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Configuration and Deployment of a scalable virtual machine cluster for molecular docking. Nara Institute of Science and technology, Nara Prefecture, Japan. Karen Rodriguez 7 /3/2013. Overview.

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configuration and deployment of a scalable virtual machine cluster for molecular docking
Configuration and Deployment of a scalable virtual machine cluster for molecular docking

Nara Institute of Science and technology, Nara Prefecture, Japan

Karen Rodriguez

7/3/2013

overview
Overview
  • Virtual machines (VMs) have been observed to yield molecular docking results that are far more consistent than those obtained from a grid configuration.
    • Inhomogeneous results obtained from a grid are thought to be due to physical differences in the cluster’s components. This is eliminated by creating and networking cloned VMs.
  • This study’s objectives consist of constructing a clustered VM environment that is scalable according to job demand and which yields consistent dock results.
    • This system is to be tested, packaged, and deployed on the PRAGMA grid. This will provide sufficient computing resources to perform a full-scale docking project of large protein databases.
week 1
Week 1:
  • Kevin Lam and I arrived at Nara Institute for Science and Technology (NAIST) June 23,2013. Met Ichikawa-sensei and received a brief tour of the laboratory and living accommodations.
  • Began installation of software necessary for VM creation and management (Debian OS, LVM configuration, and Xen) upon suggestion of Wen-waiYim, a previous PRIME student familiar with virtual clusters.
    • Further discussion with Dr. Haga and Ichikawa-sensei helped us determine that it would be more beneficial to utilize CentOS 6 with KVM and work from there since the Rocks/KVM platform is the most advanced to date.
    • Installed CentOS 6 and the necessary VM packages on a lab computer (HP Z400 Workstation). Updated software, configured host bridges.
  • Created first VM with CentOS 6 and installed docking software, cloned thrice.
future plans
Future Plans
  • Network VM’s into a single cluster.
  • Perform a small-scale docking test on the virtual cluster.
  • If results are satisfactory, will expand virtual cluster in terms of size.
  • Create an environment of layered clusters.
  • Investigate Amazon Elastic Cloud applicability in this project and how to implement.
    • Amazon Elastic Cloud (EC2) is a web service that permits automated resizing of the cluster depending on host demand. It would theoretically be capable of spawning and destroying virtual machines to adjust computing capacity.
      • If tests yield satisfactory results, will acquire necessary account and requirements for its execution.
  • Also will investigate VM packaging and preparation measures for migration and deployment.