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

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Background• Biologists need a high perfo

rmance computing system for their research process. However, they do not know how to build a cluster system by themselves.

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Meet Chie-san.

She is a biologist

with a big problem.

I borrowed slides from Condor.

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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.

http://www.ebi.ac.uk/interpro/README1.html

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Policy BarrierTechnical Skill Barrier

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

Who will help me?

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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

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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.

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Goal

• 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.

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Instant Setup Technologies

• Install-Based Deploy System– RPM-Based automatic configuration technology (Red

hat)– NPACI Rocks toolkits (UCSD)

• Image-Based Deploy System– Live-CD technology (Knoppix)

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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.

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Parallel File System on RAM Disk

Knoppix for InterProScan4.1 High Throughput Computing Edition

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500MByte500MByte

500MByte

500MByte500MByte

500MByte

Private Network

Intra Network

Inter Network

Service Sharing

Head Node

Worker Node

PXE Boot

Database download server

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Step 1: Booting image

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

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Step 2: after the successful, two setup options—EASY and ADVANCED—are

displayed on the screen.

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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.

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Step 4: building cluster system

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Download InterProScan database set

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Testing

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.

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Results

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Web site

http://big.gsc.riken.jp/index_html/Members/fumikazu/htc

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Questions