Use of Java in Computational Science

presented by

Tomasz HauptNortheast Parallel Architectures Center

at Syracuse University

Part I

Web Portals

Web Portals

• A portal is a web entrance to a set of resources and consists of a mix of information, computer simulations and various services

• For businesses portals generalize the concept of a a company Intranet and encompass domain of IBM main frames, Lotus Notes etc.

• For computing, portals are called Problem Solving Environments

Examples of Portals

• Portal to NPAC is http://www.npac.syr.edu• Portal to the world is http://www.yahoo.com/

or http://my.netscape.com/• Portal to latest news is http://www.cnn.com• Portal to computational chemistry is

http://www.osc.edu/~kenf/theGateway/• Portal to stock trading is http://quote.yahoo.com/

Example Portal: Netscape Access to:

• Search Engines

• News

• Weather

• Stocks

• Sport

• Services

• Bookmarks

• Mail

• Calendar

• ...

More Portals

Portalsare

customizable

Special Portals -- Computing

• But perhaps more interestingly computing portals involve building a web based problem solving environment to link together all the capabilities needed to compute

• run programs and access dynamically status of jobs and computers -- in particular allow a uniform interface to running a given job on one of many backend compute servers

• compile and debug programs • link diverse data sources with computations run on multiple backend machines• visualize results• web-based help systems and collections of related scientific papers• computational steering i.e. interacting with a job (change parameters) based on

dynamic results such as visualized results• See http://www.osc.edu/~kenf/theGateway/ and

http://www-fp.mcs.anl.gov/~gregor/datorr/

Portals for scientific and engineering communities

• Seamless access to HPC resources• Seamless access to instruments• Data storage• Application specific data base• Visualization Tools• Collaboratory• Scientific notepads

Remote Resources

Front-End

FRONT-END:high-level user friendly - visual programming and authoring tools - application GUI

RESOURCES:all hardware and software components needed to complete the user task, including, but not limited to, compute engines from workstations to supercomputers, storage, databases, instruments, codes, libraries, and licenses.

Desktop/Laptop

Seamless Access

Seamless Access

• Create an illusion that all resources needed to complete the user tasks are available locally.

• In particular, an authorized user can allocate the resources she needs without explicit login to the host controlling the resources.

• An analogy: NSF mounted disk or a network printer.

Example: Globus

Advantages:- platform independent mini-language (RSL) for specification of resources- can be layered on top of different schedulers- enables interoperability between resources (can allocate many resources at a time, file transfer, monitoring, etc.)

Disadvantage: - a bag of low level tools

GRAMClient

Gatekeeper Gatekeeper Gatekeeper

Contact addressResource Language Specification

MDSDirectoryService

GSS-API

Towards a complete solution ...PSE: problem description (physics, chemistry, ...)

Task description: I need 64 nodes of SP-2 at Argonne to run my MPI-based executable “a.out” you can find in “/tmp/users/haupt” on

marylin.npac.syr.edu. In addition, I need any idle workstationwith jdk1.1 installed. Make sure that the output of my a.out is

transferred to that workstation

Middle-Tier: map the user’s task description onto the resource specification; this may include resource discovery, and other services

Resource Specification

Resource Allocation: run, transfer data, run

Remote Resources

Front-End Front-End

Middle-Tier

Resource Specification

Abstract Task Specification

We need a third tier!

Target Architecture

Middle-Tier

Resource Specification

Abstract Task Specification

CTA specificknowledgedatabases

VisualAuthoring

Tools

User andGroup

Profiles

ResourceIdentificationand Access

VisualizationsCollaboration

WebFlow

Back-End Resources

Problem Solving Environment

Example of a portalNavigate and choose an existing application

to solve the problem at hand.Import all necessary data.

Retrieve data

Pre/post-processing

Run simulations

Select host

Select model

Set parameters

Run

PSE Example: CCM IPSE

Ken Flurchick, http://www.osc.edu/~kenf/Gateway

1 .Define your problem2. Identify resources (software and hardware)3. Create input file4. Run your application5. Analyze results

QS Front End

Compose interactivelyyour applicationfrom pre-existing

modules

Data-Flow Front-End

Building a Portal• We can identify a set of tools that enable the

construction of portals• These are roughly equivalent to the tools needed

to build a general application based on “object web technologies”

• There is also an architecture implying multi-tier systems with standard compliant interfaces

• A common portal architecture means that portals can be conveniently linked together– e.g. the 3 portals to biology, chemistry, and physics

naturally form portal to science

Portal Building Blocks I

• So we currently have languages (Java ..) distributed object support and standards (CORBA …), interface standards (XML), transport protocols (HTTP, TCP/IP) at various levels, rendering standard (HTML).

• We have web clients and servers

• We need certain capabilities in common to many portals. These include– security

– collaboration

– visualization (for computing portals)

– persistence, registration, look-up (part of most distributed object infrastructure)

Portal Building Blocks -- Security

• So in this course, we will discuss security as it is a common service needed by many portals– It can be implemented simply as a user name / password but there

are several special features– Encryption -- keeping information secret– Authentication -- identifying and authorizing individuals to access

particular capabilities– Different technical approaches -- especially Kerberos and Public Key

Infrastructure

• And a discussion of special difficulties as seen by spate of stories about viruses, hackers and security leaks of computer information from government facilities

Portal Building Blocks -- Distributed Object Support

• Although CORBA for instance provides (by definition) most key distributed object services such as persistence, this is not sufficient as we will inevitably mix object models and further these services are still being developed

• So as one part of this course we will discuss “discuss distributed object” and “internet” (software) infrastructure

• with special attention to issues of naming, registering, looking up (yellow pages) and addressing objects– Remember a web page is most common object and every Java program is an object

• We need to contrast classical hierarchy of naming as in DNS and web URL’s as implemented in LDAP with much more intriguing dynamic model in Sun’s Jini and UCB’s Ninja which are suitable for mobile ephemeral objects

Basic 3 Tier Computing Model• A server accepts input and produces output

– A Web Server accepts HTTP request and returns a web page

– a Database Server accepts a SQL request and returns records selected from database

– An Object Broker accepts IIOP requests to invoke methods of an “object” (e.g. run a program)

• IIOP and HTTP are two common protocols (formats of control data) for inter program messages

• A Web browser (Netscape or Microsoft) can access any server at “the click of a button” with data from user refining action

Web ServerFile System or

Database holdingWeb Pages

Object View of running a program• Similar to invoking a web page

• “CORBA” or “WIDL” (pure XMLCGI specification) is just CGIdone right …...

PressRun

ButtonObject Broker

FortranSimulation Codeon Sequential orParallel Machine

Convert GenericRun Request intoSpecific Request

on Chosen Computer

Fortran Program is an ImportantType of Object

It can be built up fromsmaller objects

e.g. Matrixlibrary could be an

object

Pragmatic Object Web Technology Model - I

• Basic Vision: The current incoherent but highly creative Web will merge with distributed object technology in a multi-tier client-server-service architecture with Java based combined Web-ORB’s

• Need to abstract entities (Web Pages, database entries, simulations) and services as objects with methods (interfaces)– CORBA .. XML is “just” CGI done right

• COM(Microsoft) and CORBA(world) are competing cross platform and language object technologies– Every Netscape4 browser has a Visigenic ORB built in

• Javabeans plus RMI and JINI is 100% pure Java distributed object technology• W3C says you should use XML which defines a better IDL and perhaps an

object model -- certainly does for documents• How do we do this while technology is still changing rapidly!

Multi-Tier Client Server Service

Old and New Useful Backend

Systems

RelationalDatabase

Web Server

Object Store

Object Broker

IIOP

Specialized Java Server

HTTP

RMI(IIOP)or Custom

Client Tier

Javabean Enterprise Javabean

Back-end TierServices

Middle TierServers

Pragmatic Object Web Technology Model - II

• Need to use mix of approaches -- choosing what is good and what will last

• For example develop Web-based databases with Java objects using standard JDBC (Java Database Connectivity) interfaces– Oracle DB2 Informix Sybase, Lotus Notes, Object database confusion becomes

an issue of performance/robustness NOT functionality

• Use XML to record small databases in flat files

• Use CORBA to wrap existing applications

• Use COM to access components of major PC applications such as Microsoft Excel and Word

• Use Jini and Java to implement dynamic registration of objects• Use HTML to render everything

1)Rendering of (Multiple)Objects2)Proxy to some backend capability used to renderinput and output to andfrom service

DatabaseMPP

TelescopeFile System

1)Server acts as a brokerand control layer2)Same software as clientbut higher performancemulti-user3)Again service representedas proxy used as a token forcontrol logic

Services withspecialized softwareand capabilities

Functionality of layers

Proxy -- Proxy -- Backend Capability

• The Proxies and actual instantiation are linked by messages whose semantic content is defined (best) in XML• The lower system level format can be HTTP RMI IIOP or …• The client proxy is for rendering input and output including specification of object • The middle tier proxy allows choice of backend provider and functional integration (the user can specify integration at client proxy level)

Real CapabilityXML XML

Basic Multi Tier architecture

• Objects (at “logical backend”) can be on client of course

• Front end can define a generic (proxy for a) object. The middle control tier brokers a particular instantiation

Broker or ServerXML

ResultXMLQuery

RenderingEngine

Browser

RenderingEngine

HTML

ObjectsUniversal InterfacesIDL or Templates

XML Requestfor servicefollowed by

return of XMLresult

Clients andtheir servers Middle Tier Custom Servers

Back End Servers andtheir services

Emerging Object Web Multi-Server Model

Database

Matrix Solver

OptimizationService

MPP

MPP

Parallel DBProxy

NEOS ControlOptimization

Origin 2000Proxy

NetSolveLinear Alg.

Server

IBM SP2Proxy

Gateway Control

Agent-basedChoice of

Compute Engine

MultidisciplinaryControl

(WebFlow)

Data AnalysisServer

Multi-Server Web Computing System

or Portal to Computing

Some caveats and comments

• Need version 5 browsers with good XML support to properly implement this

• We draw three tier as minimum architecture but as previous diagram suggests, one is likely to build a more structured system with middle tier having more layers

• Network computer breaks client tier into two with simple HTML at user and Java servlets providing heavier weight capability on a different machine– Here user is at a WebTV or Palm Pilot or similar low-end device

Palm TopUser Specific

Server

Multi-UserMiddleware

What does it take to Implement This

• Well you need some hardware -- that is either an Internet or Intranet– Internet is the world running object web software

– Intranet is a dedicated network (for a company, university department, PC cluster) running object web software

• You need some software

• You need some standards and capabilities expressed in these standards

• You need some capabilities common to many applications

• You need a specific system to solve a particular problem

More details on the implementation

• Note the hardware can be as little as 1 PC on your desk

• More interestingly it is your 64 PC Linux or Windows NT Cluster up to the cluster of 64 128 node SGI Origin’s at Los Alamos– i.e. a parallel computer is by definition a special case of an Intranet

• Software divides into several types

Fortran ProgramPLSQL Database

or …..

HTMLRendering

Java/CORBA/WIDLWrapper

Style Sheetsand Page Design

“Glue” with (multiple) tier servers and XML

inter tier communication

Implementation Continued I• The backend software can be parallel or sequential and simulation or information based

– It can be COBOL, Fortran, C++, Perl ...• We need to define in XML its interface needed to

– run it– set its parameters -- i.e. its input mechanisms– get its output -- numbers or visualization

• This backend program interface is defined as an XML file e.g.<program name=“physicssimulation1”>

<run domain=“npac” machine=“maryland” type=“pc” os=“nt” exec=c:\myprogs\a.out</run>

<input type=“htmlform” ><name>userinput</name><field default=“10” >iterations</field> ……….

</input><output> …</output>

</program>

Becomes HTML form with name userinput and text field iterations

with default value 10 on client

Implementation Continued II• For this example (running a physics program), we could use a specific

machine as defined on previous foil (the Windows NT PC maryland) or a generic machine <run domain=“any” machine=“any” type=“pc” os=“nt” >

• In this case, middle tier broker, would look in a database (XML file) to find what machines were available and either automatically or with user input choose one.

• Both Software and Hardware are defined in XML

• Note databases and an XML files are logically equivalent

• JDBC can access either Oracle (Microsoft) database or XML ASCII file

• More generally XML can be thought of as general object serialization– A database table is one type of object

Implementation Continued III

• The front end is some document consisting of a mix of HTML or XML– The HTML is whatever you want to make a nice page

– The XML is converted into some variant of HTML by• Browser default or

• XSL style sheet

• User Program -- logically in middle tier

– Note HTML can include Java applets either directly or invoked from XSL style sheets

• We will NOT discuss either how to code backend in PLSQL or Fortran or how to compose final rendered document in HTML

Collaboration I

• This is often termed groupware support and Lotus Notes is best known corporate product

• Collaboration implies sharing of electronic objects and is needed in asynchronous and synchronous modes

• AOL Yahoo etc. have Internet games which illustrate one sophisticated form of collaboration

• Chat rooms are perhaps most popular and are simplest synchronous tool. White boards next most popular

• Asynchronous mode is– shared web pages and documents (these are be shared synchronously or

asynchronously)– electronic mail, event calendars, bulletin boards

• http://www.npac.syr.edu/tango/ is a collaboration system supporting synchronous sharing of events where events signify changes in objects

Collaboration II

• Notification and linkage service can be based on object registration mechanism and allows important collaborative capabilities

• one associates with each group activity a “magic ID” (barcode)

• every digital object associated with this activity registers itself when it comes on line with some registry (registry can be distributed). A given object may have multiple barcodes attached to it– This is Jini model for registration but can be implement for pure Web

(using JavaScript) or CORBA

• Either users or Portals (PSE’s) register interest in certain barcodes

• The (Portal) event service notifies registered observers when a digital object of interest becomes available

Collaboration III

• Notification mechanism enhances collaboration as enables dynamic federation of relevant objects to be automatically maintained– Kodak would like this service to group together digital versions of

photographs taken at particular events (e.g. a wedding)

• Notification can be used for people so their presence on-line can be made known to those in particular collaborative users

• Users decide if notification causes an active signal (send electronic mail, ring a buzzer) or passively alters a list on a web page.

• Event Model unifies synchronous and asynchronous models of collaboration– Event either triggers action immediately and/or asynchronously ( sending

e-mail immediately is synchronous act generating asynchronous record)

Collaboration and Portals I• Shared Objects need to accept data from Portal compliant applications

• Portal Events need to be integrated into SPDL

• Portal federates different “event domains”

Local Event/Message Bus

Collaboration ==Sharing Event

in “Tango” Server

Local Event/Message BusLocal Event/Message Bus

PortalEvents

Collaboration and Portal II• Whiteboard and Shared Browser can be loaded with files

and data from Portal compliant systems• More generally consider any client side rendering of a

gateway system -- either data input or (visualization/data) output– These can be shared collaboratively

• Examples from Tango and Computing Portal– Shared Biology Workbench shares client side input forms

– Shared visualization (NCSA, NPAC) shares output file of a computation

Part II

WebFlow

WebFlow design

• Object Oriented, follows JavaBeans model– everything is an object

– objects interact through events

Object A(event source)

Object B(event target)

Fire event EMethod M(){…}

Firing event E by object A causes invocation of method M of object B.The association of event E and method M is achieved by an eventregistration mechanism. An event is also an object and it carries data.

A few words about CORBA

(a digression)

more information on Java, Corba, Distributed Object:

http://www.npac.syr.edu/projects/cps616spring96/index.html

Distributed objects

• Typically WebFlow objects live in different address spaces. We use CORBA to invoke methods of the remote objects.

Object A(event source)

Object B(event target)

Fire event EMethod M(){…}

ORB

How is this possible?

ORB2

Object A(event source)

Object B(event target)

Fire event EMethod M(){…}

ORB1IIOP

- Objects A and B are CORBA objects (thus not Java objects)- Objects are defined in IDL (Interface Definition Language)- IDL definitions are compiled using (Java)IDL compiler- The IDL compiler generates new classes to be used by the Java compiler (javac) instead of the original ones, on both the client and server side- The IDL compiler generates either classes to be extended, or interfaces to be implemented

Object Adapterserves also as a daemon

Example of IDL definition#include “..\BC.idl”module WebFlow { module lms{ interface runEdys:BeanContextChild { void run(); void receiveData(); void setParameter(in string p); }; interface runCasc2d:BeanContextChild{ void run(); void runAgain(); }; interface DoneEvent{ Object getSource(); }; };};

We will create 3 CORBA objects

* two modules: - runEdys - runCasc2d * one event - DoneEvent

They will be added to packageWebFlow.lms

We need more flexibility...

• WebFlow objects are developed independently of each other(reusable modules): we cannot assume that the event source knows anything about the event target and vice versa

Event binding

addEventListenerrmEventListenerfireEvent(E,M)

method M

Event Source Event TargetAdapter

Event

ORB

binding table

DII DSI

Controlling a moduleApplet

ModuleControls

Proxy Module

ModuleActionButton1ActionButton2

….

IIOP

Another complication:Java sandbox!

Adding a remote moduleLocal Host

Add module

Module Factory

Proxy Module

Remote Host

FE

requestAdd module

Module Factory

Module

Back to WebFlow design

CORBA Based Middle-Tier

Mesh of WebFlow Serversimplemented as CORBA objects

that manage and coordinate

distributed computation.

Front End

GatekeeperAuthenticationAuthorization

WebFlow Server

• The WebFlow server is a container object, a.k.a. context - in fact it implements JavaBeanContext class (Java1.2)

• The BeanContext acts as a logical container for JavaBeans (“WebFlow modules and services”) and BeanContexts.

User 1 User 2

Application 1

Application 2

App 2App 1

WebFlow Server

WebFlow server is given by a hierarchy of containers

and components

WebFlow server hosts users and services

Each user maintainsa number of applications

composed of custom modules

and common services

WebFlow Services

WebFlow Context HierarchyMaster Server (Gatekeeper)

Slave Server

Slave Server

User Context

Application Context

Module

Slave Server Proxy

Gatekeeper

Services User Modules

Browserbased

Front-End

Middle-Tier modulesserve as proxies ofBack-End Services

Browserbased

Front-End

User Space Definition and Task Specification

Metacomputing Services

Back-End Resources

Modules

• Similar to JavaBeans– full power of Java (or C++) to implement functionality

– can encapsulate legacy applications

• May serve as Proxies– JDBC

– metacomputing services (such as Globus)

– schedulers (such as PBS, CONDOR, etc)

Services

• Services are modules provided by the system and offers a generic functionality– job services (submit,monitor,kill,... a job)

– file services (edit,copy,move,… a file)

– XML parser

– database access

– mass storage access

– ...

Example of a proxy module

&(rsl_substitution = (MYDIR “/tmp/haupt”))(DATADIR $(MYDIR)/data)(EXECDIR) $MYDIR)/bin))(executable = $(EXECDIR)/a.out)(arguments=$(DATADIR)/file1)(stdout=(MYDIR)/result.dat))(count=1)

GRAM resource descriptionGenerate Data

Run Job

Analyze

The Run Job module is a proxy module. It generates the RSL on-the-fly and submits the job for execution using globusrun function.

The module knows only exec name, location and its arguments/parameters.

WebFlow over Globus

• In order to run WebFlow over Globus there must be at least one WebFlow node capable of executing Globus commands, such as globusrun

• Jobs that require computational power of massively parallel computers are directed to the Globus domain, while other jobs can be launched on much more modest platforms, such as the user’s desktop or even a laptop

running Windows NT.

Bridge between WebFlow and Globus

Secure Access: terminology• Access Control (or Authorization)

– Assurance that the person or computer at the other end of the session is permitted to do what he asks for.

• Authentication– Assurance that the resource (human or machine) at the other end of the session is

what it claims to be

• Integrity– Assurance that the information that arrives is the same as when it was sent

• Accountability (or non-repudiation)– Assurance that any transaction that takes place can subsequently proved to have

taken place

• Privacy– Assurance that sensitive information is not visible to an eavesdropper (usually

achieved using encryption)

Secure Access

• Mutual authentication of servers and users– Certificates, Keberos/SecurID

• Access control– Full autonomy of the resources owner(s)

– Akenti

• Privacy• Integrity

SECIOP

Security Model

Front End Applet

https

authentication& authorization

Gatekeeper

delegation

Stakeholders

HPCC resources

GSSAPIGSSAPI

Layer 1: secure Web

Layer 2: secure CORBA

Layer 3: Secure access to resources

Policies defined by resource owners

https (SSL)AKENTI

CORBA security service

GSSAPI (Globus)

Distributed Objects are less secure

• can play both client and server– in client/server you trust the server, but not the clients

• evolve continually– objects delegate parts of their implementation to the other objects (also dynamically composed at runtime).

Because of subclassing, the implementation of an object may change over time

• interactions are not well defined– because of encapsulation, you cannot understand all the interactions between objects

• are polymorphic (ideal for Trojan horses!)

• can scale without limit – how do you manage the access right to millions of servers?

• are very dynamic

CORBA security is built into ORB

Secure Communications

Authentication

ClientUser

Encryption Audit Authorization

Server

Encryption

Credentials

ObjectAdapterORB

Authentication

• A principal is authenticated once by ORB and given a set of credentials, including one or more roles, privileges, and an authenticated ID.

• An authenticated ID is automatically propagated by a secure ORB; it is part of the caller context

Principal Credentials

Current

Client Server

set_credentials get_attributes

authenticate

Privilege Delegation

• No delegation– The intermediary uses its own credentials

• Simple delegation– The intermediary impersonates the client

• Composite delegation– The intermediary uses both

ClientT

arge

t

Clie

nt

Tar

get

Clie

nt

Tar

get

Clie

nt TargetObject

IIOP

CORBA access model

• Based on a trusted ORB model:you must trust that your ORB will enforce the access policy on the server resource

• The ORB determines:if this client on behalf of this principal can do this operation on this object

• Server uses Access Control Lists (ACL) to control user access

Principal Role Rights Operation

Part III

WebFlow Applications

• Applications vary by the functionality of their Front-Ends– Front-End Applications

• must be pre-installed

• run fast, no restrictions

– Front-End Applets• no installation, but may take time to download

• sandbox restrictions apply, unless signed

• Applications vary by how they are composed from modules– statically

• can by prepared in the Middle-Tier

– dynamically• the user composes them from reusable components

• The modules can interact with each other in different ways:– through events (object oriented approach)

– through ports (data flow model)

– through message passing

• Applications vary on how the Front-End interacts with the Middle-Tier– A complete task description is sent to the middle-tier

• composed of reusable modules

• predefined

– Objects are added to the user context one at a time, and Front-End keeps their references

Landscape Management System

(CEWES)

LMS Objectives To develop a web based system that implements a

“navigate-and-choose” paradigm and allows the end user to: – Select (a set of) computational modules that provide answers to

the problem at hand

– Retrieve input data sets from remote sources

– Use adequate (remote) computational resources

– Visualize and analyze output data on the local host

Anytime, anywhere, using any platform

(e.g., a connected to the Internet laptop PC)

LMS: Changes in Vegetation A decision maker (the end user of the system) wants to evaluate

changes in vegetation in a geographical region over a long time period caused by short term disturbances such as a fire or human activity.

One of the critical parameters of the vegetation model (EDYS) is soil condition at the time of the disturbance.

This in turn is dominated by rainfall that possibly occurs at that time (CASC2D simulation)

Input data for the simulations are available from the Internet, such as Data Elevation Models (DEM) from USGS web site or from custom databases (spices characteristics)

LMS: Changes in Vegetation

Data retrieval Data preprocessing Simulation: two

interacting codes EDYS CASC2D

Visualization

WMS

EDYS CASC2D

DEM Land UseSoil

TextureVegetation

EDYS: vegetation model CASC2D: watershed modelWMS: Watershed Modeling System

LMS Front End

Data retrieval Data pre- and post-processing Simulations

Data RetrievalThe data wizard allows the user to

interactivelyselect the data anddownload them tothe local machine.The raw data arethen fed to the WMS system

launched from the browser to

generate input filesfor simulations.

Launching coupled simulations on different Back-End computational resources

Select host

Select model

Set parameters

Run

WMS based Visualizations

The results of the simulations are send

back to the Front-End, and can be visualized using tools included

in WMS package

Implementation of LMS

• Front-End (client) is a Java application– Data wizard, EDYS and WMS are run locally

• “navigate and choose” - no interactive composition of applications– EDYS, CASC2D, EDYS and CASC2D

• modules exchange data through message passing mediated by WebFlow

• client keeps the module references

slave

Running LMS

runCasc2d

master

UNIXWinNT

slave

runEdys

lms.class

Data wizardWMS

exeCasc2d

WebServer

WebServer

WebFlow ServersClient

- WebFlow modules

Client code

try { //add modules p1 = slaveNT.addNewModule("runEdys"); //as defined in conf.file runEdys re = runEdysHelper.narrow(p1); p2 = slaveUNIX.addNewModule("runCasc2d"); //as defined in conf.file runCasc2d rc = runCasc2dHelper.narrow(p2); //bind events master.attachEvent(p2,"Casc2dDone","Casc2dDone",p1,"run"); master.attachEvent(p1,"EdysStarted","EdysStarted",p2,"run"); master.attachEvent(p1,"EdysDone","EdysDone",p2,"runAgain"); //invoke methods of runCasc2dImp rc.run(); } catch(COMM_FAILURE ex) {System.err.println(ex.getMessage()); System.exit(1);}

Write

slave

Interactions between components

runCasc2d

master

UNIXWinNT

slave

runEdys

lms.class

Data wizardWMS

exeCasc2d

WebServer

WebServer

casc2dIIOP

http

Write

http

Quantum Simulations

Quantum Simulations

QS: WebFlow implementation

Implementation of QS

• Front-End (client) is a Java applet• applications are created dynamically from pre-

existing modules• modules exchange data through ports

(data flow model)• server keeps the module references;

the references are published on a web site

QS: Front-End

Building an application

XMLA visual representation

is converted into a XMLdocument

XMLservice

WebServer

save

parse

ApplContext

Generates Java code to add modules to ApplContextPublishes IOR

Front-End Applet

Middle-Tier

Document Type Definition <!DOCTYPE taskspec [ <!ELEMENT taskspec (task)+> <!ATTLIST taskspec UserContextRef CDATA #REQUIRED AppName CDATA #REQUIRED><!ELEMENT task ((task | module)*,connection*) > <!ELEMENT module (#PCDATA) > <!ATTLIST module modulename CDATA #REQUIRED host CDATA #REQUIRED > <!ELEMENT connection (out,in)> <!ELEMENT in EMPTY> <!ELEMENT out EMPTY> <!ATTLIST out modulename CDATA #REQUIRED eventname CDATA #REQUIRED<!ATTLIST in modulename CDATA #REQUIRED method CDATA #REQUIRED > ]>

Example XML document

<taskspec UserContextRef="123as321" AppName="TestApplication"><task> <module modulename="FileBrowser" host="localhost"> </module> <module modulename="FileEditor" host="localhost"> </module> <module modulename="Gaussian" host="localhost"> </module> <connection> <out modulename="FileBrowser" eventname="FileEvent" event="File"/> <in modulename="FileEditor" method="run"/> </connection> <connection> <out modulename="FileEditor" eventname="FileEvent" event="File"/> <in modulename="Gaussian" method="run"/> </connection></task></taskspec>

Object Oriented Applications

Mobility System’s Applications

Coordinatestransformations

databases

Remote HPCC resources

- object oriented approach - implementation:- CORBA based Middle-Tier - bean-box type API - JDBC proxy modules

- Web interface to store data in DB in variable format- Data transfer from DB to a visualization engine- Coordinates transformations on a remote server- Launching simulations on remote hosts with interactive input

Part IV

Gateway:Portal for Computing

Target Architecture

Middle-Tier

Resource Specification

Abstract Task Specification

CTA specificknowledgedatabases

VisualAuthoring

Tools

User andGroup

Profiles

ResourceIdentificationand Access

VisualizationsCollaboration

WebFlow

Back-End Resources

Problem Solving Environment

Design Issues

• Support for a seamless access (security)

• Support for distributed, heterogeneous Back-End services (HPCC, DBMS, Internet, ...) managed independently from Gateway

• Variable pool of resources: support for discovery and dynamical incorporation into the system

• Scalable, extensible, low-maintenance Middle Tier

• Web-based, extensible, customizable, self-adjusting to varying capacities and capabilities of clients (humans, software and hardware)

front end

Gateway Implementation

• Distributed, object-oriented middle tier– CORBA objects (Gateway Containers, Gateway

Modules and Gateway Services) implemented in Java. [Scalable, extensible, low-maintenance middle tier]

– Containers define the user environment.– Modules and Services serve as proxies: they accept the

user requests (Front End) and delegate them to the Back End. [Support for distributed, heterogeneous back-end services managed independently from Gateway]

Note: modules can be implemented in C++; also can be DCOM components

Gateway Implementation (2)

• Gateway operates in a keberized environment [Support for a seamless access]

– tickets are generated on the client side

– Keberos-based CORBA security service is used to manage the user sessions

– Globus GSSAPI implemented over Keberos is used for resource allocation

Gateway Implementation (3)

• Task Specification is expressed in XML– CTA independent

– Decouples implementation of the Front End and the Middle Tier

– Allows for an abstract (platform independent) task specification, and thus the Middle Tier may act as a resource broker

• Resource Specification is expressed in XML– Simplifies match-making and resource discovery

– Simplifies generating Globus RSL in-the-fly

[Support for distributed, heterogeneous Back-End services; Variable pool of resources; Scalable, extensible, low-maintenance Middle Tier]

Gateway Implementation (4)

• Component-based Front-End [extensible]

• Front-End Components (“toolbox interfaces”) are – applets (interfaces for common services)– XML pages or frames

[Web-based, extensible, customizable, self-adjusting]

• All components (Front End, Middle-Tier) are defined in XML and contain metadata (used for component mining)

Front End

CTA specific knowledge database

– requires server side support (both the middle tier and the back-end) through well defined interfaces

– should be constructed from reusable or cloneable components

– allows for identification of software components best suited to solve the problem at hand

Visual Authoring Tools

• Allows for composition of the computational task from components (reusable modules)

• Different tools to support various programming models such as data parallel, task parallel, data flow, object oriented

• No assumption on granularity

• Metadata about components and support for archiving and mining the components

• Support for instrumentation and steering

Example: Data Flow

Example: DARP

User and Group Profile

• Controls the user/group environment– file access

– job monitoring

– ...

• Allows for customization– preferences

– users with disabilities

– ...

• History of actions

• Scientific notebook

Resource Identification and Access

• Computational resources– hardware, software, licenses

– desktop applications

• Data– file systems, mass storage, distributed databases

– Internet data repositories

• Networks

Front-End infrastructure

Front-End Support

• Portal Page

• User Context

• Control Applet

• Navigator (extensible, customizable)

• PSE specific toolboxes– A placeholder for the Problem Description toolboxes

– A placeholder for the code toolbox

– Resource request toolbox – Data postprocessing toolbox

• Other (Collaboration, Visualizations, …)

User Context

• Represents a Gateway session.

• The session is associated with a user (or group) profile.

• WebFlow extends the notion of the UNIX profile via the 'User Data Base' (UDB). This UDB contains information about submitted jobs, history of the users actions, and other user state information. The user context may also contain application/front-end specific information.

Control Applet• The control applet is responsible for maintaining the

session, and direct communication with the middle-tier. • Direct communication is the most efficient, but since it is

buried into an applet, this mechanism is not readily customizable.

• The generic services, such as file service (upload, download, edit, copy, move, delete) and job services (show current jobs/show queues/kill jobs) will be supported this way. [combination of the user context and a query]

• The Gateway will also support a non-direct communication with the middle-tier through servelts.

Screen Dump of the Control Applet

Navigator

• The navigator allows the user to select and customize toolboxes.

• Embedded in a separate frame, it consists of menus, buttons, links, etc, derived from an XML document.

• The navigator is a hierarchical, extensible and customizable.

Problem description toolboxes

• The problem description is application specific, and the Gateway only provides a general framework for creating a PSE.

• The most important part is the specification of what services (middle and back tier) are needed, what is their API, and how to add new services.

• Example services: access to databases, XML parsing, generating HTML in-the-fly, file services.

Code toolboxes

• The end user see it as a mapping between the problem description and software to be used to solve the problem. Actually, it identifies WebFlow modules and their parameters to be used to construct the application (see resource request toolbox below).

• The module parameters may include input files, and if necessary, the input files are generated at this stage (using this or a separate toolbox). In addition, some parameters will be constructed from information stored in data bases, including UDB, and other sources.

Resource Request Toolbox

• The front-end activities result in an abstract task specification.

• Abstract in the sense that the user may not know nor care what actual resources are used.

• The task is composed of independently developed modules and services following different programming models.

File Formats I

• We noted that Gateway should support input and output files with certain characteristics including

• Native: internal format known to a particular application -- no checking of format matching if link output of one module to input of another

• parameter input: special file constructed in XML defining basic parameters needed by a batch job– Gateway automatically sets defaults, allows user input and applies any appropriate

checks at front end

– User provides a bridge to convert Gateway file to form understood by batch job. This can use special Gateway utilities which provide Fortan, C and Java functions to get parameter values in backend user code

– We decided such parameters would need default, min, max, type and array dimensions to be specified in XML specification of these parameters

File Formats II• Third file format is

– prescribed: data is encoded in some defined fashion known to more than one Gateway application/service

• Here HDF XML HTML are examples

– other file characteristics include database generated, realtime …

• Gateway modules need to specify nature of their input and output files and what type of linkage of modules is allowed or even required.– E.g. scientific notepad may allow data to be imported from the

visualization service or require that it be encoded in ScienceML

Other toolboxes

• Visualizations• Collaboration• Scientific notebook• ...

ScienceML

• This we define as a group of defined formats that support scientific data, note taking and sketches

• XSIL (Scientific data Interchange) defines metadata needed to specify scientific data files including high level parameters and methods needed to read data– This would a prescribed format in Gateway

• VML is Vector Graphics Mark up Language• DrawML is designed to support simple technical drawings (easier

than VML but VML should be able to do this?)• VRML (3D scenes) reimplemented in XML as X3D• MathML Mathematical Expressions• ChemML Support Chemistry

Scientific Notepad

• Presumably this allows Scientists to make notes and record thoughts in a way that it supports important scientific constructs

• At its simplest this is an authoring tool like Microsoft Word, PowerPoint or Framemaker– These will improve and support standards such as MathML (openMath) with

better WYSIWYG authoring

• One useful utility would be a whiteboard that supported scientific notes using ScienceML

• Such a collaborative whiteboard (implemented in Tango for instance) would be useful in research and teaching– Use commercial authoring tool and WebEQ or equivalent to render

Middle-Tier

User 1 User 2

Application 1

Application 2

App 2App 1

WebFlow Server

WebFlow server is given by a hierarchy of containers

and components

WebFlow server hosts users and services

Each user maintainsa number of applications

composed of custom modules

and common services

WebFlow Services

CORBA Based Middle-Tier

Mesh of WebFlow Serversimplemented as CORBA objects

that manage and coordinate

distributed computation.

Front End

GatekeeperAuthenticationAuthorization

Back End

Back End Services

• Access to HPCC (via Globus)• Access to distributed databases (via JDBC)• Access to mass storage• Access to the Internet resources• Access to desktop application and local data• Access to code repositories

Gateway Security

SECIOP

Security Model (Keberos)

Front End Applet

SECIOP

authentication& authorization

Gatekeeper

delegation

HPCC resources

GSSAPIGSSAPI

Layer 1: secure Web

Layer 2: secure CORBA

Layer 3: Secure access to resources

Policies defined by resource owners

Building Gateway Components

Middle-Tier is given by a mesh of WebFlow Servers that manage

and coordinate distributed computation

.

• Gateway applications are composed of independent reusable modules• Modules are written by module developers who have only limited knowledge of the system on which the modules will run.• The WebFlow system hides module management and coordination functions

How to develop a Gateway component (or a toolbox)

• Back-end service• Middle-tier proxy• Front-end controls

How the Back-End interacts with the rest of the system?

• Often, your job do not need to interact.– Using GRAM and GASS you stage data and

executable, submit the job and retrieve output.

– Using DUROC you can coallocate resources and run MPI-based parallel/distributed codes. The messages between nodes are sent outside Gateway control or support.

– HPF runtime will distribute your job and facilitate interprocess communication.

Implementing Back-End Services

• If you need to interact– Using a separate module, you may move files between

nodes while your jobs are executing– Your job may be a server (e.g., database, GRAM)

[if socket listener - be careful about security!]

– Your job my be a CORBA client (Java, C++)

– ...

What does it take to develop a

Gateway module (a proxy)? • Many come as a standard Gateway modules• User’s modules

– Are CORBA objects

• Define IDL (as an XML document)• Compile IDL (in the tie mode)

• Implement the functionality of the module

• Implement events

• Develop Front-End controls that invoke methods of the module

Selecting a Predefined Task

Gateway/WebFlow Mission

• seamless access to remote resources– through a Web based user interface

– customized application GUI

• high-level user friendly visual programming and runtime environment for HPDC

• portable system based on industry standards and commodity software components

Updates

• Contact person: Tomasz Haupt

• haupt@npac.syr.edu

• voice (315) 443-2087

• http://www.npac.syr.edu/users/haupt/WebFlow/