COMPUTATIONAL BIOLOGY RESEARCH GROUP

COMPBIO LINUX CLUSTER

The COMPBIO cluster is for exclusive use for our group members to run large scale simulations of biomolecules. The fully scalable (across 64 processors) parallel applications we run include Molecular Dynamics using NAMD, Born-Oppenheimer QM /MM dynamics, Car-Parrinello molecular dynamics. In addition, we run the CHARMM and the Genesis programs on 8 processors. We run multiple conformation docking on a condor grid.

Architects: The Liniac Group

64 Processor Xeon Cluster with Nocona Chips
(32 Dual Intel Xeons with Intel EM 64 Technology)

3.2GHz/1MB Cache,Xeon 800MHz FSB, PowerEdge 1850 (31 Compute Nodes)
4GB DDR and 256GB scratch disk space per node

3.2GHz/1MB Cache,Xeon 800MHz FSBus, PowerEdge 1850 (alpha login node)

3.2GHz/1MB Cache, Xeon, 800MHz FSB, PowerEdge 2850 (IO and Backup Servers)
1 Terrabyte of backed-up disk space connected to CETS managed Tape Robot

PowerEdge 750, 3.2GHz, 512K Cache, P4, 800FSB (Management Node)

Rack and Power equipment plus Extreme Networks Switch

PowerConnect 3348, 48 Port FE Stackable Managed Switch,2 GbECombo Ports

PowerVault 220S,3U,14 HDD, SCSI Storage Enclosure

Dell | EMC AX100 Array Dual Processor Enclosure

Red Hat Linux, Open PBS queuing system

Intel Fortran, C compilers, MPICH communication protocol

Additional Super-Computing Platforms we use are: