Illinois Bio-Grid Hardware

Z-Cluster

The z-cluster is an high performance Linux cluster installed at the School of Computer Science, Telecommunications and Information Systems (CTI) of DePaul University in Chicago. The z-cluster is a core computational facility at CTI.

This web site shows the current status of the cluster: http://z-login.cti.depaul.edu/ganglia

Z-cluster is constituted by 20 computational nodes. Each node consists of a 3.2 GHz P4 processor with Hyperthreading technology, 2 GBytes of Ram and 200 GBytes Hard Disk. The nodes are connected by a Gigabit switch.

Z-Cluster disk usage policy: Please do not exceed 1GB of disk utilization in your home directory. Disk usage quotas are being enforced. Error messages such as "hda8: warning, user block quota exceeded" and "hda8: write failed, user block quota exceeded too long" indicate that you are using too much disk space in your home directory. If you need more working space, please make use of the '/scratch' partition, or the new and much larger '/maxtor300gb/scratch' directory, as well as the '/maxtor300gb/data' directory. Be aware that the contents of the '/scratch' and '/maxtor300gb/scratch2/' may be deleted without warning.

A report on the Z-cluster hardware is available at the bottom of this page.

Titan and Myosin (formerly Kaveri and Mojo)

Also see IBG Storage Array

DePaul CTI and the Illinois Bio-Grid are home to many computational resources to support researchers with bioinformatics software. Titan is a Sun Fire 6800 MidFrame Server, a powerhouse incorporating 24 processors. It features the 64-bit UltraSPARC III processor with an 8MB pipelined burst level 2 cache, with a four-way associative on-chip 64-KB data and 32KB instruction level 1 cache and integrated memory controller capable of addressing up to 16 GB of main memory per processor at 2.4 GB/s. Storage is provided by a Sun T3 StorEdge array with 4 Terabytes of disk storage and a fiber optic interconnect to the SunFire. Titan is available for use without charge for researchers in the member institutions of the Illinois Bio-Grid. The Illinois Bio-Grid also has thousands of other processors available for use.

Titan is actually split in half. The other half is named Myosin. They are named after the proteins (Titan is not named after the mythical god, although the protein is). These machines were formerly named Kaveri and Mojo.

Available Software

The following software is currently available on Titan. Additionally, the Illinois Bio-Grid team is developing software for use on this machine and other machines on the grid.

• Clustering and Alignment Tool (CAT) - a program which analyzes (Screens, clusters and aligns) the DNA sequence data (DoubleTwist)
• ClustalW - a program for protein sequence analysis
• GenScan - a command line program for gene identification
• GCG - the Wisconsin Package software for comprehensive sequence analysis.
• Hmmer - a program for protein sequence analysis
• Pblast - a parallel/distributed BLAST server
• Prophecy - a search application to find data in the Annotated Human Genome Database.

System Topology

A system topology document is in process in conjunction with the Job Scheduling project. The current diagram is available here: System Topology

• z-cluster-report.zip: Z-Cluster Report by Eric Puryear

Sys Admin

* KnownIssues - Known issues with hardware that are in the process of being addressed.

* histone - Software/process issues and their solutions on histone.

-- DaveAngulo - 28 Dec 2005