Arup Chakraborty Research Group Cluster

Principle Investigator: Arup Chakraborty
Primary Contact: John Eide
Secondary Contact: Aaron Dinner

Overview

The Chakraborty Linux Cluster is a 96 processor Beowulf cluster that is used to advance two major projects in fundamental biology and bio-sensor technology. The two projects are: (1) how receptor-ligand binding, cell membrane properties, and intracellular signaling conspire together to effect T cell recognition of antigen in the adaptive immune system, and 2.) how DNA hybridization and protein-protein binding can be translated into a mechanical signal for pathogen detection.

Cluster Description

  1. Hardware

    2. Master Server Node consisting of:
    2 ea. AMD Athlon 2200+ MP processors
    Tyan Tiger MPX S2466N-4M motherboard with 10/100 onboard NIC
    2 x 512MB PC2100 ECC Registered DDR RAM
    40GB 7200 EIDE hard disk
    3Ware Escalade 7800-8 RAID controller
    8 ea. 160GB Maxtor 7200RPM EIDE disks
    Floppy and CDROM
    8MB AGP ATI
    3COM 10/100/1000BT NIC
    3U rackmount enclosure with 460W power supply

    42 Compute Nodes each with:
    2 ea. AMD Athlon 2200+ MP processors
    Tyan Tiger MPX S2466N-4M motherboard with 10/100 onboard NIC
    2 x 512MB PC2100 ECC Registered DDR RAM
    40GB 7200 EIDE hard disk
    Floppy and CDROM
    8MB VGA
    2U rackmount enclosure with 300W power supply

    6 Compute Nodes each with:
    2 ea. AMD Athlon 2800+ MP processors
    Tyan Tiger MPX S2466N-4M motherboard with 10/100 onboard NIC
    2 x 512MB PC2100 ECC Registered DDR RAM
    40GB 7200 EIDE hard disk
    Floppy and CDROM
    8MB VGA
    2U rackmount enclosure with 300W power supply

    Network Interconnect
    Cisco Catalyst 3548XL 48-port Fast Ethernet switch

  2. Software

    Red Hat Linux Release 7.3
    Warewulf 1.10 Cluster Implementation Toolkit
    Sun Grid Engine 5.3
    Ganglia distributed monitoring and execution software

  3. File Systems

    chakraborty.lbl.gov:
    Filesystem size used avail capacity Mounted on
    /dev/hda3 3099M 460M 2481M 16% /
    /dev/hda1 31.1M 22.3M 7.1M 76% /boot
    /dev/hda5 5163M 184M 4716M 4% /opt
    /dev/hda8 1035M 32M 950M 4% /tmp
    /dev/hda2 5162M 2077M 2823M 43% /usr
    /dev/hda7 1035M 286M 696M 30% /var
    /dev/sda1 945G 67G 830G 8% /home

  4. Rack Layout

Service Level

The production Chakraborty Linux Cluster is managed by the CIS UNIX Group under a Service Level Agreement as part of the Scientific Cluster Support program.

New User Accounts

User accounts on these systems should be requested or approved by the listed primary contact.

The primary users of the Chakraborty cluster are affiliated with UC Berkeley's Department of Chemistry. New users should be setup with a SecureID card so they can access their account on the cluster.

System Maintenance

  1. Scheduled Work
    Systems administration work can be performed after scheduling in advance with the Primary contact. Call the LBNL Fire Deparment to turn off the Halon file suppression system in the 50B-1275 Computer Room before proceeding if the work requires the removal of floor tiles.

Security

Unix Group Standard configuration recommendations. Users are required to use a SecureID card for login access.

System Backups

Backups of home directories are not done at this time.