Grid Chem Science Gateway In Production National Science

Grid. Chem Science Gateway In Production National Science Foundation 23 May 2007 Sudhakar Pamidighantam NCSA, University of Illinois at Urbana-Champaign sudhakar@ncsa. edu National Center for Supercomputing Applications

Outline • Grid. Chem: 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

The Big Picture National Center for Supercomputing Applications

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

Science Enabled • Azide Reactions for Controlling Clean Silicon Surface Chemistry: Benzylazide on Si(100)-2 x 1 Semyon 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 × 1 Rodriguez-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

Possible H-bonds network for P 450 cam hydroperoxy 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: THR 252 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

The Somersault Isomerization of Model Cpd 0 Robert Bach and Olga Dmytrenko, 2006 National Center for Supercomputing Applications

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

Somersault Mechanism Summary for Isobutane Hydroxylation National Center for Supercomputing Applications

Tetrakis. Dimethyl. Amino. Titanium and its derivatives on Si(100)2 x 1 Surface: Diffusion Barrier Thinfilms on Silicon Rodrigues-Reyes and Teplyakov National Center for Supercomputing Applications

Benzylazide on Si(100)-2 x 1 Surface Deposition of Aromatic Moieties on Silicon for Lateral Electron Transfer Bocharov et al. . National Center for Supercomputing Applications

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

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

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

Grid. Chem Resources New Computing Systems System Capacity (Cpus/Cores) Capability Mercury(NCSA) 1774 Small/Large Parallel Runs Abe(NCSA) 9600 Massively Parallel Runs Data. Star(SDSC) 2368 Shared. Memory Large Runs Bluegene/L(SDSC) 3456 Cluster Large Parallel Runs Teragrid. Cluster(SDSC) 564 Small/Large Parallel Runs Big. Red(IU) 1024 Shared. Memory Small/Large Runs BCX (UKy) 1360 Shared/Distributed Memory small/Large Parallel Runs National Center for Supercomputing Applications

Application Software Resources Currently Supported Suite Version Location Gaussian 03 C. 02/D. 01 Many Platforms Mol. Pro 2006. 1 NCSA NWChem 5. 0/4. 7 Many Platforms Gamess Jan 06 Many Platforms Amber 8. 0 Many Paltforms QMCPack 2. 0 NCSA National Center for Supercomputing Applications

Grid. Chem Software Resources New Applications Integration Underway • • • ADF Amsterdam Density Functional Theory Wien 2 K Linearized Augemented Plain wave (DFT) CPMD Car Parinello Molecular Dynamics QChem Molecular Energetics (Quantum Chemistry) Aces 3 Parallel Coupled Cluster Quantum Chemistry Gromacs Nano/Bio Simulations (Molecular Dynamics) NAMD Molecular Dynamics DMol 3 Periodic Molecular Systems ( Quantum Chemistry) Castep Quantum Chemistry MCCCS-Towhee Molecular Confirmation Sampling (Monte Carlo) Crystal 98/06 Crystal Optimizations (Quantum Chemistry) …. National Center for Supercomputing Applications

Gridchem Middleware Service (GMS) National Center for Supercomputing Applications

Grid. Chem 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 Grid. Chem client National Center for Supercomputing Applications

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

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

Distribution of Grid. Chem User Community National Center for Supercomputing Applications

Job Distribution National Center for Supercomputing Applications

System Wide Usage HPC System Usage (SUs) Tungsten(NCSA) 5507 Copper(NCSA) 86484 CCGcluster(NCSA) 55709 Condor(NCSA) 30 SDX(UKy) 116143 CCGCluster(UKy) . 5 Longhorn(TACC) 54 CCGCluster(OSC) 62000 TGCluster(OSC) 36936 Cobalt(NCSA) 2485 Champion(TACC) 11 Mike 4 (LSU) 14537 National Center for Supercomputing Applications

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

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

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

Grid. Chem Gamess GUI National Center for Supercomputing Applications

Grid. Chem Post Processing • IR/Raman Spectra now accessible from G 03, Mol. Pro, NWChem and Gamess Suites VCD/ROA To be Included National Center for Supercomputing Applications

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

Grid. Chem Usability Dynamic Information National Center for Supercomputing Applications

Grid. Chem 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

Grid. Chem Middleware Infrastructure Implementation Currently underway • Implementation of GRMS resource management Service http: //www. gridlab. org/Work. Packages/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

Grid. Chem In New Collaborations Resource 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 Tera. Grid) • International Partners KISTI, APAC, Daresbsry Labs National Center for Supercomputing Applications

Scientific Collaborations • Grid. Chem 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

Some New Grid. Chem 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

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