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Cluster Computing through an Application-oriented Computational Chemistry Grid

Cluster Computing through an Application-oriented Computational Chemistry Grid. Kent Milfeld and Chona Guiang, Sudhakar Pamidighantam, Jim Giuliani. April 24, 2005. Supported by the NSF NMI Program under Award #04-38312. http://www.GridChem.org. Outline.

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Cluster Computing through an Application-oriented Computational Chemistry Grid

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  1. Cluster Computingthrough an Application-orientedComputational Chemistry Grid Kent Milfeld and Chona Guiang, Sudhakar Pamidighantam, Jim Giuliani April 24, 2005 Supported by the NSF NMI Program under Award #04-38312 http://www.GridChem.org

  2. Outline • Computational Chemistry Grid Overview • HPC Application Computing through a Client Interface • Architecture for the GridChem Client • Supporting the Virtual Organization

  3. The Big Picture

  4. Computation Chemistry Grid (CCG)“GridChem” • A collection of “grid-enabled” resources to routinely run chemical physics applications • Integrates a desktop environment into an infrastructure for a specific community of users • comp. chemists with large/small scale needs • experimental chemists who occasionally need simulation capabilities to verify experimental results • Establishes a distributed infrastructure for open scientific research– a virtual organization

  5. Electronic Structure Atoms, Small Molecules, Clusters Cluster Systems Client Interface to the Grid The Components • Applications • Resources • Desktop Environmentthe GridChem Client Compute Intensive 0.1-100 hrs runs High Speed Infrastructure Not Needed Batch Support Secure Access (grid-enabled) 4 – 16 CPUS/job Multi-platform support (XP, OS X, Linux) Responsive

  6. Applications • GridChem supports some apps already • Gaussian 98/03, GAMESS, MolPro • Schedule of integration of additional software • NWChem • ACES-2 • Crystal • Q-Chem • NBO • Wein2K • MCCCS Towhee • homegrown computational chemistry codes developed at LSU

  7. Computational Chemistry Resource Providers NCSA CCS OSC CCT TACC

  8. Resources Over 400 processors and 3,525,000 CPU hours available annually

  9. Gigaflop Processors GigaBytes for Storage Intel: GMA 900 Graphics,… Mac: ATI Radeon 9200 with 32MB DDR 596 MB for Internet Files Desktop Use your workstation! Computing Resource Data Storage Graphics

  10. Desktop -- GridChem • Java Based Client • “Same” Look and Feel on “every” machine. • Consistent Environment • No Globus Installation • Designed for “Application Services” through a Server; but • Can be used as Stand-Alone Client for job submission

  11. GridChem Client GC Middleware Server HPC Resources Site Monitors Kerberos MyProxy SSH modules Kerb. & MyProxy Servers Authentication inputs, resource specs. & temp. cert. transfer Input Preparation Molecular Editor Application Options Site Info (stat./dyn.) MySQL Site Preference Job Submission • Resource specs.  • into Local Batch Specs • Batch Script • Queue Submission Resource Management File Management Application Execution + Output & File Transfers Molecular Editor + Visualization Remote Storage J2EE User See Two-Tier Architecture 3-tier Architecture

  12. Infrastructure (now) * • Server, GridChem Client* • MyProxy (X-500 Certs), Kerberos (Security) • CGI Scripts  GSI ( for Data Movement & Job Launch) • Job Monitoring • Perl filters, MySQL • Support • PCS, Portable Consulting Service • EOT • OSU

  13. Infrastructure (future) • Server • Condor + ? (Job Launch) • GSI ( Data Transfer, uberftp) • Information Repository (IGRID, GPIR,…?) • Support • GridPort 3.0  Monitoring, Consulting (PCS), Accounting…

  14. Infrastructure (future) • GridClient • 3-rd party file transfers (Trebuchet) • More intelligence in input construction • Increase Application Space • Web Start • Indirect DB access for preferences • Advanced visualization support (Molden,…) • Resource Sites • Condor • Globus Utils

  15. GridChem Client

  16. GridChem Client

  17. GridChem Nanocad Molecular Editor

  18. Lexical Analysis And Parsing • Follows the progress of the calculation while it is still running or has completed. • Plots the energy, gradient, etc versus iteration number.

  19. Filter Monitoring Storage HTTP HTML,PHP,… DB Service User Login Batch cron

  20. Job-Status-Monitor = JSM

  21. Consulting User Interface Report Problem Problem Form Personalized Monitor Page Further Interaction Email Notification Notifications Database Consultant Monitor Page Front-line triage Ticket Owner & CCs Ticket Transfer & Response Page Email Notification Consultant Interface

  22. User Submission

  23. Consultant View Consultant’s View

  24. Molecule Viewers Post Processing2d and 3d Orbital isosurfaces Using NCSAChem/Slice/Molden/Cartona/Free Software

  25. Electron Structure: Orbitals or electron densities,… 5-dehydro-m-xylylene triradical

  26. Transcription Regulator(molecular modeling)

  27. Summary • GridChem Client • Resources • Community •  “Better Living Through Chemistry”

  28. References • www.gridchem.org • www.grids-center.org • www.gridlab.org/

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