GridChem: Science Gateway for High-End Computing Systems

1. GridChem Science GatewayIn ProductionNational Science Foundation 23 May 2007 Sudhakar Pamidighantam NCSA, University of Illinois at Urbana-Champaign sudhakar@ncsa.edu National Center for Supercomputing Applications

2. Outline • GridChem: A Brief Overview • Scientific Impact • Resources High End Computing Systems Applications Software • Middleware Infrastructure • Portal/Gateway Client • User Community • Usage • Critical Gateway Issues • Future Plans National Center for Supercomputing Applications

3. The Big Picture National Center for Supercomputing Applications

4. Science Enabled • Chemical Reactivity of the Biradicaloid (HO...ONO) Singlet States of Peroxynitrous Acid. The Oxidation of Hydrocarbons, Sulfides, and Selenides. Bach, R. D et al. J. Am. Chem. Soc. 2005, 127, 3140-3155. • The "Somersault" Mechanism for the P-450 Hydroxylation of Hydrocarbons. The Intervention of Transient Inverted Metastable Hydroperoxides. Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006, 128(5), 1474-1488. • The Effect of Carbonyl Substitution on the Strain Energy of Small Ring Compounds and their Six-member Ring Reference Compounds Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006,128(14), 4598. National Center for Supercomputing Applications

5. Science Enabled • Azide Reactions for Controlling Clean Silicon Surface Chemistry: Benzylazide on Si(100)-2 x 1Semyon Bocharov et al..J. Am. Chem. Soc.,128 (29), 9300 -9301, 2006 • Chemistry of Diffusion Barrier Film Formation: Adsorption and Dissociation of Tetrakis(dimethylamino)titanium on Si(100)-2 × 1Rodriguez-Reyes, J. C. F.; Teplyakov, A. V.J. Phys. Chem. C.; 2007; 111(12); 4800-4808. • Computational Studies of [2+2] and [4+2] Pericyclic Reactions between Phosphinoboranes and Alkenes. Steric and Electronic Effects in Identifying a Reactive Phosphinoborane that Should Avoid Dimerization Thomas M. Gilbert* and Steven M. Bachrach Organometallics, 26 (10), 2672 -2678, 2007. National Center for Supercomputing Applications

6. Possible H-bonds network for P450camhydroperoxy intermediate Nagano, S.; Poulos, T.L. J. Biol. Chem. 2005, 250, p.1668 • Auclair, K.; Hu, Z.; Little, D. M.; Ortiz de Montellano, P. R.; Groves, J. T. J. Am. Chem. Soc. 2002, 124, 6020. Suggested: THR252 accepts an H-bond from the hydroperoxy (Fe(III)-OOH that promotes the second protonation on the distal oxygen, leading to the O-O bond cleavage National Center for Supercomputing Applications

7. The Somersault Isomerization of Model Cpd0 Robert Bach and Olga Dmytrenko, 2006 National Center for Supercomputing Applications

8. Energy Diagram for the Concerted Non-synchronous Hydroxylation of Isobutane Energy diagram (kcal/mol) for the oxidation of the isobutane with ground state, 24a (GS-8 hydrogen bonded to isobutane). MIN-24b [model oxidant MIN-10 (PorFe(SH)OHO) hydrogen bonded to isobutene] is not necessarily on the reaction pathway. National Center for Supercomputing Applications

9. Somersault Mechanism Summary for Isobutane Hydroxylation National Center for Supercomputing Applications

10. TetrakisDimethylAminoTitanium and its derivatives on Si(100)-2x1 Surface: Diffusion Barrier Thinfilms on SiliconRodrigues-Reyes and Teplyakov National Center for Supercomputing Applications

11. Benzylazide on Si(100)-2x1 SurfaceDeposition of Aromatic Moieties on Silicon for Lateral Electron TransferBocharov et al.. National Center for Supercomputing Applications

12. [2+2] Cyclo Additions involving B=P BondsGilbert and Bachrach Ethyne Addition Ethene Additions Dimerization National Center for Supercomputing Applications

13. [4+2] Cycloadditions involving B=P BondsGilbert and Bachrach Cis-Butadiene Addition Cyclopentadiene Addition National Center for Supercomputing Applications

14. GridChem Resources http://portal.gridchem.org:8080/gridsphere/gridsphere?cid=home National Center for Supercomputing Applications

15. GridChem ResourcesNew Computing Systems National Center for Supercomputing Applications

16. Application Software ResourcesCurrently Supported National Center for Supercomputing Applications

17. GridChem Software ResourcesNew ApplicationsIntegration Underway • ADF Amsterdam Density Functional Theory • Wien2K Linearized Augemented Plain wave (DFT) • CPMD Car Parinello Molecular Dynamics • QChem Molecular Energetics (Quantum Chemistry) • Aces3 Parallel Coupled Cluster Quantum Chemistry • Gromacs Nano/Bio Simulations (Molecular Dynamics) • NAMD Molecular Dynamics • DMol3 Periodic Molecular Systems ( Quantum Chemistry) • Castep Quantum Chemistry • MCCCS-Towhee Molecular Confirmation Sampling (Monte Carlo) • Crystal98/06 Crystal Optimizations (Quantum Chemistry) • …. National Center for Supercomputing Applications

18. Gridchem Middleware Service (GMS) National Center for Supercomputing Applications

19. GridChem User Services • Allocation https://www.gridchem.org/allocations/index.shtml Community and External Registration Reviews, PI Registration and Access Creation Community User Norms Established • Consulting/User Services https://www.gridchem.org/consult Ticket tracking, Allocation Management • Documentation, Training and Outreach https://www.gridchem.org/doc_train/index.shtml FAQ Extraction, Tutorials, Dissemination Help is integrated into the GridChem client National Center for Supercomputing Applications

20. GridChem Client Download Statistics http://download.gridchem.org/usage/ National Center for Supercomputing Applications

21. Users and Usage • 222 Users Under 168 Projects Include Academic PIs and colleagues, graduate classes and training users (typically used in tutorials/workshops/demo sessions etc..) More than a 380000 CPU Wallhours Delivered since Jan 05 for over 5690 Individual Jobs National Center for Supercomputing Applications

22. Distribution of GridChem User Community National Center for Supercomputing Applications

23. Job Distribution National Center for Supercomputing Applications

24. System Wide Usage National Center for Supercomputing Applications

25. GridChem Client Enhancements • New Molecular Editor JMolEditor (ANU) Integration • VMD Is integrated • Nanotube Generator (Tubegen) Will be available • Gamess Graphical User Interphase National Center for Supercomputing Applications

26. Java Molecular Editor • JMolEditor Three Dimensional Visual with Java 3D Intuitive Molecule Manipulation Interactive Bond, Angle and Dihedral Settings A Gaussian input generator Interface National Center for Supercomputing Applications

27. Nanotube Generator:TubegenCourtesy: Doren Research Group at the University of Delaware Crystal Cell Types Output Formats National Center for Supercomputing Applications

28. GridChem Gamess GUI National Center for Supercomputing Applications

29. GridChem Post Processing • IR/Raman Spectra now accessible from G03, MolPro, NWChem and Gamess Suites VCD/ROA To be Included National Center for Supercomputing Applications

30. GridChem Post Processing • Normal Mode Viewing in 3D VRML • Other Spectra With MO Integration NMR Electronic Spectra National Center for Supercomputing Applications

31. GridChem UsabilityDynamic Information National Center for Supercomputing Applications

32. GridChem Usability • Information on Potential Start and End Time for a given set of Job parameters • Automated Resource Selection • Possible Job Migration In case of dropped nodes or incomplete job • Monitoring Multiple Jobs • Automated Monitoring Job Output National Center for Supercomputing Applications

33. GridChem Middleware InfrastructureImplementation Currently underway • Implementation of GRMS resource management Service http://www.gridlab.org/WorkPackages/wp-9 • Moving toward Service based job submission eliminating gateway interfaces • Infrastructure for multiple input files for single application • Infrastructure for multiple inputs in High Throughput processing • Integrated workflow for multi scale coupled modeling • Meta-scheduling for High Throughput Processing Match Making Round-robin scheduling Preferred Host Set usage National Center for Supercomputing Applications

34. GridChem In New CollaborationsResource Providers • New Resource Providers Open Science Grid Initially for Bio-related applications (open source preferably) • PRAGMA Partner sites University of Hyderabad • ORNL (Could be via TeraGrid) • International Partners KISTI, APAC, Daresbsry Labs National Center for Supercomputing Applications

35. Scientific Collaborations • GridChem Extension to Molecular Sciences (Bio, Nano, Geo and Materials Sciences) (NSF Proposal) • Parameter Sweep for Potential Energy Hyper Surfaces (Faculty Fellows, NCSA) • Automated Parameterization of Force fields (NSF Proposal) • Ab initio Molecular Dynamics (Faculty Fellows, NCSA) • Education (CI-TEAM) (NSF Proposals) • Multi-Scale Modeling (IACAT, UIUC) National Center for Supercomputing Applications

36. Some New GridChem Infrastructure • Workflow Editors • Coupled Application Execution • Large Scale Computing • Metadata and Archiving • Rich Client Platform Refactorization • Intergrid Interactions • Open Source Distribution http://cvs.gridchem.org/cvs/ • Open Architecture and Implementation details http://www.gridchem.org/wiki National Center for Supercomputing Applications

37. Critical Gateways Issues • Science Gateways compete with business as usual for the end user research scientist • No direct access to HPC systems may be possible leading to apparent lack of control for users • No “End to end solutions” If part of the research needs require old ways Gateways may be avoided • Learning to use Gateways should provide substantial added benefit –Cost/Benefit Issues for users • Flexibility to integrate new applications as needed by community quickly is critical to keep the user community engaged National Center for Supercomputing Applications