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Integrated Environment for Computational Chemistry on the APAC Grid

Integrated Environment for Computational Chemistry on the APAC Grid. Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University, ACT 0200, Canberra, Australia. Concept of the National Grid. Research Teams. Data Centres. grid-based portals distributed computation

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Integrated Environment for Computational Chemistry on the APAC Grid

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  1. Integrated Environment for Computational Chemistry on the APAC Grid Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University, ACT 0200, Canberra, Australia

  2. Concept of the National Grid Research Teams Data Centres grid-based portals distributed computation federated data access remote control collaboratories Sensor Networks Other Grids: Institutional National International Instruments

  3. APAC National GridComputing Grid Infrastructure Job Submission: Command Line Portals • Systems coverage • Users can access ALL systems at APAC partners • About 4600 processors and 100’s of Tbytes of disk • Around 3Pbytes of disk cached HSM systems QPSF (JCU) Job Monitoring: Scope QPSF APAC National Facility Job Management: Globus, PBS Nimrod LCG IVEC ac3 ANU SAPAC Computing Systems: Peak Mid-range Special CSIRO VPAC TPAC

  4. Integrated Environment for Computational Chemistry on the APAC Grid Supercomputer(s) Client

  5. What does it mean “Integrated Environment”?

  6. “Integrated Environment”: Overall Architecture There are two standalone programs, JMolEditor and Shelves Providers: GT2 GT4 SSH Local Database PDB JMolEditor Tripos Mol2 Gaussian Job submission Job Monitoring Getting results Gaussian Amber Input File Formats Input File Preparation Amber Gamess Shelves Gromacs Gamess JMolEditor Gromacs

  7. “Integrated Environment”: Rich User Interface High-performance 3D rendering Intuitive interface for unexperienced users

  8. “Integrated Environment”: Support for popular Computational Chemistry Formats Gaussian GAMESS Mopac PBD Tripos Mol2 Amber Gromacs etc.

  9. The most popular Computational Chemistry Programs on the National Facility (1920 CPUs) Of total wall time on the Altix cluster (1920 CPUs) Our primary targets are the most popular programs in the Computational Chemistry community

  10. “Integrated Environment”:Preparation of input files for popular programs Simple Gaussian Input Editor

  11. “Integrated Environment”: On-line and in-built help system and tutorials Tracking Help Help

  12. “Integrated Environment”: Molecular Builder/Editor Adding/deleting Atoms Adding Fragments Adding Molecules Modifying atoms, bonds, angles, dihedral angles Automatic filling of empty valences with hydrogens

  13. “Integrated Environment”: Visualizing Volumetric Data (Gaussian cubes)

  14. “Integrated Environment”: Implementing a Full Production Cycle Structure Preparation Input File Preparation Job Submission Calculated Structure Visualization Output Files Download Job Status Query

  15. “Integrated Environment”: Job Submission All complexities of the Grid job submission are hidden behind a dialog Common options for all programs Provider Specific Options Scheduler Specific Options Program specific options

  16. “Integrated Environment”: Job Status Monitoring To download output files To kill selected jobs

  17. System requirements • Mac OS All is already there… • MS Windows and Linux 1) The Java Runtime Environment (JRE)≥ 1.5 2) Download and install Java3d (freeware optional component)

  18. Download Site for JMolEditor • http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html Option 1: Download a program to run it on a desktop Option 2: Run from a website using Java Web Start • On-line Help

  19. What will be next? • Support for more Computational Chemistry Programs (visualization, input files preparation, analysis of final results) • Adding new features according to the user’s requests…

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