A Grid Enabled Collaboratory for Scientific Research (GESCR) Charles Severance University of...

A Grid Enabled Collaboratory for Scientific Research (GESCR)

Charles SeveranceUniversity of Michigan

Sakai Project, NEESGrid Project, OGCE Project

www.dr-chuck.com

csev@umich.edu

Outline

• Collaborative Software

• Historical Context

• The Sakai Project

• NEESGrid Experience

• Comparing Civil Engineering and HENP

• The Concepts of GESCR

• Going Forward

Collaboration Happens

• As individuals, we are parts of many groups and have many roles in those groups

SakaiWLAP

OGCE

uPortal

Architecture

Tools

Board

Board

UM Sakai June MTG

Dec MTG Next Grant

Support

Support

Database

Next Ver

JSR-168 FusionGridNEESGrid

Data Model

Data Repo

Minnesota

Texas

Version 3Post Oct.

HENP

GESCRUM IssuesOne View of

Chuck’s Context Map

Another View

Another View

Maintaining the Map

• Read E-Mail and move to proper folders

• Copy attachments into folders

• Searching for information

• Making calendar entries from E-Mail

Imagine Software

• That could create a new “context” in a few clicks– Enroll/invite others to the context as necessary in a few more clicks

• Context capabilities– E-Mail list (automatically extracts attachments and places them in

folders which appear on your desktop)– Schedule (you can either see a “federated” schedule across all

contexts or look at one context)– Persistent browser-based chat - quite useful during meetings when

the Polycom or VRVS messes up :)– Resource area where anyone can upload files which appear on

everyone’s desktop at the same time (WebDAV) – Threaded discussion area for the context

• Problem: There are literally hundreds of solutions to portions of this problem.

More Software

• A single place to see new activity in your “contexts”• These contexts are stored on backed-up production

servers rather than your desktop for many years• A search across your contexts - that would be really

cool• The ability to customize each context in terms of look,

feel, and capabilities• The ability to build unique domain specific tools and

interfaces to extend the mechanism using Portlets, Servlets, or Applets

A 10-Year Collaborative Mission @ UM

19981991 - 1997 1999 2000 2001 2002 2003 2004 2005

SPARC

Science of Collaboratories

Sakai

Worktools (Notes Based) WTNG

Coursetools (Notes Based) CTNG

CHEF 1 CHEF 2

OGCE Grid Portal

NEESGrid

Portal TechnologyJetspeed 2.0uPortal 3.0

Websphere …

Channels, Teamlets

JSR-168 Portlets

CHEF Services

JSR-168 Technology

OKI Services

Legacy

SakaiTeamlet

OtherServices

Sakai GUI

SakaiTeamlet

Sakai GUI

Java Swing

SPARC

2/2001 600 users 800 data sources

CourseTools

Over 42,000 users at the end of 2003

WorkTools

Over 9000 users (2000 active) at the end of 2003

Digital libraries & documents

groups-to-information

groups-to-facilities

people-to-people

Communication,Collaboration

Services

Distributed,media-richinformationtechnology

Remote instruments

http://www.scienceofcollaboratories.org/

Science of Collaboratories

NSF Funded ITR

CHEF 1.0

• Fall 2001: CHEF Development begins – Generalized extensible framework for building collaboratories– “Best-of” CourseTools, SPARC, WorkTools

• Integrate across current UM projects and adopt relevant standards

• Funded internally at UM as replacement for CourseTools

• All JAVA - Open Source– Jakarta Jetspeed Portal– Jakarta Tomcat Servlet Container– Jakarta Turbine Service Container

• Build community of developers through workshops and outreach

Not “just” a portal

• Portals are a framework to deploy tools (aka rectangles) and focus on how the user wants to arrange their own “rectangles”

• While CHEF technically is a portal, the goal is for the tools to work together closely and seem to really be parts of a larger “tool”

• CHEF has a lot of features, (services, presence, notification, etc..) which bridge the gap between portal and application framework

CHEF Applications

• CourseTools Next Generation

• WorkTools Next Generation

• NEESGrid

• NSF National Middleware Grid Portal

CourseTools Next Generation

Over 5000 users at the end of 2003http://coursetools.ummu.umich.edu/

Worktools Next Generation

New WorkTools Sites being created in WTNG as of 12/2003Run on the same servers as CTNG.

NEESGrid - The EquipmentNetwork for Earthquake Engineering Simulation

NSF Funded. NCSA, ANL, USC/ISI, UM, USC, Berkeley, MSU

CHEF-Based NEESGrid Software

NMI / OGCE www.ogce.org

NSF National Middleware IniativeIndiana, UTexas, ANL, UM, NCSA

What we learned in 10 years.

• Portal technology is a good idea - forces component approach - functionality does not “smear”

• Portals are not just aggregators of independent information - but can be an application framework

• Many (but not all) tools can be used for both teaching and learning and research collaboration

• Separating functionality into lightweight GUI components and pluggable services with strong and well-specified APIs allows significant reusability

• GUI elements program to abstract service interfaces - not databases, file systems, LDAP, etc. - this allows great flexibility.

While we were building collaboratories…

• The Open Knowledge Initiative (OKI) at MIT was developing APIs for learning management systems - involving many universities (UM, Indiana, Stanford, and MIT were strong participants)

• Indiana, Stanford, MIT all developed learning management system

• Java Community Process (JCP) produced JSR-168 - The “unified” portal standard API

• Oasis developed the Web Services for Remote Portals (WSRP) standard

• The open-source uPortal portal project had quietly moved into the #1 open source portal (#4 including commercial vendors)

Jan 04 July 04 May 05

Michigan•CHEF Framework•CourseTools•WorkTools

Indiana•Navigo Assessment•Eden Workflow•Oncourse

MIT•Stellar

Stanford•CourseWork•Assessment

OKI•OSIDs

uPortal

SAKAI 1.0 Release•Tool Portability Profile•Framework•Services-based Portal•Refined OSIDs & implementations

SAKAI Tools•Complete CMS•WorkTools•Assessment

SAKAI 2.0 Release•Tool Portability Profile•Framework•Services-based Portal

SAKAI Tools•Complete CMS•Assessment•Workflow•Research Tools•Authoring Tools

Primary SAKAI ActivityArchitecting for JSR-168 Portlets,

Refactoring “best of” features for toolsConforming tools to Tool Portability Profile

Primary SAKAI ActivityRefining SAKAI Framework,

Tuning and conforming additional toolsIntensive community building/training

Activity: Ongoing implementation work at local institution…

Dec 05

Activity: Maintenance &

Transition from aproject to

a community

So we got together and drew an über collaboration picture…

Sakai Core Members

• Universities– Indiana– Michigan– MIT– Stanford

• Projects– Open Knowledge Initiative (OKI)– uPortal - JaSIG

• Funding ($6.8M - 2 Years)– Mellon Foundation– Hewlett Foundation– Partners Program– Core member match

KYOU / sakai

Boundary, Situation

Sakai Concepts

• It is neither research nor teaching, it is all “collaboration” - many common tools– Teaching: Courses, tools, drop-boxes– Research: Putting the user interface on the

Grid and Virtual Organizations

Teaching and Learning

CollaborativeResearch

Collaboration andLearning Environment

What we agreed to build…

• A Collaborative Learning Environment– Open Source– Uses OKI (Open Knowledge APIs)– Uses uPortal as its portal framework

• Similar to– Blackboard– WebCT

• And all four core institutions would deploy the commonly developed software

Collaboration and Learning Environment

• Learning management systems are really just a form of collaboration– Freshman Calculus– Chess Club– Group of 5 faculty members working on

curriculum– 2000 physics researchers collaborating

across the world on a 15-year physics experiment

Sakai 1.0

• Site based collaboration environment– Worksite management– E-Mail Lists– Threaded Discussion– Resources (folders) with WebDav support– Chat– No search yet :(– Many other tools

• Beta Release July 15, 2004• Production site available at ctools.umich.edu

More Sakai Beta Tools Admin: Alias Editor (chef.aliases) Admin: Archive Tool (chef.archive) Admin: Memory / Cache Tool (chef.memory) Admin: On-Line (chef.presence) Admin: Realms Editor (chef.realms) Admin: Sites Editor (chef.sites) Admin: User Editor (chef.users)Announcements (chef.announcements) Assignments (chef.assignment) C. R. U. D. (sakai.crud) Chat Room (chef.chat) Discussion (chef.discussion) Discussion (chef.threadeddiscussion) Dissertation Checklist (chef.dissertation) Dissertation Upload (chef.dissertation.upload) Drop Box (chef.dropbox)Email Archive (chef.mailbox)

Help (chef.contactSupport)Membership (chef.membership) Message Of The Day (chef.motd) My Profile Editor (chef.singleuser) News (chef.news) Preferences (chef.noti.prefs) Recent Announcements (chef.synoptic.announcement) Recent Chat Messages (chef.synoptic.chat) Recent Discussion Items (chef.synoptic.discussion) Resources (chef.resources) Sample (sakai.module) Schedule (chef.schedule) Site Browser (chef.sitebrowser) Site Info (chef.siteinfo) Web Content (chef.iframe) Worksite Setup (chef.sitesetup) WebDAV

Sakai Going Forward

• Focus on the”Learning” of Collaborative Learning Environment through 2Q05– Getting ready for production deployment at the four partner

sites– Improving the look and feel of the software– Many feature enhancements (to satisfy four + 60 schools)– New GUI Programming Environment based on Java Server

Faces– Building new set of Sakai APIs (Java)

• Based on OKI - Enabling RDF

• Move into OGCE and NEESGrid starting 3Q04• Release 2.0 - 2Q04

The George E. Brown, Jr. Network for Earthquake Engineering

Simulation (NEES)

NEES Founding

• George E. Brown, Jr. Network for Earthquake Engineering Simulation (NEES).

• Funded in 1999 - > $100M• Goal: Transform the nation’s ability to carry out

earthquake engineering research, to obtain information vital to develop improved methods for reducing the nation’s vulnerability to catastrophic earthquakes, and to educate new generations of engineers, scientists and other specialists committed to improving seismic safety.

• To be Completed: October 2004

• NEESgrid facilitates research capabilities previously unavailable• NEESgrid links earthquake researchers across the U.S. with

leading-edge computing resources and research equipment and allowing collaborative teams (including remote participants) to plan, perform, and publish their experiments

• NEESgrid is a coordinated and secure architecture/environment • NEESgrid is a modular and extensible environment with a

customizable user interface• NEESgrid provides common tools that allow leveraging resources

and experiences• Rather than having to worry about the required cyber

infrastructure, NEESgrid allows researchers to focus on the earthquake engineering challenges at hand

• The goal of the System Integrator (SI) is to develop NEESgrid as the Cyber Infrastructure that will facilitate this next generation of experimentation/simulation in earthquake engineering

NEES Components

• New experimental facilities (15) – Oregon State University, Rensselaer Polytechnic

Institute, University of Buffalo, University of Colorado at Boulder, University of Minnesota, University of Nevada at Reno, University of Texas at Austin, and the University of California campuses at Berkeley, Davis and Los Angeles

• Collaborative Software System: NEESGrid– Collaboration– Data capture and sharing– Tele-presense and Tele-operation– Simulation– Support for Hybrid Simulation and Physical Experiments

Shake table: Nevada, Reno

Reaction wall: Minnesota

Centrifuge: UC Davis

Wave basin: Oregon State

Field structural: UCLA

Field geotechnical: Texas

If we build it, they will collaborate

• Data and access to data represent fundamental barriers to dispersed collaboration

• Efficient movement of vast amounts of data is a prime rationale for cyberinfrastructure

• Federating, visualizing and mining data are principle challenges

Researchers

DataFacilities

Synchronized dataSynchronized data and imagesData discovery

Automatic archivingSimulation codesHybrid experiments

TeleoperationTeleobservation

Synchronous communicationAsynchronous communication

The collaboratory concept

NEES Resources

Field Equipment

Laboratory Equipment

Remote Users

Remote Users: (K-12 Faculty and Students)

Instrumented Structures and Sites

Leading Edge Computation

Curated Data Repository

Laboratory Equipment

Global Connections

(Faculty, Students, Practitioners) Simulation

Tools Repository

The Grid in NEESgrid

NEESpop A

Experimental Equipment

Video I/O

Audio I/O

Site A: Experimental Data Producer

Hub A

Telepresence Equipment

Active PI

Data Cache

Site B: Remote Lead Investigator

Hub B

Internet Fabric and Operations

Site C: Passive Collaborator

Teleobservation Equipment

Passive co-PI

Data Cache

Hub C

Grid Data Repository

Grid Operations

Center

Experimental Component

Campus Net Component

NEESgrid Component

NEESGrid Software

• Founding NMI Technologiess– Globus Toolkit– OGCE Collaboration Toolkit

• New Work– Data and Metadata Repository - NCSA– Data Acquisition, Storage, and Visualization– Simulation Portal– Synchronized data and video (live and stored)

NEESgrid Experiment Data FlowNEESgrid Experiment Data Flow

NEESGridData

Repository

ProjectBrowser

DataTurbine

DataIngestion

ExperimentControl

StreamingViewer

DAQC

D

SiteSpecific

ProjectRelated

ExperimentalSetup

ExperimentalElement

DataElement

Data Model

DAQDisk

StoredViewer

DT Main System

PTZ/USB

StillCapture

DT Client

BT848Video

Frames

DT Client

Capturing Video and Data

Camera ControlGateway

DAQData

CaptureDT Client

SimulationCoordinator

Site A Site B

DT Main System

Data Monitoring Tools

Still Image / Camera Control

~

< >^

^

< >

Camera ControlGateway

Creareviewers

Still imagecameracontrol

Thumb-nail

Video andData Tivo

Thumbnail + Audio + Data

< > +

SimulationCoordinator

NTCPServer

DAQ

CompSim

DAQ

NTCPServer

LiveExtractor

Quicktime

DAQ Data

DataRepository

SampleExperimentSetup

Data Models

• Data models are developed in RDF• Local repository supports multiple simultaneous data

models with cross-model linkages• Metadata browser (aka Project browser) becomes

the Project Browser, Notebook Browser, Site Specification Database Browser

• Metadata browser can federate multiple sources of Metadata

InstrumentationSetup

SensorGroup

Sensor

Specimen

EquipmentSetup

CalibrationSet

Equipment

CameraDataEquipment

Overall Data Modeling EffortsOverall Data Modeling Efforts

NEES

Site A Site CSite B

Equipment People

Experiments Trials

Equipment People

Experiments Trials

Data Data Data

TsnumaiSpecimen

Shake TableSpecimen

GeotechSpecimen

CentrifugeSpecimen

Units Sensors Descriptions

SiteSpecificationsDatabase

ProjectDescription

Domain Specificmodels

Common Elements

Data / Observations

Ref. Source: Chuck Severance

Models + Data Model

Repo

Models

Configure

Data

Load

Con

figur

e

RDF/OWL

RDF<owl:ObjectProperty rdf:ID="hasPublications"> <rdfs:domain> <owl:Class> <owl:unionOf rdf:parseType="Collection"> <owl:Class rdf:about="#Project"/> <owl:Class rdf:about="#Task"/> </owl:unionOf> </owl:Class> </rdfs:domain> <rdfs:range rdf:resource="#Publications"/> </owl:ObjectProperty>

Protégé - 2K

Models + Data Model

Repo

Models

Configure

Data

Load

Con

figur

e

RDF/OWL

RDF

DOE ELN / Example

NEESgrid: Simulation

Lessons Learned in NEESGrid (Chuck’s views)

• A collaborative environment *must* have a user interface• Just asking about requirements is a tiny part of the problem -

CS developers must learn to “walk in the shoes” of the scientists.

• Scientists know a lot about Computer Science - listen to them and involve them

• The real work begins after software is “delivered” - Version 1.0 is usually just a conversation starter - but a very important step

• There are some things that are useful across fields - but the most valuable elements are field-unique

• Data models, data repositories, and long-term curation is difficult!

HENP/Civil Similarities

HENP/Civil: Differences

• Willingness to collaborate– CE: Not too keen on the idea - NSF forcing the issue

using “carrot and stick”– HENP: It is part of the fabric of the field (at least within

Atlas and CMS :) )

• Technology Savvy– CE: It is all about the “within lab” electronics– HENP: In lab electronics is difficult, important and

different. The internet is a tool to be used both for human communication and data manipulation - have tried everything - use simple reliable stuff because the work cannot wait.

NEES Going Forward

• Release 3.0 complete July 31, 2004– Improve documentation and bug fixes through

September 30, 2005

• As of October 1, 2004, NEESGrid will transition from development lead by NCSA to maintenance led by SDSC– Focus on deployment and support– UM will continue involvement - move to Sakai -

improving data modeling, internationalization (Japan)

GESCR* - The Vision

* A Grid Enabled Collaboratory for Scientific Research

HENP: Unique Aspects

• Already highly collaborative as a scientific field

• Globally distributed in space and time (both time-zones and years)

• Technology savvy but wary :)• Solutions underway (iVDGL, GriPhyn,

etc) without significant user interface component

GESCR in a sentence..

….. will combine the best open-source applications from within the HENP communities (and from allied Grid and National Middleware efforts) within a common portal interface.

Put another way: There is a lot of work going on in HENP that does not really have much of a user interface yet. We want to put a user interface on the Grid and other activities.

GESCR in a sentence..

….. will combine the best open-source applications from within the HENP communities (and from allied Grid and National Middleware efforts) within a common portal interface.

What I tell people:GESCR will be a tri-corder for the Atlas and CMS collaborations. Starting with inter-human communication and moving towards data processing and analysis.

Elements of GESCR

• Sakai with Grid Support (from OGCE / NEESGrid)

• Sakai Collaboration Tools• Well funded analysis of application,

requirements, and challenges throughout the project

• Additional new capabilities– VRVS Integration (rooms, record, playback)– Web Lecture Archive (WLAP)– VNC support

GESCR Elements (cont)

• MonaLisa integration• Collaborative LaTeX editing environment• Peer-to-Peer file sharing• Language of Access to handle “over-

collaboration”• Adaption of HEPBook• GESCR support office (Y3)• Education and outreach activities

GESCR Project

• Planned: Four years - Medium ITR (NSF)• Partners: Caltech, Fermilab, Florida International

University, Lawrence Berkeley, Maryland, University of Michigan, University of Texas Austin, University of Iowa

• Joint between Atlas and CMS• Has been submitted twice to the NSF ITR program at

the urging of the Physics directorate to create a CMS/Atlas joint IT effort

GESCR - Going Forward

• Waiting for funding decision on most recent submission– If funded, work on unique physics capabilities

(VRVS, MonaLISA, etc) will begin immediately– If not funded, leverage NEESGrid / Open Grid

Computing Environment / Sakai - focus on the generic tools - deploy in a physics context

• Immediately, we can begin some experimental usage for interested groups using the University of Michigan CTools service

University of Michigan: Ctools

• University of Michigan runs a large scale professional server cluster for teaching and learning and research collaboration– Research collaboration simply needs a single UMich

member of each group - the rest of the members have no-charge “friend” accounts based on E-Mail addresses.

– For multiple accounts, it is best to have a UM person to act as your “problem solver” familiar with your group. If there is interest, we can provide staff from the MGrid (www.mgrid.umich.edu) organization to support HEP collaborative activities.

• ctools.umich.edu

Sakai-Based CTools @ UM

In production August 1, 2004.

Summary

• We will deploy collaboration software for Atlas / CMS sooner or later

• If / when we get funding it will accelerate the process and provide Physics specific capabilities

• Collaborative portals is a well-funded and well-coordinated activity (Sakai 30+FTE, NEESGrid 10+FTE, OGCE 5+ FTE)

• It is (almost) a no-lose situation - the longer we wait, the more mature the software will be

Questions

• Thank you for your time…

• Questions to csev@umich.edu