PRAGMA18 Demonstration 2-4 March 2010 Kei Kokubo, Yasuyuki Kusumoto, Susumu Date Osaka University, Cybermedia Center Wen-Wai Yim, Jason Haga Department.

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Presentation transcript:

PRAGMA18 Demonstration 2-4 March 2010 Kei Kokubo, Yasuyuki Kusumoto, Susumu Date Osaka University, Cybermedia Center Wen-Wai Yim, Jason Haga Department of Bioengineering, University of California, San Diego

Overlay Network Organization A Organization B Organization C Physical network VM Virtual Cluster  The concept:  Dynamically aggregate available resources from different organizations on the basis of user’s request  Provide a user with a private virtual cluster Virtual node

1. Utilize three nodes from each of two clusters located at Osaka University 2. Flow of Demonstration 1. access to a Web portal to build a virtual cluster 2. set and submit some requirements for the deployment 3. submit an example job into the virtual cluster Overlay Network mocalatte VM Web Portal Virtual Cluster

 Xen  Need for virtualization  OpenVPN  Need to provide a single private network address space among virtual machines and user’s machine  PIAX  Need to organize an overlay network  Discover appropriate resources for a user  Realize IP-based end-to-end communication on the overlay network relaying the connection of the OpenVPN  Java 5 or latter versions are needed

 We believe our system will help scientists and researchers to deploy their private virtual cluster on available resources from different organizations.  Wen-wai actually verified the possibility of our proposed virtual cluster  The virtual cluster deploys an appropriate computational environment for her application.

Developed by UCSF Free, constantly improving Models ligand/receptor interactions – Dock score: sum of the van der Waals attractive, van der Waal dispersive and Coulombic electrostatic energies – Time – Ligands/Receptor from ZINC database –

Developer's nacona komolongm aocikbpraauroracafe01tea01 OS-bit6432 machine bit6432 gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Graph I. Visualization of DOCK 6.2 scores over PRAGMA Grid Graph I. DOCK 6.2 scores from virtual screenings across PRAGMA clusters Developer's naconakomolongmaocikbpraauroracafe01tea01 OS-bit6432 machine bit6432 gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Developer's naconakomolongmaocikbpraauroracafe01tea01 OS-bit6432 machine bit6432 gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E

Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E coregridlatteVC_coregridVC_latte Time Per Molecule13.5 ± ± ± ± 7 Total674.6 ± ± 5953 ± ± 6 Table II. DOCK 6.2 Scores of Virtual Clusters Compared with Physical Clusters Table III. DOCK 6.2 Execution Times on Virtual Clusters Compared with Physical Clusters Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E Developer'scoregridLatteVC_coregridVC_latte OS-bit6432 machine bit gcc version IDScores ZINC ZINC ZINC ZINC ZINC ZINC E

 Performing DOCK 6.2 experiments on a heterogeneous Grid can lead to inconsistent results.  For any scientific application, this can be a problem.  Virtual clusters can provide a solution with affordable overhead costs.

Overlay Network Organization A Organization B Organization C Physical network VM Virtual Cluster  Develops P2P overlay network on every resources  Dynamically gathers unused computational resources from different organizations  Forms a virtual private network among the virtual machines Virtual node

1. Utilize computational resources of two clusters located at Osaka University 2. access to a Web portal to develop a virtual cluster 3. submit some requirement for the development Overlay Network mocalatte VM Virtual Cluster Web Portal