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Enabling Science with Grid Technology

Enabling Science with Grid Technology. Jamie Rintelman , Kerstin Kleese-Van Dam, Rik Tyer STFC-Daresbury Laboratory; Daresbury, Cheshire, UK. Who am I?. STFC Daresbury laboratory eScience Dept - Computational Science and Engineering Dept Liaison Chemist

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Enabling Science with Grid Technology

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  1. Enabling Science with Grid Technology • Jamie Rintelman, Kerstin Kleese-Van Dam, Rik Tyer • STFC-Daresbury Laboratory; Daresbury, Cheshire, UK

  2. Who am I? • STFC Daresbury laboratory • eScience Dept - Computational Science and Engineering Dept Liaison • Chemist • Specializing in Quantum Chemistry, electronic structure theory, GAMESS

  3. Traditional Way of Working • eMinerals Grid Computing Framework • Background on eMinerals Program • Grid Computing Framework • Input preparation • Monty - bulk job submission • RMCS - integrated compute/data/metadata framework • Rgem - analysis of results • Scientific Examples • QDGA • BTG • eMinerals

  4. Traditional Way of Working I Comp01 Comp03 Files on local computer Comp02 Check for available remote resource Comp04

  5. Traditional Way of Working I Comp01 Comp03 Files on local computer Comp02 Check for available remote resource Comp04

  6. Traditional Way of Working I Comp01 Comp03 SCP files over Files on local computer

  7. Traditional Way of Working I Comp01 Comp03 Run job Output files on remote resource

  8. Traditional Way of Working I Comp01 Comp03 Check on progress (many times?) Output files on remote resource

  9. Traditional Way of Working I Comp01 Comp03 SCP files back Output files on remote resource

  10. Traditional Way of Working I Comp01 Comp03 Files on local computer

  11. Traditional Way of Working II Collaborator asks for files Find files Place them on ftp server, or put in email Email collaborator with files or with location of files

  12. eMinerals / RMCS framework A new way of working

  13. eMinerals Project • NERC funded • Collaborators throughout the UK • Pragmatic approach to development = Science Driven

  14. TheeMinerals team

  15. eMinerals Project - Scope • Set of tools to facilitate scientific work • Building and configuring grids • Job submission tools • Data management • Metadata management • Data processing / Information extraction • Simulation output visualization

  16. eMinerals Project - Scope • Set of tools to facilitate scientific work • Building and configuring grids • Job submission tools • Data management • Metadata management • Data processing / Information extraction • Simulation output visualization

  17. RMCS Framework • Components: • Input Preparation • Bulk Job Submission • Running Jobs • Analysis of Results • Additional Building Blocks: • Storage Resource Broker (SRB) - Data Storage and Collaborative Sharing • AgentX - XML data, sharing between programs, metadata capture (developed by Phil Couch, STFC)

  18. Input preparation • Bespoke scripts to automate generation of input files for parameter sweep type calculations Simulation Template input Simulation Simulation Simulation

  19. Monty - Bulk Job Submission SRB • set up structure in SRB for staging of input files and binary; storage of output files • set up structure in database for metadata capture • submit jobs to RMCS Monty Metadata Database RMCS

  20. Metadata Database Study • Metadata in database are divided into study, data set, and data object • Study = entire proj • Data Set = group of calculations • Data Objects = piece of data from each calculation Data Set Data Set Data Objects (i.e. “parameters”)

  21. RMCS - integrated compute/ data/ metadata framework3 tier model Client tools GUIs (SOAP library), Command Line Tools (gSOAP) RMCS Server The Grid

  22. “The Grid” so far The Grid Northwest Grid National Grid Service eMineralsMiniGrid Cambridge Condor Pool Scarf Cluster (coming soon)

  23. RMCS - integrated compute/data/metadata framework • Meta-schedule • Stage input files and binary • Run job/submit to batch queue • Transfer output to SRB • Use Rcommands + AgentX to put metadata into database /extract XML data if available

  24. Rgem - Collect Results • Analyze Results • Collect parameters from a chosen dataset -> tab separated file -> graph Data Set Data Objects

  25. Scientific Examples • Quantum Directed Genetic Algorithm • Transition metal oxides, Perovskites • eMinerals

  26. Quantum Directed Genetic Algorithm (QDGA)Marcus Durant (Univ of Northumbria), Jens Thomas (STFC-Daresbury) • The QDGA project uses a genetic algorithm to try and determine an optimal catalyst for the conversion of nitrogen (N2) to hydrazine (N2H4)

  27. Template Input GAMESS-UK

  28. DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search Template Input GAMESS-UK BespokeScripts

  29. DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search SRB Input files + binary Output files Template Input GAMESS-UK BespokeScripts Monty Create directory structure

  30. DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search SRB Input files + binary Output files Template Input GAMESS-UK BespokeScripts Monty Create metadata containers in database Metadata Database

  31. DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search SRB Input files + binary Output files Template Input GAMESS-UK BespokeScripts Monty RMCS Submit jobs via RMCS Metadata Database

  32. SRB Input files GAMES-UK binary Template Input GAMESS-UK DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search RMCS Stage input files + binary Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  33. SRB Input files GAMES-UK binary Template Input GAMESS-UK DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search RMCS Metaschedule Submit to batch queues Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  34. SRB Input files GAMES-UK binary Output files Template Input GAMESS-UK DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search RMCS Transfer output to SRB Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  35. SRB Input files GAMES-UK binary Output files Template Input GAMESS-UK DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search RMCS Using AgentX and Rcommands, place metadata in database Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  36. SRB Input files GAMES-UK binary Output files Template Input GAMESS-UK Rgem Collect and plot Total Energy from each optimized geometry DFT Transition State Search DFT Transition State Search DFT Transition State Search DFT Transition State Search Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  37. SRB Input files GAMES-UK binary Output files Template Input GAMESS-UK Rgem Collect and plot Total Energy from each optimized geometry DFT Transition State Search DFT Transition State Search DFT Transition State Search BespokeScripts DFT Transition State Search Monty RMCS Metadata Database NWGrid (Daresbury, Manchester, Liverpool, Lancaster)

  38. Simulation Simulation Simulation Simulation RGem XML data XML data XML data Database XML data RCommands AgentX Transition metal oxides; Perovskites (e.g. LaMnO3)Band Theory Group; W. Temmerman, M. Lueders, L. Petit, R. Tyer Use of RMCS Framework with XML output allows each of these steps to be linked together seamlessly

  39. Level of theory Quantum Monte Carlo Natural organic matter Linear-scaling quantum mechanics Oxides/hydroxides Aluminosilicates Clays, micas Sulphides Phosphates Carbonates Large empirical models Organic molecules Adsorbing surface Metallic elements Halogens Contaminant “Grand Challenge” science and the eMinerals VO

  40. Some Recent eMinerals Projects • Calculation of compressibility of diopside (CaMgSi2O6) between 0 and 22 Gpa - Andrew Walker • Equation of State of Silica Glass - Andrew Walker • Adsorption of Polychlorinated Dibenzo-p-Dioxins (PCDDs) onto Mineral Surfaces - Kat Austen

  41. GCOMS: (Proudman Oceanographic Laboratory) Global Coastal Ocean Modelling System Shelf seas are omitted or poorly resolved in global ocean models ……… ….... but they are a disproportionately important part of the earth system 37% of the Earth’s population live within 100km of the coast Shelf seas are 7% of ocean area but account for up to 30% of production Shelf seas modify and transport terrestrial inputs: freshwater, nutrients, pollutants Strong role in dense water formation, mixing on slopes etc.

  42. acknowledgements • Cambridge eMinerals Group - Prof. Martin Dove, Kat Austen, Andrew Walker, Richard Bruin • STFC eScience - Rik Tyer, Kerstin Kleese Van Dam, Rob Allan, Phil Couch • STFC CSED - Jens Thomas, Martin Lueders, Walter Temmerman

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