Introduction to Scientific Workflows and the KEPLER System Instructors: Bertram Ludaescher Ilkay Altintas Instructors: Bertram Ludaescher Ilkay Altintas

Introduction to Scientific Workflows Introduction to Scientific Workflows and the KEPLER Systemand the KEPLER SystemIntroduction to Scientific Workflows Introduction to Scientific Workflows and the KEPLER Systemand the KEPLER System

Instructors:

Bertram LudaescherIlkay Altintas

Instructors:

Bertram LudaescherIlkay Altintas

2Scientific Workflows, B. Ludaescher & I. Altintas

Overview

• 10:30-11:15 Introduction to Scientific Workflows

• 11:15-12:00 Scientific Workflows in KEPLER live demo, brains-on session

• … but first, one more time … (déjà déjà vu)

TM



Information Integration Challenges: S4 Heterogeneities• Systems Integration

– platforms, devices, data & service distribution, APIs, protocols, … Grid middleware technologies + e.g. single sign-on, platform independence, transparent use of remote

resources, …

• Syntax & Structure– heterogeneous data formats (one for each tool ...)– heterogeneous data models (RDBs, ORDBs, OODBs, XMLDBs, flat files, …) – heterogeneous schemas (one for each DB ...) Database mediation technologies+ XML-based data exchange, integrated views, transparent query rewriting,

…

• Semantics– fuzzy metadata, terminology, “hidden” semantics, implicit assumptions, … Knowledge representation & semantic mediation technologies+ “smart” data discovery & integration+ e.g. ask about X (‘mafic’); find data about Y (‘diorite’); be happy

anyways!


Information Integration Challenges: S5 Heterogeneities

• Synthesis of applications, analysis tools, data & query components, … into “scientific workflows” – How to make use of these wonderful things & put them

together to solve a scientist’s problem? Scientific Problem Solving Environments

(PSEs)GEON Portal and Workbench (“scientist’s view”)+ ontology-enhanced data registration, discovery,

manipulation+ creation and registration of new data products from

existing ones, … GEON Scientific Workflow System (“engineer’s

view”)+ for designing, re-engineering, deploying analysis pipelines

and scientific workflows; a tool to make new tools … + e.g., creation of new datasets from existing ones, dataset

registration,…


What is a Scientific Workflow (SWF)?• Goals:

– automate a scientist’s repetitive data management and analysis tasks

– typical phases: • data access, scheduling, generation, transformation, aggregation,

analysis, visualization design, test, share, deploy, execute, reuse, … SWFs

• Typical requirements/characteristics:– data-intensive and/or compute-intensive– plumbing-intensive– dataflow-oriented– distributed (data, processing)– user-interaction “in the middle”, …– … vs. (C-z; bg; fg)-ing (“detach” and reconnect)– advanced programming constructs (map(f), zip, takewhile, …)– logging, provenance, “registering back” (intermediate) products…

• … easy to recognize a SWF when you see one!


Promoter Identification Workflow

Source: Matt Coleman (LLNL)Source: Matt Coleman (LLNL)


Source: NIH BIRN (Jeffrey Grethe, UCSD)Source: NIH BIRN (Jeffrey Grethe, UCSD)


Ecology: GARP Analysis Pipeline for Invasive Species Prediction

Training sample

(d)

GARPrule set

(e)

Test sample (d)

Integrated layers

(native range) (c)

Speciespresence &

absence points(native range)

(a)EcoGridQuery

EcoGridQuery

LayerIntegration

LayerIntegration

SampleData

+A3+A2

+A1

DataCalculation

MapGeneration

Validation

User

Validation

MapGeneration

Integrated layers (invasion area) (c)

Species presence &absence points

(invasion area) (a)

Native range

predictionmap (f)

Model qualityparameter (g)

Environmental layers (native

range) (b)

GenerateMetadata

ArchiveTo Ecogrid

RegisteredEcogrid

Database

RegisteredEcogrid

Database

RegisteredEcogrid

Database

RegisteredEcogrid

Database

Environmental layers (invasion

area) (b)

Invasionarea prediction

map (f)

Model qualityparameter (g)

Selectedpredictionmaps (h)

Source: NSF SEEK (Deana Pennington et. al, UNM)Source: NSF SEEK (Deana Pennington et. al, UNM)



Digression: (Business) Workflows and

Systems

or: what you need to know when someone wants to sell you one ;-)

or: the remote relatives (2nd-3rd cousins?) of scientific workflows


What is a (Business) Workflow?• Workflow management (also called Business Process

Management) is the coordination of work processes through software.

• A workflow management system routes pending activities to process participants according to a model of the process.

• WF management systems have been around since the late 1970s (e.g. Officetalk, Xerox PARK)– marketing waves: Office Automation (70’s-80’s), Business Process

Reengineering (90’s), Web Services Choreography (00’s)– roots/related: document management apps, email system apps, database

apps (active DBMS’s, federated DBMS’s)

– Meanwhile (69’-71’) elsewhere: Flow-based programming (J. Paul Morrison)– … not quite workflow but rather dataflow … (we’ll come to that…)

Src/cf: http://www.workflow-research.de/index.htm, M.z. Muehlen, 2003

Src/cf: http://www.workflow-research.de/index.htm, M.z. Muehlen, 2003


Some History

Commercial Workflow Systems

Source: http://www.workflow-research.de/index.htm, M.z. Muehlen, 2003



Some History

Commercial Workflow Systems




Play Time @ Petri Nets World

• Petri Nets are the underlying abstract model of many B-WfMS’s (who said I can’t do bad acronyms, too? ;-)

• http://www.daimi.au.dk/PetriNets/

• http://www.daimi.au.dk/PetriNets/introductions/aalst/

• Let’s see the basic ideas first …


Formal Basis: Petri Nets• Mathematical model of discrete distributed systems (named

after Carl Adam Petri, 1960’s)• Provides a modeling language w/ rich theory, analysis tools, … • A Petri net consists of places (P), transitions (T) and directed

arcs (PT or TP). Places can hold tokens. • A transition is enabled if each of its input places contains at

least one token.• An enabled transition can fire, removing input tokens and

producing output tokens

P1

P2

P3 P4T1 T2

Enabled not enabled


Formal Basis: Petri Nets• Mathematical model of discrete distributed systems (named

after Carl Adam Petri, 1960’s)• Provides a modeling language w/ rich theory, analysis tools, … • A Petri net consists of places (P), transitions (T) and directed

arcs (PT or TP). Places can hold tokens. • A transition is enabled if each of its input places contains at

least one token.• An enabled transition can fire, removing input tokens and

producing output tokens

P1

P2

P3 P4T1 T2

Enablednot enabled


Why Petri Nets • Modeling and designing concurrent systems w/

competing resources (dining philosophers), …

• Lots of analysis techniques, tools, theory– boundedness (state space), – liveness (good things do happen), – safety (bad things do not happen), – reversibility, – deadlock(-freeness), – reachability (of certain states),– …


In a Flux: WS-XX-“Standards”

Source: W.M.P. van der Aalst et al. http://tmitwww.tm.tue.nl/research/patterns/http://tmitwww.tm.tue.nl/staff/wvdaalst/Publications/publications.htmlSource: W.M.P. van der Aalst et al. http://tmitwww.tm.tue.nl/research/patterns/http://tmitwww.tm.tue.nl/staff/wvdaalst/Publications/publications.html


Everything Flows? But what exactly?

• Dataflow – Data flows through operations (zoom into your

CPU…)– Activity diagrams: data flows through actions– Process networks: data flows between processes

• Control-flow– Nodes are control-flow operations that start other

operations on a state

• Mixed approaches– Statecharts: events trigger state transitions– Petri nets: tokens mark control and dataflow– Workflow languages: mix control and dataflow– … many others …


Scientific “Workflows” vs Business Workflows

• Business Workflows (BPEL4WS* …)– Task-orientation: travel reservations; credit approval; BPM; …– Tasks, documents, etc. undergo modifications (e.g., flight reservation

from reserved to ticketed), but modified WF objects still identifiable throughout

– Complex control flow, complex process composition (danger of control flow/dataflow “spaghetti”)

Dataflow and control-flow are often divorced!

• Scientific “Workflows”– Dataflow and data transformations– Data problems: volume, complexity, heterogeneity – Grid-aspects

• Distributed computation • Distributed data

– User-interactions/WF steering– Data, tool, and analysis integration Dataflow and control-flow are often married! (can be a happy marriage…

at times…)*Business Process Execution Language for Web Services (in case you wondered)


Scientific “Workflows”: Some Findings

• More dataflow than (business control-/) workflow– DiscoveryNet, Kepler, SCIRun, Scitegic, Triana, Taverna, …,

• Need for “programming extensions” – Iterations over lists (foreach); filtering; functional composition;

generic & higher-order operations (zip, map(f), …)

• Need for abstraction and nested workflows• Need for data transformations (WS1DTWS2)• Need for rich user interaction & workflow steering:

– pause / revise / resume– select & branch; e.g., web browser capability at specific steps

as part of a coordinated SWF

• Need for high-throughput data transfers and CPU cyles: “(Data-)Grid-enabling”, “streaming”

• Need for persistence of intermediate products and provenance


Perspectives on Systems

Source: Workflow-based Process Controlling, Michael zur Muehlen, 2003

Source: Workflow-based Process Controlling, Michael zur Muehlen, 2003

/ Dataflow View


A Dataflow Component (“Actor”)

“actor” /component

inputchannels

outputchannels

ports

parameters$1, $2, …


Actor-Oriented Design

• Object orientation:class name

data

methods

call return

What flows through an object is

sequential control (cf. CCA, MPI)

• Actor/Dataflow orientation:actor name

data (state)

portsInput data

parameters Output data

What flows through an object is a

stream of data tokens

(in SWFs/KEPLER also references!!)

Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/


Object-Oriented vs.Actor-Oriented Interfaces

Actor/DataflowOriented

AO interface definition says “Give me text and I’ll give you speech”

OO interface gives procedures that have to be invoked in an order not specified as part of the interface definition.

TextToSpeech

initialize(): voidnotify(): voidisReady(): booleangetSpeech(): double[]

Object Oriented



Ptolemy II

see!see!see!see!

try!try!try!try!

read!read!read!read!

Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/ptolemyII/Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/ptolemyII/


History• Gabriel (1986-1991)

– Written in Lisp– Aimed at signal processing– Synchronous dataflow (SDF) block diagrams – Parallel schedulers– Code generators for DSPs– Hardware/software co-simulators

• Ptolemy Classic (1990-1997)– Written in C++– Multiple models of computation– Hierarchical heterogeneity– Dataflow variants: BDF, DDF, PN– C/VHDL/DSP code generators– Optimizing SDF schedulers– Higher-order components

• Ptolemy II (1996-2022)– Written in Java– Domain polymorphism– Multithreaded– Network integrated– Modal models– Sophisticated type system– CT, HDF, CI, GR, etc.

• PtPlot (1997-??)– Java plotting package

• Tycho (1996-1998)– Itcl/Tk GUI framework

• Diva (1998-2000)– Java GUI framework

• Copernicus (code generator)

• KEPLER (2003-2028)– scientific workflow extensions

Source (Ptolemy): Edward Lee et al. http://ptolemy.eecs.berkeley.edu/Source (Ptolemy): Edward Lee et al. http://ptolemy.eecs.berkeley.edu/

Ptolemy II: A laboratory for investigating designKEPLER: A problem-solving environment for Scientific Workflows

KEPLER = “Ptolemy II + X” for Scientific Workflows


An “early” example: An “early” example: Promoter Identification Promoter Identification

SSDBM, AD 2003SSDBM, AD 2003

• Scientist models application as a “workflow” of connected components (“actors”)

• If all components exist, the workflow can be automated/ executed

• Different directors can be used to pick appropriate execution model (often “pipelined” execution: PN director)


Why Ptolemy II (and thus KEPLER)?• Ptolemy II Objective:

– “The focus is on assembly of concurrent components. The key underlying principle in the project is the use of well-defined models of computation that govern the interaction between components. A major problem area being addressed is the use of heterogeneous mixtures of models of computation.”

• Dataflow Process Networks w/ natural support for abstraction, pipelining (streaming) actor-orientation, actor reuse

• User-Orientation– Workflow design & exec console (Vergil GUI)– “Application/Glue-Ware”

• excellent modeling and design support• run-time support, monitoring, …• not a middle-/underware (we use someone else’s, e.g. Globus, SRB, …)• but middle-/underware is conveniently accessible through actors!

• PRAGMATICS– Ptolemy II is mature, continuously extended & improved, well-documented

(500+pp) – open source system– Ptolemy II folks actively participate in KEPLER


The KEPLER/Ptolemy II GUI (Vergil)

“Directors” define the component interaction & execution semantics

Large, polymorphic component (“Actors”) and Directors libraries (drag & drop)


Ptolemy II: Actor-Oriented Modeling

• Component (“actor”) interaction semantics not hard-wired inside components, but “factored out” in a “director”

• Different directors for different modeling and execution needs (… can even be combined!)

Better abstraction, modeling, component reuse, …


Behavioral Polymorphism in Ptolemy

«Interface»Receiver

+get() : Token+getContainer() : IOPort+hasRoom() : boolean+hasToken() : boolean+put(t : Token)+setContainer(port : IOPort)

These polymorphic methods implement the communication semantics of a domain in Ptolemy II. The receiver instance used in communication is supplied by the director, not by the component.(cf. CCA, WS-??, [G]BPL4??, … !)

produceractor

consumeractor

IOPort

Receiver

Director

Behavioral polymorphism is the idea that components can be defined to operate with multiple models of computation and multiple middleware frameworks. Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/


Domains and Directors: Semantics for

Component Interaction• CI – Push/pull component interaction• CSP – concurrent threads with

rendezvous• CT – continuous-time modeling• DE – discrete-event systems• DDE – distributed discrete events• FSM – finite state machines• DT – discrete time (cycle driven) • Giotto – synchronous periodic• GR – 2-D and 3-D graphics• PN – process networks• SDF – synchronous dataflow• SR – synchronous/reactive• TM – timed multitasking


For (coarse grained) Scientific Workflows!

For (finer-grained) concurrent jobs!?


Polymorphic Actor Components Working Across Data Types and

Domains• Actor Data Polymorphism:

– Add numbers (int, float, double, Complex)– Add strings (concatenation)– Add complex types (arrays, records, matrices)– Add user-defined types

• Actor Behavioral Polymorphism:– In dataflow, add when all connected inputs have data– In a time-triggered model, add when the clock ticks– In discrete-event, add when any connected input has

data, and add in zero time– In process networks, execute an infinite loop in a

thread that blocks when reading empty inputs– In CSP, execute an infinite loop that performs

rendezvous on input or output– In push/pull, ports are push or pull (declared or

inferred) and behave accordingly– In real-time CORBA, priorities are associated with

ports and a dispatcher determines when to add

By not choosing among these when defining the component, we get a huge increment in component re-usability. But how do we ensure that the component will work in all these circumstances?



Directors and Combining Different Component Interaction

Semantics

Source: Edward Lee et al. http://ptolemy.eecs.berkeley.edu/ptolemyII/

Possible app. in SWF:• time-series aware …• parameter-sweep aware … • MPI aware• XYZ aware … … execution models


Component Composition & Interaction

• Components linked via ports• Dataflow (and msg/ctl-flow)• Where is the component

interaction semantics defined?? – each component is its own director!

• But still useful for special applications, e.g. parallel programs (MPI, …)

Source: GRIST/SC4DEVO workshop, July 2004, CaltechSource: GRIST/SC4DEVO workshop, July 2004, Caltech

DIR1DIR2

DIR3

DIR4

???


CCA via special (“look the other way”) Director(s)?

CCA!?

• Dataflow in CCA• a CCA “convention” can be used to accommodate actor-

oriented/dataflow modeling• CCA/Message Passing in KEPLER

• Kepler/Ptolemy can be extended to accommodate message passing semantics (CSP is already in Ptolemy II)


Data/Control-Flow Spectrum

• Data (tokens) flow– (almost) no other side effects– WYSIWYG (usually)

• References flow – token reference type may be “http-get”, “ftp-get”, “hsi put”… – generic handling still possible

• Application specific tokens flow– e.g. current Nimrod job management in Resurgence– “invisible contract” between components– Director is unaware of what’s going on … (sounds familiar? ;-)

• Specific messages passing protocols (e.g., CSP, MPI) – for systems of tightly coupled components

“clean” data(=ctl)-flow special tokens flow message passing, control flow

“actor”


KEPLER/CSP: Contributors, Sponsors, Projects

(or loosely coupled Communicating Sequential Persons ;-)Ilkay Altintas SDM, Resurgence

Kim Baldridge Resurgence, NMI Chad Berkley SEEK Shawn Bowers SEEKTerence Critchlow SDM Tobin Fricke ROADNetJeffrey Grethe BIRNChristopher H. Brooks Ptolemy II Zhengang Cheng SDM Dan Higgins SEEKEfrat Jaeger GEON Matt Jones SEEK Werner Krebs, EOLEdward A. Lee Ptolemy II Kai Lin GEONBertram Ludaescher SEEK, GEON, SDM, BIRN, ROADNetMark Miller EOLSteve Mock NMISteve Neuendorffer Ptolemy II Jing Tao SEEK Mladen Vouk SDM Xiaowen Xin SDM Yang Zhao Ptolemy IIBing Zhu SEEK •••

Ptolemy IIPtolemy II


KEPLER: An Open Collaboration• Initiated by members from NSF SEEK and DOE SDM/SPA; now

several other projects• Open Source (BSD-style license)• Intensive Communications:

– Web-archived mailing lists– IRC (!)

• Co-development: – via shared CVS repository– joining as a new co-developer (currently):

• get a CVS account (read-only)• local development + contribution via existing KEPLER member• be voted “in” as a member/co-developer

• Software & social engineering– How to better accommodate new groups/communities?– How to better accommodate different usage/contribution models (core

dev … special purpose extender … user)?


GEON Dataset Generation & Registration

(a co-development in KEPLER)

Xiaowen (SDM)

Edward et al.(Ptolemy)

Yang (Ptolemy)

Efrat(GEON)

Ilkay(SDM)

SQL database access (JDBC)Matt,Chad,

Dan et al. (SEEK)

% Makefile$> ant run

% Makefile$> ant run


KEPLER then …


… and KEPLER today…

Whatis

HPC?

… so,you see,scientific workflows

need domain and data-polymorphic

actors & must scale to HPC!

What’s a scientific workflow?

What’sa poly-

morphic actor?

BTW: Kepler is NOT a GUI (Vergil

is)

BTW: Kepler is NOT a GUI (Vergil

is)


KEPLER Pedigree (to be determined…)

Ptolemy KEPLERPtolemy IIGabriel

SCIRunKhoros

AVS

• Graphical dataflow environments• Problem solving environments• Grid workflows

DiscoveryNet

Taverna

Triana

Pegasus

Matrix

openDX


A Few Specific Kepler Features


Web Services Actors (WS Harvester)

12

3

4

“Minute-made” (MM) WS-based application integration• Similarly: MM workflow design & sharing w/o implemented

components


Recent Actor Additions


Digression: Who are the clients?

• Domain scientists1. C/Perl/Python/Java/WS/DB-enabled ones2. others (e.g. visually-inclined rest of us?)

• Goal: make the life better for both!– Workflow automation– Plumbing support– Execution monitoring, steering, runtime

revision (pause-inspect-modify-resume cycle)


For the Geoscientist: GEON Mineral Classification

Workflow


… inside the Classifier

BrowserUI actor w/ SVG client display


in KEPLER (interactive session)

Source: Dan Higgins, Kepler/SEEKSource: Dan Higgins, Kepler/SEEK


in KEPLER (w/ editable script)

Source: Dan Higgins, Kepler/SEEKSource: Dan Higgins, Kepler/SEEK


A Closer Look at Dataflow … (or: Do you know what’s going on under your carpet? )

control tokens flow, e.g., from “$”-actor to FileReader and ImageReader

actors

actual dataflow is “under the carpet” and through handles

(file system, GridFTP, scp, SRB, …)

• Dataflow: what you see is what you get (almost…)

• Need for a general way to handle references!


GEON Data Registration UI


GEON Data Registration in KEPLER


Registered Resources show up in Vergil (joint SEEK, SPA, GEON, …

Registry!?)


Data Analysis: Biodiversity Indices


Traffic info for a list of highways: Uses iterate (higher-order “map”) actor to access highway info web service repeatedly, sending out one email per highway.






Re-engineered PIW w/ Iteration Constructs AD 2004

map(GenbankWS) Input: {“NM_001924”, “NM020375”} Output: {“CAGT…AATATGAC",“GGGGA…CAAAGA“}


Streaming Real-time Data

Laser Strainmeter Channels in; Scientific Workflow;

Earth-tide signal out

Straightforward Example:

Seismic Waveforms


ORB


Job Management (here: NIMROD)

• Job management infrastructure in place• Results database: under development• Goal: 1000’s of GAMESS jobs (quantum mechanics) – Fall/Winter’04


KEPLER Today

• Support for SWF life cycle– Design, share, prototype, run, monitor, deploy, …

• Coarse-grained scientific workflows, e.g.,– web service actors, grid actors, command-line actors, …

• Fine grained workflows and simulations, e.g.,– Database access, XSLT transformations, …

• Kepler Extensions– SDM Center/SPA: support for data- and compute-intensive

workflows!– real-time data streaming (ROADNet)– other special and generic extensions (e.g. GEON, SEEK)

• Status– first release (alpha) was in May 2004– nightly builds w/ version tests– “Link-Up Sister Project” w/ other SWF systems (UK Taverna, Triana,

…)– Participation in various workshops and conferences (GGF10,

SSDBMs, eScience WF workshop, …)


KEPLER Tomorrow• Application-driven extensions:

– access to/integration with other IDMAF components • SciRUN?, PnetCDF?, PVFS(2)?, MPI-IO?, parallel-R?, ASPECT?, FastBit, …

– support for execution of new SWF domains• Astrophysics: TSI/Blondin (SPA/NCSU)• Nuclear Physics: Swesty (SPA/LLNL)• …

• Generic extensions:– addtl. support for data-intensive and compute-intensive workflows

(all SRB Scommands, CCA support, …) – (C-z; bg; fg)-ing (“detach” and reconnect)– workflow deployment models

• Additional “domain awareness” (e.g. via new directors)– time series, parameter sweeps, job scheduling, … – hybrid type system with semantic types

• Consolidation– More installers, regular releases, improved documentation, …


Desiderata for and Features of Scientific Workflow Automation

• SWF design support – step-wise refinement, component/actor-oriented design, flow-oriented

design, sharing (visual) design with others, …– better component reuse through actor-oriented modeling w/ (largely)

independent directors

• Rapid prototyping support– Web service actors and harvester– Shell/command line actor– Data transformations (e.g., via Perl, Python, XSLT, … actors)

• Workflow “plumbing” support– data transformation actors e.g., in Perl, Python, XSLT, …

• Runtime support– Execution monitoring

• animation for SDF, planned “heartbeat” for PN, … • listening to and logging of token flow through ports and control messages of

directors

– Pause-inspect-modify-resume cycle


F I N

Additional material ahead


Research (and Development) Issues

…some challenges and ideas…


“Service Composition, Orchestration” and all that stuff

• Instead of asking which WS-XXX solves this for you, ask: What is my WF composition problem?

• Also: there is a good amount of previous work, most notably from the Ptolemy group itself:– How do you model systems as interacting

components– How do you model component interaction – How can you make components and interaction

patterns as reusable as possible– … Check out actor-oriented modeling and design!


“Programming Patterns”(Higher-Order FP Constructs)








hand-crafted control solution; also: forces sequential execution!

designed to fit

designed to fit

hand-craftedWeb-service

actor

Complex backward control-flow

No data transformations

available

[Altintas-et-al-PIW-SSDBM’03][Altintas-et-al-PIW-SSDBM’03]


A Scientific Workflow Problem: More Solved (Computer Scientist’s view)

• Solution based on declarative, functional dataflow process network(= also a data streaming

model!)

• Higher-order constructs: map(f) no control-flow spaghetti data-intensive apps free concurrent execution free type checking automatic support to go

from piw(GeneId) to PIW :=map(piw) over [GeneId]

map(f)-style

iterators Powerful type

checking Generic,

declarative “programming”

constructs

Generic data transformation

actors

Forward-only, abstractable sub-workflow piw(GeneId)


A Scientific Workflow Problem: Even More Solved (domain&CS coming

together!)

map(GenbankWS) Input: {“NM_001924”, “NM020375”} Output: {“CAGT…AATATGAC",“GGGGA…CAAAGA“}


A Research Problem: Optimization by Rewriting

• Example: PIW as a declarative, referentially transparent functional process optimization via functional rewriting

possiblee.g. map(f o g) = map(f) o map(g)

• Technical report &PIW specification in Haskell

map(f o g) instead of map(f) o

map(g)

Combination of map and zip

http://kbis.sdsc.edu/SciDAC-SDM/scidac-tn-map-constructs.pdfhttp://kbis.sdsc.edu/SciDAC-SDM/scidac-tn-map-constructs.pdf


KEPLER Today

• Support for SWF life cycle– Design, share, prototype, run, monitor, deploy, …

• Coarse-grained scientific workflows, e.g.,– web service actors, grid actors, command-line actors, …

• Fine grained workflows and simulations, e.g.,– Database access, XSLT transformations, …

• Kepler Extensions– support for data- and compute-intensive workflows!– real-time data streaming (ROADNet)– other special and generic extensions (e.g. GEON, SEEK)

• Status– first release (alpha) was in May 2004– nightly builds w/ version tests– “Link-Up Sister Project” w/ other SWF systems (UK Taverna, Triana,

…)– Participation in various workshops and conferences (GGF10,

SSDBMs, eScience WF workshop, …)


KEPLER Tomorrow• Application-driven extensions:

– access to/integration with other IDMAF components • SciRUN?, PnetCDF?, PVFS(2)?, MPI-IO?, parallel-R?, ASPECT?, FastBit, …

– support for execution of new SWF domains• Astrophysics: TSI/Blondin (SPA/NCSU)• Nuclear Physics: Swesty (SPA/LLNL)• …

• Generic extensions:– addtl. support for data-intensive and compute-intensive workflows

(all SRB Scommands, CCA support, …) – (C-z; bg; fg)-ing (“detach” and reconnect)– workflow deployment models

• Additional “domain awareness” (e.g. via new directors)– time series, parameter sweeps, job scheduling, … – hybrid type system with semantic types

• Consolidation– More installers, regular releases, improved documentation, …


Towards a more concise Presentation Style …

Due to lack of time, some slides will be “by reference” only ;-)

– …Each speaker was given four minutes to present his paper, as there were so many scheduled -- 198 from 64 different countries. To help expedite the proceedings, all reports had to be distributed and studied beforehand, while the lecturer would speak only in numerals, calling attention in this fashion to the salient paragraphs of his work. ... Stan Hazelton of the U.S. delegation immediately threw the hall into a flurry by emphatically repeating: 4, 6, 11, and therefore 22; 5, 9, hence 22; 3, 7, 2, 11, from which it followed that 22 and only 22!! Someone jumped up, saying yes but 5, and what about 6, 18, or 4 for that matter; Hazelton countered this objection with the crushing retort that, either way, 22. I turned to the number key in his paper and discovered that 22 meant the end of the world… [The Futurological Congress, Stanislaw Lem, translated from the Polish by Michael Kandel, Futura 1977]


References• Kepler: http://kepler-project.org • Ptolemy: http://ptolemy.eecs.berkeley.edu/ • Flow-based Programming: http://www.jpaulmorrison.com/fbp/index.shtml• Wiki with links to others: http://www.jpaulmorrison.com/cgi-bin/wiki.pl

– http://c2.com/cgi/wiki?FlowBasedProgramming– http://c2.com/cgi/wiki?DataflowProgramming – http://c2.com/cgi/wiki?ActorsModel

Documents

Introduction to Scientific Workflows and the KEPLER System Instructors: Bertram Ludaescher Ilkay Altintas Instructors: Bertram Ludaescher Ilkay Altintas