1. 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

2. Condor Week 2006 Background Biologists need a high performance computing system for their research process. However, they do not know how to build a cluster system by themselves.

3. Condor Week 2006 Meet Chie-san. She is a biologist with a big problem. I borrowed slides from Condor.

4. Condor Week 2006 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

5. Condor Week 2006 Policy Barrier Technical Skill Barrier I have 103,000 sequences to search a gene functional domain. And I am Non-Cluster Experts. Who will help me?

6. Condor Week 2006 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

7. 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.

8. Condor Week 2006 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.

9. Condor Week 2006 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)

10. Condor Week 2006 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.

11. Condor Week 2006 Parallel File System on RAM Disk

12. Knoppix for InterProScan4.1 High Throughput Computing Edition

13. Condor Week 2006 Head Node Worker Node PXE Boot Database download server

14. Condor Week 2006 Step 1: Booting image Boot the head node, IP address leased by the DHCP server is displayed after the boot sequence.

15. Condor Week 2006 Step 2: after the successful, two setup options—EASY and ADVANCED—are displayed on the screen.

16. Condor Week 2006 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.

17. Condor Week 2006 Step 4: building cluster system

18. Condor Week 2006

19. Download InterProScan database set

20. Condor Week 2006 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.

21. Condor Week 2006 Results

22. Condor Week 2006

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

24. Condor Week 2006 Questions