pricing and email with questions.

 

CGRB Biocomputing Staff:

  Name Contact Information Email
Chris Sullivan Chris Sullivan
Assistant Director for Biocomputing
3132 Ag & Life Sciences Bldg.
541-737-5254
 Contact person by email
Brent Kronmiller Brent Kronmiller
Bioinformatics Analyst

3129 Ag & Life Sciences Bldg.
541-737-3611

Contact person by email
Ian Munoz Ian Muñoz
Assistant Computational Scientist

3132 Ag & Life Sciences Bldg.
541-737-5254

Email Ian Muñoz
Matthew Peterson Matthew Peterson
Computational Scientist

3122 Ag & Life Sciences Bldg.
541-737-3897

Contact person by email

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