Grid. Chem A Computational Chemistry Cyber-infrastructure Using Web services Sanibel Symposium 23 Feb 07 Sudhakar Pamidighantam NCSA, University of Illinois at Urbana-Champaign sudhakar@ncsa. edu
Acknowledgements
Outline • • Historical Background Grid Chemistry Current Status Web Services Usage Brief Demo Future
Motivation 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
Background Qauntum Chemistry Remote Job Monitor ( Quantum Chemistry Workbench) 1998, NCSA Chemviz 1999 -2001, NSF Technologies Web Based Client Server Models Visual Interfaces Distributed computing
Grid. Chem 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
Extended Tera. Grid Facility www. teragrid. org
Grid and Gridlock Alliance lead to Physical Grid lead to Tera. Grid Homogenous Grid was planned but it was difficult to keep it homogenous Things got more complicated and we have heterogeneous grids now! Interoperability and Standards and Openness Are Critical
Current Grid Status Interfaces Grid Hardware Middleware Scientific Applications
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
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
Computational Chemistry Grid Integrated Cyber Infrastructure for Computational Chemistry Integrates Applications, Middleware, HPC resources, Scheduling and Data management Allocations, User Services and Training
Resources System (Site) Intel Cluster (OSC) Procs Avail 36 Total CPU Hours/Year Status 315, 000 SMP and Cluster nodes HP Integrity Superdome (UKy) 33 IA 32 Linux Cluster (NCSA) 64 Intel Cluster (LSU) 1024 IBM Power 4 (TACC) Teragrid (Multiple Institutions) 290, 000 TB Replaced with an SMP/ Cluster nodes 16 560, 000 1, 000 140, 000 250, 000 New Allocation Expected
Other Resources Extant HPC resources at various Supercomputer Centers (Interoperable) Optionally Other Grids and Hubs/local/personal resources These may require existing allocations/Authorization
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 Mass Storage
Applications • Grid. Chem supports some apps already – Gaussian 98/03, GAMESS, NWChem, Molpro, QMCPack, Amber • Schedule of integration of additional software – – – ACES-2 Crystal Q-Chem Wein 2 K MCCCS Towhee More …. .
Gridchem Middleware Web Services Oriented
WS Web Services is different from Web Page Systems or Web Servers: There is no GUI Web Services Share business logic, data & processes through API with each other (not with user) Web Services describe Standard way of interacting with “web based” applications XML is used to tag the data, SOAP is used to transfer the data, WSDL is used for describing the services available and UDDI is used for listing what services are available. A client program connecting to a web service can read the WSDL to determine what functions are available on the server. Any special datatypes used are embedded in the WSDL file in the form of XML Schema. Universal Description, Discovery, and Integration. WSRF Standards Compliant.
Client Objects Database Interaction Client DTO (Data Transfer Object) Serialize transfer through XML DAO (Data Access Object) How to get the DB objects hb. xml (Hibernate Data Map) describes obj/column data mapping Business Model DTO DAO WS Resources Objects Hibernate hb. xml Database
Database Table Relationships Users Projects Resources User. Project. Resource user. ID project. ID resource. ID login. Name SUs. Local. User. Used Users Jobs job. ID job. Name user. ID proj. ID soft. ID cost Software. Resources Network. Resoruces Resources Compute. Resources resoruce. ID Type host. Name IPAddress site. ID Storage. Resources
Computational Chemistry Resource
GMS_WS Use Cases http: //www. gridchem. org: 8668/space/GMS/usecase • • Authentication Job Submission Resource Monitoring File Retrieval
GMS_WS Authentication http: //www. gridchem. org: 8668/space/GMS/usecase GC Client Contact GMS Creates Session, Session RP and EPR Sends EPR Login Request (username: passwd) Validates, Loads User. Projects Sends acknowledgement Retrieve User. Projects (Get. Resource. Property port Type PT) • • • WSDL (Web Service Definition Language) is a language for describing how to interface with XML-based services. It describes network services as a pair of endpoints operating on messages with either document-oriented or procedure-oriented information. The service interface is called the port type WSDL FILE: <? xml version="1. 0" encoding="UTF-8"? > <definitions name="Math. Service" target. Namespace="http: //www. globus. org/namespaces/examples/core/Math. Service_instance" xmlns="http: //schemas. xmlsoap. org/wsdl/" …
GMS_WS Authentication http: //www. gridchem. org: 8668/space/GMS/usecase GC Client Selects project Load. VO port type (w. MAC address) GMS Verifies user/project/MACaddr Load User. Resources RP Sends acknowledgement Retrieve User. Resources [as user. VO/ Profile] (Get. Resource. Property port Type PT) Validates, Loads User. Projects Sends acknowledgement
GMS_WS Job Submission GC Client Create Job object Predict. Job. Start. Time PT + Job. DTO If decision OK, Submit. Job PT + Job. DTO GMS Job. Start Prediction RP Create Job object API—Submit Store Job Object Send Acknowledgement PT = port. Type RP = Resource Properties DTO = Data Transfer Object Submission Co. GKit GAT “gsi-ssh” Completion: Email from batch system to GMS server cron@GMS DB Need to check to make sure allocation-time is available.
GMS_WS Monitoring GC Client Request for Job, Resource Status Alloc. Balance GMS User. Resource RP Updated from DB Send info Parse XML, Display PT = port. Type RP = Resource Properties DTO = Data Transfer Object DB = Data Base Resources/Kits/DB cron@GMS server cron@HPC Servers Job Launcher Notifications VO Admin email parses email DB (status + cost)
GMS_WS File Retrieval GC Client Load. File PT Get. Resource. Property PT File. DTO(? ) Load. File PT (project folder+job) Retrieve. Files PT (+file rel. path) GMS Resources/Kits/DB Job Completion: Send Output to MSS Retrieve Root Dir. Listing on MSS with Co. GKit or GAT or “gsi-ssh” MSS query User. Files RP + File. DTO object Validates project folder owned by user. Send new listing API file request Store locally Create File. DTO Load into User. Data RP Retrieve file: Co. GKit or GAT or “gsi-ssh” Get. Resource. Property PT Should whole directory be evaluated (may be large)— why not just those owned by user? PT = port. Type RP = Resource Properties DTO = Data Transfer Object MSS = Mass Storage System
GMS_WS File Retrieval GC Client Retrieve. Job. Output PT (+Job. DTO) GMS Resources/Kits/DB Job Record from DB. Running: from Resource Complete: from MSS Create File. DTO (? ) Load into User. Data RP Retrieve file: Co. GKit or GAT or “gsiftp” Get. Resource. Property PT Should whole directory be evaluated (may be large)— why not just those owned by user? PT = port. Type RP = Resource Properties DTO = Data Transfer Object MSS = Mass Storage System
Web Services WSRF (Web Services Resource Framework) Compliant WSRF Specifications: WS-Resource. Properties (WSRF-RP) WS-Resource. Lifetime (WSRF-RL) WS-Service. Group (WSRF-SG) WS-Base. Faults (WSRF-BF) %ps -aux | grep ws Logging Configuration /usr/java/jdk 1. 5. 0_05/bin/java Where to find Globus -Dlog 4 j. configuration=container-log 4 j. properties -DGLOBUS_LOCATION=/usr/local/globus -Djava. endorsed. dirs=/usr/local/globus/endorsed -DGLOBUS_HOSTNAME=derrick. tacc. utexas. edu Where to get random seed -DGLOBUS_TCP_PORT_RANGE=62500, 64500 for encryption key generation -Djava. security. egd=/dev/urandom -classpath /usr/local/globus/lib/bootstrap. jar: Classpath (required jars) /usr/local/globus/lib/cog-url. jar: /usr/local/globus/lib/axis-url. jar org. globus. bootstrap. Bootstrap org. globus. wsrf. container. Service. Container -nosec
Software Organization • CVS for Grid. Chem
GMS_WS • Package: org. gridchem. service. gms
GMS_WS + Should these each be a separate package?
GMS_WS gms client dao dto exceptions model credential file. task job. task notification resource user persistence audit query synch gpir test Classes for WSRF service implementation (PT) Cmd line tests to mimic client requests Data Access Obj – queries DB via persistent classes (hibernate) Data Transfer Obj – (job, File, Hardware, Software, User) XML How to handle errors (exceptions) CCG Service business mode (how to interact) Contains user’s credentials 4 job sub. file browsing, … “Oversees correct” handling of user data (get/putfile). Define Job & util & enumerations (Submit. Task, Kill. Task, …) util Contains utility and singleton classes for the service. Encryption of login password Mapping from GMS_WS enumeration classes DB GAT util classes: GATContext & GAT Preferences generation Classes deal with Co. GKit configuration. crypt enumerators gat proxy Autonomous notification via email, IM, textmesg. CCGResource&Util, Synched by GPIR, abstract classes Network. Res. , Compute. Res. , Software. Res. , Storage. Res. , Visualization. Res. User (has attributes – Preference/Address) DB operations (CRUD), OR Maps, pool mgmt, DB session, Classes that communicate with other web services Periodically update DB with GPIR info (GPIR calls) JUnit service test (gms. properties): authen. VO retrieval, Res. Query, Synch, Job Mgmt, File Mgmt, Notification
GMS_WS external jars • Testing • For XML Parsing • “Java” Document Object Model – Lightweight – Reading/Writing XML Docs – Complements SAX (parser) & DOM – Uses Collections**
Authentication
Resource Status
Job Editor
Job Submission
Job Monitoring
Gradient Monitoring
Energy Monitoring
Post Processing
Visualization Molecular Visualization Electronic Properties Spectra Vibrational Modes
Molecular Visualization Better molecule representations (Ball and Stick/VDW/MS) In Nanocad Molecular Editor Third party visualizer integration Chime/VMD Export Possibilities to others interfaces Deliver standard file formats (XML, SDF, MSF, Smiles etc…)
Eigen Function Visualization • Molecular Orbital/Fragment Orbital • MO Density Visualization • MO Density Properties • Other functions Radial distribution functions
Some example Visuals Arginine Gamess/6 -31 G* Total electronic density 2 D - Slices
Electron Density in 3 D Interactive (VRML)
Orbital 2 D Displays N 2 6 -31 g* Gamess
Orbital 3 D VRML
Spectra • IR/Raman Vibrotational Spectra • UV Visible Spectra • Spectra to Normal Modes • Spectra to Orbitals
Grid. Chem Use • Allocation Community and External Registration • Consulting/User Services Ticket tracking, Allocation Management • Documentation Training and Outreach FAQ Extraction, Tutorials, Dissemination
Users and Usage • 170 Users Include Academic PIs, two graduate classes And about 15 training users • NCSA 57000 SUs + A 7 node dedicated system • UKy around 106766 SUs • OSC 13, 820 SUs + A 14 node dedicated system • Usage at LSU and TACC as well More than a 335000 CPU Wallhours since Jan 06.
Science Enabled • Chemical Reactivity of the Biradicaloid (HO. . . ONO) Singlet States of Peroxynitrous Acid. The Oxidation of Hydrocarbons, Sulfides, and Selenides. Bach, R. D. ; Dmitrenko, O. ; Estévez, C. M. 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.
Science Enabled • Azide Reactions for Controlling Clean Silicon Surface Chemistry: Benzylazide on Si(100)-2 1 Semyon Bocharov, Olga Dmitrenko, Lucila P. Mendez De Leo, and Andrew V. Teplyakov* Department of Chemistry and Biochemistry, Uni. Versity of Delaware, Newark, Delaware 19716 Received April 13, 2006; E-mail: andrewt@udel. edu http: //pubs. acs. org. proxy 2. library. uiuc. edu/cgibin/asap. cgi/jacsat/asap/pdf/ja 0623663. pdf [May require ACS access]
Third Year Plans • • Post Processing New Application Support Expansion of Resources Extension Plan
Acknowledgments • • • 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 Scott Brozell, OSC, Applications and Testing Michael Sheetz, UKy, Application Interfaces Vikram Gazula, UKy, Server Administration Tom Roney, NCSA, Server and Database Maintaienance
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