BeSTGRID Auckland Cluster

From BeSTGRID

The new BeSTGRID SGI Altix XE based Auckland Cluster has been ordered (23/01/2008) and expected arrival is late February 2008.

This SGI Altix XE [1] cluster is based on:

• Intel® Quad-Core Xeon® Processor-based architecture
• 1600 MHz front-side bus,
• 16GB of memory per compute node,
• an ultra-dense architecture that packs sixteen cores in a slim 1U form factor,
• fully-buffered DDR2 memory,
• driving the cluster with an Altix XE250 head node for advanced extensibility, redundancy, reliability, and I/O rich-features.

Contents 1 Preparation 2 Configuration 2.1 Hardware 2.2 Operating System 2.3 Cluster Software 2.4 Computation Packages 3 Installation 3.1 Naming 3.2 Hosting Location 4 Testing 5 Projects 5.1 Ocean Biogeographic Information System (OBIS)

[edit] Preparation

• Presentation on BeSTGRID Auckland Cluster by SGI to:
  • ITS Operations
  • System Management
  • Users

[edit] Configuration

[edit] Hardware

	SGI Altix XE250	SGI Altix XE320
Purpose	Head Node	Compute Nodes
Quantity	1	5 systems x 2 Nodes each = 10 Nodes
Processors	2x Dual Core Xeon 3.4GHz 6M 1600 FSB 80W X5272 (Harpertown)	2x Quad Core Xeon 2.8GHz 12M 1600 FSB 80W E5462 (Harpertown) = 8 Cores per Node
Total Cores	4	80
Memory	16GB Fully Buffered DIMM 800 MHz	16GB Fully Buffered DIMM 800 MHz for each Node, 2GB per Core = 160 GB memory
Disk space	4x 750GB SATA with HW RAID	1x 250GB SATA for each Node

See here for more detailed configuration

[edit] Operating System

Linux CentOS is a standard de-facto for BeSTGRID computing environment.

[edit] Cluster Software

Cluster software should be chosen to install. There are the following options:

• Rocks Cluster Suit
• OSCAR Cluster Suit
• Set of separated packages:
  • Torque - Resource Manager
  • LAM-MPI or MPI-CH - Message Passing Interface Libraries
  • C3 - The Cluster Command and Control

[edit] Computation Packages

[edit] Installation

[edit] Naming

The cluster is known as the BeSTGRID Auckland Cluster, with the canonical name being:

• [cluster].[bestgrid].auckland.ac.nz

[edit] Hosting Location

The Cluster will be hosted within the Tier 1 University of Auckland ITS Data Centre, within the Owen G Glenn Building.

• ITS Data Center
• BeSTGRID Auckland Cluster install notes
  • List of MAC Addresses
  • Hardware positions

[edit] Testing

Auckland Cluster Testing

[edit] Projects

[edit] Ocean Biogeographic Information System (OBIS)

Project Lead

Dr Mark J. Costello

Usage

OBIS virtual machine on Pleyads, 20GB of disk space.

Project Description

• OBIS publishes data on behalf of scientists from government agencies, museums, universities, commercial companies, and non-governmental organisations. OBIS is always seeking new contributors.
• OBIS is a marine biogeographic information system, meaning that we concentrate on datasets that record particular species (or higher taxonomic group) from particular marine locations, at particular times. At present, we can only publish data where the locations are recorded as latitude and longitude, not as place names. Our focus is on high taxonomic quality, so datasets where organisms have been identified by professional or trained biologists are our priority. In the near future, we will be expanding to take in environmental datasets (i.e. coverage of physical, chemical, and geological parameters) that are relevant to understanding the distribution of species. So we are interested in hearing from potential contributors of these datasets, and welcome your contact, but are still in the process building this facility.

www

http://www.iobis.org