Priority Research Centre for
BIOINFORMATICS, BIOMARKER DISCOVERY AND INFORMATION-BASED MEDICINE

Super Computing

CIBM Cluster Summary

The CIBM owns a High Performance GPU Computing cluster with a combined performance of 34 Tera FLOPS in single precision, and 1.3 Tbytes of RAM. In addition, all our workstations are GPU equipped. We advocate for Open Source tools and software development, and acknowledge we just are nanos gigantum humeris insidentes. This is why our machines are named after some of the past great minds, not because we share their social or cultural views, but rather for their scientific contribution.

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Darwin

16 Server High Performance Computing Cluster

Specifications

16 Dell PowerEdge III servers, each;

  • Dual Xeon 5550 2.67 GHz (8 cores each machine - 128 cores total)
  • 32 Gb RAM (512 Gb RAM total)
  • 42 Gb Local Hard Disk (672 Gb total)

Operating System

Red Hat Enterprise Linux AS release 4 (Nahant Update 8)

Commissioned

December 2007. Our "senior" cluster, about to volunteer for retirement.

Name Significance

Darwin is named in honor of Sir Charles Darwin, naturalist.

Research_Centres_CIBM_Research_SuperComputing_Galton.jpg

Galton

Storage and High Performance Computing

Specifications

Dell PowerEdge server with PowerVault RAID array;

  • Dual Xeon 5520 2.3 GHz (16 cores)
  • 64 Gb RAM
  • 10 Tb RAID Disk Array

Operating System

Red Hat Enterprise Linux Server release 5.5 (Tikanga)

Commissioned

May 2008

Name Significance

Galton is named in honor of Sir Francis Galton, naturalist and half cousin to Darwin.

Sir Ronald Fisher

Fisher

GPU High Performance Computing

Specifications

Xenon Nitro T5 Supermicro server;

  • Dual Xeon 5520 2.3 GHz (16 cores)
  • 48Gb RAM
  • 4x NVIDIA Tesla C2050 "Fermi" GPU cards (1792 GPU Cores and 12 Gb RAM total)
  • 800Gb Local Hard Disk

Operating System

Ubuntu 10.04 LTS Linux Server (Lucid Lynx)

Commissioned

January 2010

Name Significance

Fisher is named in honor of Sir Ronald Fisher, naturalist.

Gregor Mendel

Mendel

GPU High Performance Computing

Specifications

Xenon Nitro T5 Supermicro server;

  • Dual Xeon 5620 2.4GHz (16 cores)
  • 48Gb RAM
  • 4x NVIDIA Tesla C2050 "Fermi" GPU cards (1792 GPU Cores and 12 Gb RAM total)
  • 800Gb Local Hard Disk

Operating System

Red Hat Enterprise Linux Server release 5.5 (Tikanga)

Commissioned

June 2010

Name Significance

Mendel is named in honor of Gregor Mendel, father of genetics.

Marie Skłodowska-Curie

Marie Curie

GPU High Performance Computing, Radiation Oncology research

Specifications

Xenon Nitro T5 Supermicro server;

  • Dual Xeon 5650 2.7GHz (24 cores)
  • 96Gb RAM
  • 4x NVIDIA Tesla C2070 "Fermi" GPU cards (1792 GPU Cores and 25 Gb RAM total)
  • 2Tb Local Hard Disk

Operating System

Red Hat Enterprise Linux Server release 5.5 (Tikanga)

Commissioned

May 2011

Name Significance

Marie Curie is named in honour of Marie Skłodowska-Curie, physicist and chemist, first female Nobel Prize, relentless researcher in a male-dominated science. Her pioneering work in radioactivity was foundational of radiation cancer therapies.

Nikolai Konstantinovich Koltsov

Koltsov

GPU High Performance Computing

Specifications

Xenon Nitro T5 Supermicro server;

  • Dual Xeon 5620 2.4GHz (16 cores)
  • 48Gb RAM
  • 4x NVIDIA Tesla C2050 "Fermi" GPU cards (1792 GPU Cores and 12 Gb RAM total)
  • 800Gb Local Hard Disk

Operating System

Red Hat Enterprise Linux Server release 5.5 (Tikanga)

Commissioned

June 2010

Name Significance

Koltsov is named in honor of Nikolai Konstantinovich Koltsov, geneticist and molecular biologist whose ideas anticipated Watson & Crick in describing the DNA structure.

Claude Elwood Shannon

Shannon

GPU High Performance Computing

Specifications

Xenon Radon 6170 Supermicro server;

  • Quad E5-4650 Sandy Bridge 2.7GHz (32 cores)
  • 512Gb RAM
  • 4x NVIDIA Tesla K20 "Kepler" GPU cards (9984 GPU Cores and 20 Gb RAM total)
  • 600Gb Redundant Solid State Disk

Operating System

In commissioning.

Commissioned

June 2013

Name Significance

Shannon is named in honour of Claude Elwood Shannon, mathematician, electronic engineer and cryptographer, "the father of information theory", whose ideas deeply changed how we understand knowledge and data mining.

CIBM

Workstations

10 Developer Work Stations

The CIBM has 10 developer workstations furnished with "Fermi" and "Tesla" GPUs, Intel single i7 or E5-26xx and double Xeon E26xx processor.

Some workstations have dual boot linux / Windows or virtualised dual OS.

The CIBM has been the major driving force behind the nomination of The University of Newcastle as a CUDA Teaching Centre since 2011. We have also obtained hardware donations to equip a Computer Science Honours Lab with 9 High Performance GPU workstations.