Cloud Resources in Production Cyberenvironments for E-Science Virtual Organizations Grid. Chem/Param. Chem Interoprability NSF Cloud Computing. Workshop Arlington, VA 17 -18 Mar 2011 Sudhakar Pamidighantam NCSA, University of Illinois at Urbana-Champaign sudhakar@ncsa. Illinois. edu National Center for Supercomputing Applications
Acknowledgements Open Gateways Computing Environments National Center for Supercomputing Applications
Acknowledgments • • • Jayeeta Ghosh, NCSA, Param. Chem Suresh Marru, Indiana U. OGCE Ye Fan, Indiana U. OGCE Kenno Vonnommeslaeghe, U. Maryland/Paramchem, Narendra Polani, UKy, Middleware/Param. Chem Michael Sheetz, UKy, Application Interfaces/ Param. Chem Vikram Gazula, UKy, Server Administration Tom Roney, NCSA, Server and Database Maintenance Nikhil Singh, NCSA, Paramchem • • Liu Yang, NCSA, Grid. Chem Scott Brozell, OSC, Applications and Testing Rion Dooley, TACC Middleware Infrastructure Stelios Kyriacou, OSC Middleware Scripts Chona Guiang, TACC Databases and Applications Kent Milfeld, TACC Database Integration Kailash Kotwani, NCSA, Applications and Middleware National Center for Supercomputing Applications
Outline • Historical Background : --- Grid Computational Chemistry • Production Environments • Current Status Web Services • Usage: Grid and Science Achievements • Cloud in Hybrid Environments • Interoperability • Future National Center for Supercomputing Applications
Motivation Integrating Services for E-Science and Engineering in Research, Education and Training Software - Reasonably 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 - Distributed and heterogeneous National Center for Supercomputing Applications
Extended Tera. Grid Facility www. teragrid. org National Center for Supercomputing Applications
NSF Petascale Road Map • Track I Scheme Multi-petaflop single site system to be deployed by 2011 at NCSA Blue. Waters http: //www. ncsa. illinois. edu/Blue. Waters/ • Track 2 Sub-petaflop systems Several to be deployed until Track 1 is online System OS Cores • Dell Power. Edge(NCSA) EM 64 T 9600 • SGI-Altix(PSC) IA 64 768 • SGI UV-Ice(NCSA) EM 64 T 1568 • IBM Power 4 Cluster(NCSA) Pwr 4 48 • IBM Power. PC(Indiana) Pwr 4 1536 • Sun Constellation (TACC) EM 64 T 50000 Additional Systems to be online soon (currently being allocated ) SGI UV-Ice(PSC) EM 64 T 4096 Future. Grid Diverse on demand National Center for Supercomputing Applications
Grids and New Opportunities Alliance to Tera. Grid Homogenous Grid with predefined fixed software and system stack was planned (Teragrid) but it was difficult to keep it homogenous Local preferences and diversity leads to heterogeneous grids now! (Operating Systems, Schedulers, Policies, Software and Services) Grid Hardware Interfaces Scientific Applications Middleware Openness and standards that lead interoperability are critical for successful services National Center for Supercomputing Applications
User Community Chemistry and Computational Biology NRAC AAB Small Allocations As of Oct 04 #PIs 26 23 64 #SUs 5, 953, 100 1, 374, 100 640, 000 Tera. Grid Allocations in 2010 Discipline # PIs Initial Alloc. SUs Physics Molecular Biosciences Chemistry Chemical, Thermal Systems Materials Research 125 308 264 143 207 920, 254, 700 689, 733, 465 255, 479, 494 232, 905, 769 210, 602, 367 2101 Users using Chemistry Software 230 ASC 30 AST 18 ATM 8 BCS 30 CCR 28 CDA 653 CHE 11 CTS 1 DBS 2 DEB 805 DMR 10 DMS 18 EAR 1 ECS 23 IBN 2 IRI 153 MCB 10 MSS 3 NCR 4 OCE 37 PHY 6 SEE 5 SES 3 STA National Center for Supercomputing Applications
National Center for Supercomputing Applications
Computational Chemistry Grid This is a Virtual Organization 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
Other Resources Extant HPC resources at various Supercomputer Centers, Cloud resources (Interoperable) Optionally Other Grids and Hubs/local/personal resources These may require existing allocations/Authorization National Center for Supercomputing Applications
National Center for Supercomputing Applications
Grid. Chem System user application user Portal Client user application Grid Middleware Proxy Server Grid Services Grid http: //www. nsf. gov/awardsearch/show. Award. do? Award. Number=0438312 National Center for Supercomputing Applications Mass Storage
Applications • Grid. Chem supports some apps already – Gaussian, GAMESS, NWChem, Aces 3 Molpro, ADF, Quild, QMCPack, Castep, DMol 3, Amber, Charmm • Schedule of integration of additional software – – – Crystal Q-Chem Wein 2 K MCCCS Towhee Others. . . Workflows National Center for Supercomputing Applications
Gridchem Middleware Service (GMS) National Center for Supercomputing Applications
Grid. Chem Resources Monitoring http: //portal. gridchem. org: 8080/gridsphere? cid=home 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 QChem Aces 3 Gromacs • • 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) …. • • Car Parinello Molecular Dynamics Molecular Energetics (Quantum Chemistry) Parallel Coupled Cluster Quantum Chemistry Nano/Bio Simulations (Molecular Dynamics) 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
Users and Usage • 433 Users under 221 Projects Include Academic PIs, two graduate classes And about 15 training users More than a 2, 000 CPU Wallhours More than 35500 Jobs processed 5 Dissertations, More than 50 Publications National Center for Supercomputing Applications
User Research 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
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
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
Force Field Parameterization Molecular Force Fields require constant improvement as new reference data becomes available (that can not be accommodated easily with existing sets) New molecular systems become amenable for computational analysis New models/potential energy functions/Hamiltonians force are established Coverage of force fields should constantly be extended to cover new fields of research/new functionality (nanomaterials, biomaterials and medicine, . . . )"
Cyberenvironments for Molecular Force Fields • Extension of currently available models, with the • • resulting parameters sets to be made available publicly Databases of experimental and quantum mechanical reference data to be used in the parameterization process Integration of computational resources for data acquisition, automation of QM reference data generation Automation Extensible infrastructure for parameterization management for rapid and systematic parameterization of novel Hamiltonians (empirical and semi-empirical) Systematic improvement of parameter optimization processes
Accurate Force Fields Are needed
Science Gateways Layer Cake User Interfaces Gateway Services Web/Gadget Container Web/Gadget Interfaces Application Abstractions Fault Tolerance Workflow System Auditing & Reporting Resource Middleware Cloud Interfaces Compute Resources Computational Clouds Color Coding Web Enabled Desktop Applications Application Monitoring Gateway Abstraction Interfaces User Management Information Services Security Provenance & Metadata Management Registry Grid Middleware SSH & Resource Managers Computational Grids Local Resources OGCE Gateway Components Complimentary Gateway Components Dependent resource provider components
XSUL/Apache Axis 2 GFac Current & Future Features Input Handlers Registry Interface Scheduling Monitoring Interface Output Handlers Fault Tolerance Data Management Abstraction Auditing Checkpoint Support Job Management Abstraction Color Coding Existing Features Planned/Requested Features Globus Campus Resourc es Amazon Eucalyptus Unicore Condor
OGCE Layered Workflow Architecture: Derived from LEAD Workflow System Workflow Interfaces (Design & Definition) XBaya GUI (Composition, Deploying, Steering & Monitoring) BPEL 2. 0 Gadget Interface for Input Binding Python BPEL 1. 0 Flex/Web Composition Java Code Scufl Workflow Specification Workflow Execution & Control Engines Apache ODE GBPEL Pegasus DAG Dynamic Enactor Condor DAGMan Jython Interpreter Taverna
Putting It All Together
Pegasus WMS 35
Param. Chem-Xbaya-Pegasus • Input Workflow for Grid. Chem/Param. Chem created using Pegasus JAVA DAX API -- DAX can have combinations of tasks ( like Charmm/ multiple Gaussian tasks) each taking respective input file. • The tasks can be mapped to either respective specific applications (like charmm/amber/g 03 or g 09 )based on a simple configuration. • Input data (instructions, structure, topology, parameters) will be staged from middleware using Grid. FTP to the execute clusters (such as Tera. Grid systems Mercury and Abe at NCSA). • Jobs will be distributed across the multiple execute clusters using Round-Robin or other schema. -- Any heuristics based scheduling is also possible. • Output files will be staged back from execute clusters to middleware using Grid. FTP for post processing/archiving. 36
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
• • • Param. Chem Apache Axis 2 Services Notification. Service Resource. Service Trigger. Service Session. Service Software. Service Job. Service Workflow Service File. Service User. Service Project. Service
Cloud HPC Interoperability § The Cloud in our case is a part of over all resources for computing and storage § They have to be usable interoperably along with other HPC and local resources §Particular use will be for on-demand computing and high throughput computing §Certain routine sensor enabled data dependent computing hydrological event monitoring and simulation could be handled by clouds for rapid on demand prediction of short term events §The interoperability requirements that enable data and computation movement from one resource to other should be explored. National Center for Supercomputing Applications
sarv. E jan. Ah Sukhin. O bhavantu May every person be happy Questions? Imaginations unbound
Скачать презентацию Cloud Resources in Production Cyberenvironments for E-Science
b4d9ccd275ea57662db87438d7b282f7.ppt