Installation and Integration of Virtual Clusters onto Pragma Grid NAIST Nara, Japan Kevin Lam 07/17/13.

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Installation and Integration of Virtual Clusters onto Pragma Grid NAIST Nara, Japan Kevin Lam 07/17/13

Week 5: Finishing the Tests There was a problem with assigning different tasks to each virtual machine. The cause seemed to stem from Open MPI not being compatible with Dock6.  MPICH, another implementation of MPI, was installed and used instead. firewall problem which prevented jobs from being sent out was declared a non-issue. It would be taken down for local cluster usage. During and after the integration onto public clusters, a solution would be devised. Dock6.2 was upgraded to Dock6.6, the newest version. In order to determine the variability in results, Dock6.6 and Dock6.2 were run using the compounds from the Dock5 test suite.

Week 5: Finishing the Tests (Continued) A previous prime student, Wen-wai, did research on virtual clusters. Her tests compared the results from running docking simulations on physical clusters against the results from running them on her virtual clusters.  Our results from running the same proteins on Dock6.6 were compared to the results from the physical clusters. MPICH and Dock6.6 were compatible. They were able to run on all of the virtual machines. Different tasks were also assigned to individual machines.

Results Zinc ID Wen-Wai's Results Dock 6.6 Results (Grid)naconakomolongmaocikbpraauroracafe01tea01 ZINC ZINC ZINC ZINC ZINC ZINC ZINC ZINC ZINC ZINC ZINC

Results PDB CodeDock 5 PublishedDock 6.2 TestDock 6.6 TestDock 5 PublishedDock 6.2 TestDock 6.6 Test GridAmber 1A ABE ABF ACJ ACM AI AOE AQW AZM BYG C5C C5X C CBX CIL GBP H4N MCP PCP PK GPB HVT AAH LBD ABP

Coming Up Next Week The results need to be evaluated to ensure that the tests are precise if not accurate. As soon as that is done, the virtual cluster can be moved to the NAIST cluster. The firewall issue will then need to be fixed.

Exploring the Culture

Acknowledgments UCSD + PRIME  Dr. Jason Haga  Dr. Gabriele Wienhausen  Dr. Peter Arzberger  Teri Simas  Tricia Taylor  Jim Galvin  Wen-wai Yim  Olivia Yang  Joshua Wei Host Institute (NAIST)  Dr. Kohei Ichikawa  Dr. Hajimu Iida Funding  JASSO  National Science Foundation