Web 2 0 for E Science Environments

1

Web 2.0 for e-Science

Environments

SKG2007

Xi’an Hotel, Xi’an China October 29 2007

Geoffrey Fox and Marlon Pierce

Computer Science, Informatics, Physics Community Grids Laboratory

Indiana University Bloomington IN 47401

Applications, Infrastructure,

Technologies

n This field is confused by inconsistent use of terminology; I define n Web Services, Grids and (aspects of) Web 2.0 (Enterprise 2.0) are

technologies

n Grids could be everything (Broad Grids implementing some sort of managed web) or reserved for specific architectures like OGSA or Web Services (Narrow Grids)

n These technologies combine and compete to build electronic

infrastructures termed e-infrastructure or Cyberinfrastructure

n e-moreorlessanything is an emerging application area of broad importance that is hosted on the infrastructures e-infrastructure

or Cyberinfrastructure

n e-Science or perhaps better e-Research is a special case of

Relevance of Web 2.0

n

They say that Web

1.0

was a

read-only

Web while Web

2.0

is the wildly

read-write collaborative

Web

n

Web 2.0

can

help e-Science

in many ways

n

Its tools can enhance scientific collaboration, i.e.

effectively

support virtual organizations

, in different

ways from grids

n

The popularity of Web 2.0 can provide

high quality

technologies and software

that (due to large

commercial investment) can be very useful in e-Science

and preferable to Grid or Web Service solutions

n

The

usability

and

participatory

nature of Web 2.0 can

bring science and its informatics to a

broader audience

n

Web 2.0 can even help the emerging challenge of using

multicore

chips i.e. in improving

parallel computing

4

“Best Web 2.0 Sites” -- 2006

n Extracted from http://web2.wsj2.com/ n All important capabilities for e-Science n Social Networking

n Start Pages

n Social Bookmarkin

n Peer Production News

n Social Media Sharing

Web 2.0, Grids and Web Services I

n Web Services have clearly defined protocols (SOAP) and a well defined mechanism (WSDL) to define service interfaces

• There is good .NET and Java support

• The so-called WS-* specifications provide a rich sophisticated but

complicated standard set of capabilities for security, fault tolerance, meta-data, discovery, notification etc.

n “Narrow Grids” build on Web Services and provide a robust managed environment with growing but still small adoption in Enterprise systems and distributed science (so called e-Science) n Web 2.0 supports a similar architecture to Web services but has

developed in a more chaotic but remarkably successful fashion with a service architecture with a variety of protocols including those of Web and Grid services

• Over 500 Interfaces defined at http://www.programmableweb.com/apis n Web 2.0 also has many well known capabilities with Google

Maps and Amazon Compute/Storage services of clear general relevance

n There are also Web 2.0 services supporting novel collaboration modes and user interaction with the web as seen in social

Web 2.0 Systems like Grids have Portals, Services, Resources

n

Captures the incredible development of interactive

Web 2.0, Grids and Web Services II

n I once thought Web Services were inevitable but this is no longer clear to me

n Web services are complicated, slow and non functional

• WS-Security is unnecessarily slow and pedantic

(canonicalization of XML)

• WS-RM (Reliable Messaging) seems to have poor adoption

and doesn’t work well in collaboration

• WSDM (distributed management) specifies a lot

n There are de facto Web 2.0 standards like Google Maps and powerful suppliers like Google/Microsoft which “define the architectures/interfaces”

n One can easily combine SOAP (Web Service) based

Distribution of APIs and Mashups per

Protocol

REST SOAP XML-RPC REST,

XML-RPC XML-RPC,REST, SOAP

REST,

SOAP JS Other

google maps netvibes live.com virtual earth google search amazon S3 amazon ECS flickr ebay youtube 411syncdel.icio.us yahoo! search yahoo! geocoding technorati yahoo! images trynt yahoo! local Number of Mashups Number of APIs

Where did Narrow Grids and Web Services go wrong?

n Too much Computing: historically one (including narrow grids) has tried to increase computing capabilities by

• Optimizing performance of codes at cost of re-usability

• Exploiting all possible CPU’s such as Graphics co-processors and “idle

cycles” (across administrative domains)

• Linking central computers together such as NSF/DoE/DoD

supercomputer networks without clear user requirements

n Next Crisis in technology area will be the opposite problem – commodity chips will be 32-128way parallel in 5 years time and we currently have no idea how to use them – especially on clients

• Only 2 releases of standard software (e.g. Office) in this time span

n Interoperability Interfaces will be for data not for infrastructure

• Google, Amazon, TeraGrid, European Grids will not interoperate at the

resource or compute (processing) level but rather at the data streams

flowing in and out of independent Grid islands

• Data focus is consistent with Semantic Grid/Web but not clear if latter

has learnt the usability message of Web 2.0

n One needs to share computing, data, people in e-moreorlessanything, Grids initially focused on computing but data and people are more important

n eScience is healthy as is e-moreorlessanything

n Most Grids are solving wrong problem at wrong point in stack with a

Some Web 2.0 Activities at IU

n

Use of

Blogs

, RSS feeds, Wikis etc.

n

Use of

Mashups

for Cheminformatics Grid workflows

Moving from

Portlets

to

Gadgets

in portals (or at least

supporting both)

n

Use of

Connotea

to produce tagged document collections

such as htt

p://www.connotea.org/user/crmc for

parallel

computing

n

Semantic Research Grid

integrates multiple tagging and

search systems and copes with overlapping inconsistent

annotations

n

MSI-CIEC portal

augments Connotea to tag a mix of

URL and URI’s e.g. NSF TeraGrid use, PI’s and

Proposals

• Hopes to support collaboration (for Minority Serving

Institution faculty)

Use blog to create posts.

Semantic Research Grid (SRG)

n Integrates tagging and search system that allows users to use

multiple sites and consistently integrate them with traditional citation databases

n We built a mashup linking to del.icio.us, CiteULike, Connotea allowing exchange of tags between sites and between local

repositories

n Repositories also link to local sources (PubsOnline) and Google

Scholar (GS) and Windows Academic Live (WLA) • GS has number of cited publications.

• WLA has Digital Object Identifier (DOI)

n We implement a rather more powerful access control mechanism n We build heuristic tools to mine “web lists” for citations

n We have an “event” based architecture (consistency model)

allowing change actions to be preserved and selectively changed • Supports integrating different inconsistent views of a given document and

its updates on different tagging systems

MSI-CIEC Portal

MSI-CIEC

NSF Grants Tag System

n

NSF has the ability to get information (in XML) on all of the

grants a particular person worked on

n

We downloaded, parsed, and bookmarked this info using a

little scavenger robot.

• Each grant is represented by a bookmark and tagged with

relevant information in MSI-CIEC Portal

• Grant tags point to URLs of the NSF award page. n

The investigators

are imported as users

n

Each has a bookmark for each project they worked on

n

Can now

form research collaborations

by linking

researchers with common tags

n

Hopefully will enable

broader collaborations

and not

Superior (from broad usage)

technologies of Web 2.

Mash-ups can replace Workflo

Gadgets can replace Portlet

16

Mashups v Workflow?

n Mashup Tools are reviewed at

http://blogs.zdnet.com/Hinchcliffe/?p=63

n Workflow Tools are reviewed by Gannon and Fox

http://grids.ucs.indiana.edu/ptliupages/publications/Workflow-overview.pdf

n Both include scripting in PHP, Python, sh etc. as both implement

distributed

programming at level of services

n Mashups use all types of service interfaces and perhaps do not have the potential

robustness (security) of Grid service approach n Mashups typically

17

Grid Workflow Datamining in Earth Science

n Work with Scripps Institute

n Grid services controlled by scripting workflow process

real time data from ~70 GPS Sensors in Southern California

Streaming Data Support

Transformations Data Checking

Hidden Marko Datamining (JPL)

Display (GIS)

NASA GPS

Earthquake

Grid Workflow Data Assimilation in Earth Science

n Grid services triggered by abnormal events and controlled by workflow process real

time data from radar and high resolution simulations for tornado forecasts

Typical graphical interface to service

composition

Taverna another well known Grid/Web Service workflow tool

Major Companies entering mashup area

n Web 2.0 Mashups (by definition the largest market) are likely to drive composition tools for Grid and web

n Recently we see Mashup tools like Yahoo Pipes and Microsoft Popfly which have familiar graphical interfaces

n Currently only simple examples but tools could become powerful

Web 2.0 Mashups

and APIs

n

http://www.programmable

web.com/apis

has (Sept 12

2007) 2312 Mashups and

511

Web 2.0 APIs

and with

GoogleMaps the most often

used in Mashups

n

This is the

Web 2.0 UDDI

The List of

Web 2.0 API’s

n

Each site has API and

its features

n

Divided into broad

categories

n

Only a few used a lot

(

49 API’s

used in

10

or more

mashups

)

n

RSS feed of new APIs

Google maps

dominates but

Amazon S3

growing

Now to Portals

22

Grid-style portal as used in Earthquake Grid

The Portal is built from portlets – providing user interface fragments for each service that are composed into the full interface – uses OGCE technology as does planetary science VLAB portal with University of Minnesota

QuakeSim has a typical Grid technology portal

23

Portlets v. Google Gadgets

n

Portals for Grid Systems are built using portlets with

software like GridSphere integrating these on the

server-side into a single web-page

n

Google (at least) offers the Google sidebar and Google

home page which support Web 2.0 services and do not

use a server side aggregator

n

Google is more user friendly!

n

The many Web 2.0 competitions is an interesting model

for promoting development in the world-wide

distributed collection of Web 2.0 developers

n

I guess Web 2.0 model will win!

Typical Google Gadget Structure

 … Lots of HTML and JavaScript </Content> </Module>

Portlets build User Interfaces by combining fragments in a standalone Java Server

Google Gadgets build User Interfaces by combining fragments with JavaScript on the client

Google Gadgets are an example of Start Page Web 2.0 term for portals) technolog

Web 2.0

can also help

address

long standing difficulties

with

parallel programming

environments

Too much computing addresses too much data an implies need for multicore datamining algorithms

Clustering

Principal Component Analysis (SVD)

Expectation-Maximization EM (mixture models)

Multicore S

A

LS

A

at CGL

n

S

ervice

A

ggregated

L

inked

S

equential

A

ctivities

• http://www.infomall.org/multicore

n

Ai

ms to

link parallel and distributed

(Grid) computing

by developing parallel applications as

services

and

not

as programs or libraries

• Improve traditionally poor parallel programming

development environments

n

Can use messaging to link parallel and Grid services

but performance – functionality tradeoffs different

• Parallelism needs few µs latency for message latency and

thread spawning

• Network overheads in Grid 10-100’s µs

n

Developing set of

services (library)

of

multicore parallel

Parallel Programming Model

n If multicore technology is to succeed, mere mortals must be able to build effective parallel programs

n There are interesting new developments – especially the Darpa HPCS Languages X10, Chapel and Fortress

n However if mortals are to program the 64-256 core chips expected in 5-7 years, then we must use today’s technology and we must make it easy

• This rules out radical new approaches such as new languages

n The important applications are not scientific computing but most of the

algorithms needed are similar to those explored in scientific parallel computing

• Intel RMS analysis

n We can divide problem into two parts:

• High Performance scalable (in number of cores) parallel kernels or

libraries

• Composition of kernels into complete applications

n We currently assume that the kernels of the scalable parallel algorithms/applications/libraries will be built by experts with a

n Broader group of programmers (mere mortals) composing library

Scalable Parallel Components

n There are no agreed high-level programming environments for building library members that are broadly applicable.

n However lower level approaches where experts define

parallelism explicitly are available and have clear performance models.

n These include MPI for messaging or just locks within a single shared memory.

n There are several patterns to support here including the

collective synchronization of MPI, dynamic irregular thread parallelism needed in search algorithms, and more specialized cases like discrete event simulation.

n We use Microsoft CC

http://msdn.microsoft.com/robotics/ as it supports both MPI

and dynamic threading style of parallelism

Composition of Parallel Components

n The composition step has many excellent solutions as this does not have the same drastic synchronization and correctness constraints as for scalable kernels

• Unlike kernel step which has no very good solutions

n Task parallelism in languages such as C++, C#, Java and Fortran90; n General scripting languages like PHP Perl Python

n Domain specific environments like Matlab and Mathematica n Functional Languages like MapReduce, F#

n HeNCE, AVS and Khoros from the past and CCA from DoE

n Web Service/Grid Workflow like Taverna, Kepler, InforSense KDE, Pipeline Pilot (from SciTegic) and the LEAD environment built at Indiana University.

n Web solutions like Mash-ups and DSS

n Many scientific applications use MPI for the coarse grain composition as well as fine grain parallelism but this doesn’t seem elegant

n The new languages from Darpa’s HPCS program support task parallelism (composition of parallel components) decoupling

“Service Aggregation” in

SALSA

n

Kernels and Composition must be supported both

inside

chips

(the multicore problem) and

between machines

in

clusters (the traditional parallel computing problem) or

Grids.

n

The scalable parallelism (kernel) problem is typically only

interesting on true parallel computers as the algorithms

require low communication latency.

n

However

composition is similar in both parallel and

distributed scenarios

and it seems useful to allow the use of

Grid

and

Web 2.0

composition tools for the parallel problem.

•

This should allow parallel computing to exploit large

investment in service programming environments

n

Thus in SALSA we express parallel kernels not as traditional

libraries but as (some variant of) services so they can be used

by non expert programmers

n

For

parallelism expressed in CCR

,

DSS

represents the

Parallel Programming 2.0

n

Web 2.0 Mashups

(by definition the largest market)

will drive

composition tools

for Grid, web and

parallel

programming

n

Parallel Programming 2.0

can build on Mashup tools

like Yahoo Pipes and Microsoft Popfly

Inside the SALSA Services

n

We generalize the well known

CSP

(Communicating

Sequential Processes) of Hoare to describe the low level

approaches to fine grain parallelism as “

L

inked

S

equential

A

ctivities” in

SALSA

.

n

We use term “

activities

” in

SALSA

to allow one to build

services from either

threads

,

processes

(usual MPI choice)

or even just other

services

.

n

We choose term “

linkage

” in

SALSA

to denote the

different

ways of synchronizing

the parallel activities that may

involve

shared memory

rather than some form of

messaging or communication.

n

There are several engineering and research issues for

SALSA

•

There is the critical

communication optimization

problem area for communication inside chips, clusters

and Grids.

25.8

4 Thread

CCR

XP Intel4(4 core 2.8 Ghz)

16.3 4 Thread CCR XP 39.3 4 Process MPICH2 99.4 4 Process mpiJava 152 4 Process MPJE Redhat 185 4 Process MPJE XP AMD4

(4 core 2.19 Ghz)

20.2 8 Thread CCR (C#) Vista 100 8 Process mpiJava Fedora 142 8 Process MPJE Fedora 170 8 Process MPJE Vista Intel8b

(8 core 2.66 Ghz)

64.2 8 Process MPICH2 111 8 Process mpiJava 157 8 Process MPJE Fedora Intel8c:gf20

(8 core 2.33 Ghz)

4.21 8 Process Nemesis 39.3 8 Process MPICH2: Fast 40.0 8 Process MPICH2 (C) 181 8 Process MPJE (Java) Redhat Intel8c:gf12

(8 core 2.33 Ghz) (in 2 chips)

MPI Exchange Latency Parallelism

Grains Runtime

OS Machine

MPI Exchange Latency in µs (20-30 µs computation between messaging)

SALSA Performance

The macroscopic inter-service DSS Overhead is about 35µs

DSS is composed from CCR threads that hav

4µs overhead for spawning threads in dynamic search applications

Renters Total

Asian

Hispanic

Renters

IUB Purdue

10 Clusters

Total

Asian

Hispanic

Renters

30 Clusters

Clustering is typical of data mining methods that are needed for tomorrow’s clients or servers bathed in a data rich environment

Clustering Census data in Indiana on dual quadcore processors

Implemented with CCR and DS

Use deterministic annealing that uses multiscale method to avoid local minima

Parallel Multicore GI

Deterministic Annealing

Clustering

Parallel Overhea on 8 Threads Intel 8b

Speedup = 8/(1+Overhead)

10000/(Grain Size n = points per core) Overhead = Constant1 + Constant2/n

Constant1 = 0.02 to 0.1 (Windows) due to threa runtime fluctuations

10 Clusters

Web 2.0 v Narrow Grid I

n Web 2.0 and Grids are addressing a similar application class although Web 2.0 has focused on user interactions

• So technology has similar requirements

n Web 2.0 chooses simplicity (REST rather than SOAP) to lower

barrier to everyone participating

n Web 2.0 and Parallel Computing tend to use traditional (possibly

visual) (scripting) languages for equivalent of workflow whereas Grids use visual interface backend recorded in BPEL

n Web 2.0 and Grids both use SOA Service Oriented Architectures n Services will be used everywhere: Grids, Web 2.0 and Parallel

Computing

n “System of Systems”: Grids and Web 2.0 are likely to build systems hierarchically out of smaller systems

• We need to support Grids of Grids, Webs of Grids, Grids of

Services etc. i.e. systems of systems of all sorts

• Web 2.0 suggest data not infrastructure system linkage

Web 2.0 v Narrow Grid II

 Web 2.0 has a set of major services like GoogleMaps or Flickr but the world is composing Mashups that make new composite services

• End-point standards are set by end-point owners

• Many different protocols covering a variety of de-facto standards

 Narrow Grids have a set of major software systems like Condor and Globus and a different world is extending with custom

services and linking with workflow

 Popular Web 2.0 technologies are PHP, JavaScript, JSON,

AJAX and REST with “Start Page” e.g. (Google Gadgets)

interfaces

 Popular Narrow Grid technologies are Apache Axis, BPEL

WSDL and SOAP with portlet interfaces

 Robustness of Grids demanded by the Enterprise?

 Not so clear that Web 2.0 won’t eventually dominate other application areas and with Enterprise 2.0 it’s invading Grids

Web 2.0 v Narrow Grid III

n Narrow Grids have a strong emphasis on standards and structure n Web 2.0 lets a 1000 flowers (protocols) and a million developers

bloom and focuses on functionality, broad usability and simplicity

• Interoperability at user (data) level not at service level

• Puts semantics into application (user) level (like KML for maps)

and minimizes general system level semantics

n Semantic Web/Grid has structure to allow reasoning

• Annotation in sites like del.icio.us and uploading to

MySpace/YouTube is unstructured and free text search replaces structured ontologies?

• Flickr has geocoded (structured) and unstructured tags

n Portals are likely to feature both Web and “desktop client”

technology although it is possible that Web approach will be adopted more or less uniformly

n Web 2.0 has a very active portal activity which has similar architecture to Grids

• A page has multiple user interface fragments

n Web 2.0 user interface integration is typically Client side using

Gadgets AJAX and JavaScript while

• Grids are in a special JSR168 portal server side using Portlets

WSRP and Java

The Ten areas covered by the 60 core WS-*

Specifications

WSRP (Remote Portlets) 10: Portals and User

Interfaces

WS-Policy, WS-Agreement 9: Policy and Agreements

WSDM, WS-Management, WS-Transfer 8: Management

WSRF, WS-MetadataExchange, WS-Context 7: System Metadata and State

UDDI, WS-Discovery 6: Service Discovery

WS-Security, WS-Trust, WS-Federation, SAML, WS-SecureConversation

5: Security

BPEL, WS-Choreography, WS-Coordination 4: Workflow and

Transactions

WS-Notification, WS-Eventing (Publish-Subscribe)

3: Notification

WS-Addressing, WS-MessageDelivery; Reliable Messaging WSRM; Efficient Messaging MOTM 2: Service Internet

XML, WSDL, SOAP 1: Core Service Model

WS-* Areas and Web 2.0

Start Pages, AJAX and Widgets(Netvibes) Gadgets 10: Portals and User

Interfaces

Service dependent. Processed by application 9: Policy and Agreements

WS-Transfer style Protocols GET PUT etc. 8:

Management==Interaction

Processed by application – no system state –

Microformats are a universal metadata approach 7: System Metadata and

State

http://www.programmableweb.com 6: Service Discovery

SSL, HTTP Authentication/Authorization, OpenID is Web 2.0 Single Sign on

5: Security

Mashups, Google MapReduce

Scripting with PHP JavaScript …. 4: Workflow and

Transactions (no

Transactions in Web 2.0)

Hard with HTTP without polling– JMS perhaps? 3: Notification

No special QoS. Use JMS or equivalent? 2: Service Internet

XML becomes optional but still useful SOAP becomes JSON RSS ATOM

WSDL becomes REST with API as GET PUT etc. Axis becomes XmlHttpRequest

1: Core Service Model

Looking to the Future

n Web 2.0 has momentum as it is driven by success of social web sites and the user friendly protocols attracting many developers

of mashups

n Grids momentum driven by the success of eScience and the

commercial web service thrusts largely aimed at Enterprise

n We expect applications such as business and military where

predictability and robustness important might be built on a Web Service (Narrow Grid) core with perhaps Web 2.0 functionality enhancements

• But even this Web Service application may not survive

n Multicore usability driving Parallel Programming 2.0

n Simplicity, supporting many developers are forces pressuring

Grids!

n Robustness and coping with unstructured blooming of a 1000