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Acknowledgements

GridChem: Integrated Cyber Infrastructure for Computational Chemistry http://www.gridchem.org Sudhakar Pamidighantam Sudhakar@ncsa.edu 10 Oct 2005. Acknowledgements. Motivation. Software - Mature and easy to use to address chemists questions of interest Community of Users

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Acknowledgements

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  1. GridChem: Integrated Cyber Infrastructure for Computational Chemistryhttp://www.gridchem.orgSudhakar PamidighantamSudhakar@ncsa.edu10 Oct 2005 National Center for Supercomputing Applications

  2. Acknowledgements National Center for Supercomputing Applications

  3. Motivation Software - Mature and easy to use to address chemists questions of interest Community of Users - Need and capable of using the software Some are non traditional computational chemists Resources - Various in capacity and capability National Center for Supercomputing Applications

  4. Background Qauntum Chemistry Remote Job Monitor ( Quantum Chemistry Workbench) 1998, NCSA Chemviz 1999-2001, NSF National Center for Supercomputing Applications

  5. Technologies Web Based Client Server Models Visual Interfaces Distributed computing National Center for Supercomputing Applications

  6. GridChem NCSA Alliance was commissioned 1998 Diverse HPC systems deployed both at NCSA and Alliance Partner Sites Batch schedulers different at sites Policies favored different classes and modes of use at different sites/HPC systems National Center for Supercomputing Applications

  7. Grid and Gridlock Alliance lead to Physical Grid Grid lead to TeraGrid Homogenous Grid was planned but it was difficult to keep it homogenous Things got more complicated and we have heterogeneous grid now! National Center for Supercomputing Applications

  8. Extended TeraGrid Facility www.teragrid.org National Center for Supercomputing Applications

  9. Initial Grid Status Grid Hardware Scientific Applications Middleware National Center for Supercomputing Applications

  10. Current Grid Status Grid Hardware Interfaces Scientific Applications Middleware National Center for Supercomputing Applications

  11. User Community Chemistry and Computational Biology User Base Sep 03 – Oct 04 NRAC AAB Small Allocations ------------------------------------------------------------- #PIs 26 23 64 #SUs 5,953,100 1,374,100 640,000 National Center for Supercomputing Applications

  12. User Issues • New systems meant learning new commands • Porting Codes • Learning new job submissions and monitoring protocols • New proposals for time • Computational modeling became more popular and users increased • Batch queues are longer / waiting increased • Find resources where to compute - probably multiple distributed sites • Multiple proposals/allocations/logins • Authentication and Data Security • Data management National Center for Supercomputing Applications

  13. Computational Chemistry Grid Integrated Cyber Infrastructure for Computational Chemistry Integrates Applications, Middleware, HPC resources, Scheduling and Data management Allocations, User Services and Training National Center for Supercomputing Applications

  14. Resources • Over 400 processors and 3,525,000 CPU hours available annually National Center for Supercomputing Applications

  15. Other Resources Extant HPC resources at various Supercomputer Centers NCSA Tungsten and Copper Optionally TeraGrid/local/personal resources These may require existing allocations/Authorization National Center for Supercomputing Applications

  16. Applications • GridChem supports some apps already • Gaussian 98/03, GAMESS, Molpro, NWChem • Schedule of integration of additional software • ACES-2 • Crystal • Q-Chem • Wein2K • MCCCS Towhee • More ….. National Center for Supercomputing Applications

  17. Details • Three tiered architecture • GridChem client • middleware server • computational resources National Center for Supercomputing Applications

  18. GridChem System user user user user user Portal Client application application Grid Middleware Proxy Server Grid Services MassStorage Grid http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0438312 National Center for Supercomputing Applications

  19. GridChem Client • Graphical user interface (GUI) • Java desktop application • Pre and Post Processing • helps scientists generate input • submit and monitor quantum chemistry jobs remotely • visualize output data • Leverages internal development projects National Center for Supercomputing Applications

  20. Composed of several modules authentication job-editor molecule builder visual molecular editor molecular fragment database crystal structure database job submission job manager job status info output monitoring and retrieval GridChem Client Architecture National Center for Supercomputing Applications

  21. Allocation • GridChem is in friendly user mode • GridChem allocations are ready! Visit https://www.gridchem.org/allocations/policy.htm Simple one page submission Password is user generated ( with strong suggestions of the type) Registration of External allocations possible “Add Users” Facility Available for PI’s National Center for Supercomputing Applications

  22. GridChem Client Launch National Center for Supercomputing Applications

  23. GridChem Authentication Requires a GridChem Login National Center for Supercomputing Applications

  24. GridChem Allocation Information National Center for Supercomputing Applications

  25. User Preferences National Center for Supercomputing Applications

  26. Creating Jobs National Center for Supercomputing Applications

  27. GridChem Job Editor National Center for Supercomputing Applications

  28. GridChem Job EditorGamess Template National Center for Supercomputing Applications

  29. GridChem Job EditorNWChem Template National Center for Supercomputing Applications

  30. GridChem Nanocad Molecular Editor National Center for Supercomputing Applications

  31. Molecular Editor Based Input National Center for Supercomputing Applications

  32. GridChem Job Submission Job Object . National Center for Supercomputing Applications

  33. Submit Jobs National Center for Supercomputing Applications

  34. GridChem Job Management National Center for Supercomputing Applications

  35. Job Status Information National Center for Supercomputing Applications

  36. Monitor Output National Center for Supercomputing Applications

  37. Post-Processing • 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. • Displays the current (optimized) structure in the Molecular Editor National Center for Supercomputing Applications

  38. Post ProcessingResults National Center for Supercomputing Applications

  39. Allocations Existing allocations at various extant resources are supported Community allocation to reduce proposal writing/review “headaches” for already “funded” research. National Center for Supercomputing Applications

  40. User/Community Support • Support provided by distributed set of staff involved in the project - Chemists, Programmers, Systems Engineers • Problems tracking through single mechanism - PCS Ticketing System https://www.gridchem.org/consult/ • Online documentation to be provided on the CCG website - FAQs, Benchmarking Informations, Tips/Tricks etc.. National Center for Supercomputing Applications

  41. Training and Outreach Integration • Develop modules on a set of topics • interface fundamentals (e.g., inputs, choice lists, controls, etc.)authentication/authorization molecular builderjob manager resource managementpost-processing visualizationintegration of additional applications • Provide as workshops and seminars • 5th Annual Computational Chemistry Conference at the UIUC, April 17-19, 2005 • Annual updates • track advancements and additional technologies developed and integrate them into CCG National Center for Supercomputing Applications

  42. Work In Progress New Resource Integration Easily manageable Resource Description Facility to add or remove resources and validation Software Provide Pre and Post Processing for additional Application Software Automated Distributed computing Metascheduling across Grid National Center for Supercomputing Applications

  43. Applications • Gamess • NWChem • MolPro Pre and Post Processing Support National Center for Supercomputing Applications

  44. Post Processing Some example Visuals Arginine Gamess/6-31G*Total electronic density 2D - Slices National Center for Supercomputing Applications

  45. Molecular Orbitals 2D National Center for Supercomputing Applications

  46. 3D VRML Views National Center for Supercomputing Applications

  47. Questions We would like to be responsive to community requests Source is OPEN. Contributions welcome! https://www.gridchem.org/software/software.htm National Center for Supercomputing Applications

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