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Installation and Integration of Virtual Clusters onto Pragma Grid

Installation and Integration of Virtual Clusters onto Pragma Grid. NAIST Nara, Japan Kevin Lam 07/31/13. Week 5: Aiming for Accurate Results.

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Installation and Integration of Virtual Clusters onto Pragma Grid

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  1. Installation and Integration of Virtual Clusters onto Pragma Grid NAIST Nara, Japan Kevin Lam 07/31/13

  2. Week 5: Aiming for Accurate Results • The comparison between the results from Dock5, Dock6.2, and Dock6.6 showed a major difference between Dock 6.x and Dock 5.x. The results between the physical clusters and our virtual cluster were close, but it could be closer. • A new cluster was created containing 1 masternode and 1 slavenode. Machine version: CentOS 5.9 32-bit utilizing gcc 4.1.2. • The results were different. However, the difference between our results and the developer’s results remained roughly the same.

  3. Week 5: Aiming for Accurate Results (Continued) • The test suite that Wenwai used was also run. Out of twelve ligands that were run, two were drastically different from Wenwai’s results. The other ten were accurate. • The PRAGMA administrator was contacted about deploying the VM. It seems that more information pertaining to the VMs and the network would be needed to proceed forward. A skype session is being setup to discuss this further.

  4. Coming Up Next Week • VM deployment needs to be discussed with the PRAGMA administrator over Skype. • There is a possibility that we will need to write instructions on how to setup, configure, and run the VM. This needs to be given to the PRAGMA administrator. • A solution needs to be found for the Dock6.2 test suite results. Two of the results are do not match with Wenwai’s results. • We need to look more into N2N which is to be set up after the VMs are deployed.

  5. Exploring the Culture

  6. Acknowledgment • UCSD + PRIME • Dr. Jason Haga • Dr. Gabriele Wienhausen • Dr. Peter Arzberger • Teri Simas • Tricia Taylor • Jim Galvin • Wen-waiYim • Olivia Yang • Joshua Wei • Nadya Williams • Host Institute (NAIST) • Dr. Kohei Ichikawa • Dr. Hajimu Iida • Funding • JASSO • National Science Foundation

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