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Improving the Research Bootstrap of Condor High Throughput Computing for Non-Cluster Experts Based on Knoppix Instant Computing Technology. RIKEN Genomic Science Center Fumikazu KONISHI. Background.

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Improving the Research Bootstrap of Condor High Throughput Computing for Non-Cluster Experts Based on Knoppix Instant Computing Technology

RIKEN Genomic Science Center

Fumikazu KONISHI

  • Biologists need a high performance computing system for their research process. However, they do not know how to build a cluster system by themselves.

Condor Week 2006

meet chie san

She is a biologist with a big problem.

Meet Chie-san.

Condor Week 2006

I borrowed slides from Condor.

chie san s application
Chie-san’s Application …

Run a Sequence Sweep of InterProScan for Mouse cDNAs of a total of 103,000 clones .

  • InterProScan takes on the average 1 minute to compute on a “typical” workstation (total = 103000 × 1 = 103000 minutes = 1716 hours )
  • InterProScan requires 6G bytes Public Database set for each.

Condor Week 2006


Technical Skill Barrier

Policy Barrier

I have 103,000 sequences to search a gene functional domain. And I am Non-Cluster Experts.

Who will help me?

Condor Week 2006

getting knoppix for interproscan high throughput computing edition
Getting Knoppix for InterProScan High Throughput computing Edition
  • Available as a free download from

Google Search “fumikazu”.

Download the image file.

The image includes:

      • InterProScan4.1
      • Condor 6.6.10
      • PVFS2 1.2
      • Ganglia 3.0.1

Condor Week 2006

Chie-san can boot up by an image of Instant High Throughput Computing with an Application on lab’s machines…

She can borrow lab’s computers on weekend without any software installation.

Condor Week 2006

  • This research goal is to provide an instant high performance bioinformatics research workbench for all biology researchers, and allow us easy setup in collaborative project without side effect to local system.


Condor Week 2006

instant setup technologies
Instant Setup Technologies
  • Install-Based Deploy System
    • RPM-Based automatic configuration technology (Redhat)
    • NPACI Rocks toolkits (UCSD)
  • Image-Based Deploy System
    • Live-CD technology (Knoppix)

Condor Week 2006

key solutions
Key Solutions
  • Knoppix
    • A GNU/Linux distribution that construct a machine without hard disk instillation.
  • Parallel File System
    • PVFS is intended a high-performance parallel file system for cluster computing. This system provides high bandwidths access and huge volume storage area.

Condor Week 2006


Worker Node

PXE Boot

Head Node

Condor Week 2006

Database download server

step 1 booting image
Step 1: Booting image

Boot the head node, IP address leased by the DHCP server is displayed after the boot sequence.

Condor Week 2006

step 2 after the successful two setup options easy and advanced are displayed on the screen
Step 2: after the successful, two setup options—EASY and ADVANCED—are displayed on the screen.

Condor Week 2006

step 3 boot work nodes
Step 3: Boot work nodes

All nodes must support PXE boot; The system must automatically assess whether sufficient resources are available for the database arrangement of InterProScan4.1.

Condor Week 2006


The system submits a single test job. The test jobs are completed in a few minutes. The condor job status is displayed on the browser, and Ganglia provides a large amount of information on all nodes. All configurations can be tested in this phase.

Condor Week 2006


Condor Week 2006

web site
Web site

Condor Week 2006


Condor Week 2006