8th biennial ptolemy miniconference berkeley, ca april 16, 2009 kepler project overview, status,...

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8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California, Davis

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Page 1: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

8th Biennial Ptolemy Miniconference

Berkeley, CAApril 16, 2009

Kepler Project Overview, Status, Future Directions

Bertram Ludäscher

University of California, Davis

Page 2: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Overview

• History– Origins, Diversity, Challenges

• Kepler, Kepler/CORE: – Issues, Status– Next steps

• Research: Scientific Workflows … – Business (workflows) as usual? – Or… ?

Page 3: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler: Some History

• The Origins:– AD 2002: NSF/SEEK, DOE/SDM

• Similar requirements for “scientific workflows”• Can we avoid reinventing the wheel (twice…) !? Grass-roots effort, open source collaboration

• The Head-start:– Adopting, extending Ptolemy II from Berkeley– Common software platform facilitates grass-root collaboration– More than software: Research Results

• Heterogeneous Modeling & Design, dataflow-, actor-oriented MoCs

Page 4: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Scientific Workflows: Cyberinfrastructure “Upperware”

Underware

Middleware

UpperMiddleware

Upperware

NSF/SEEK ITR, 5 Year collaboration: SDSC, UCSB, UCD, UNM, UK, …

Page 5: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Scientific Workflow

Capture how a scientist works with data and analytical tools– data access, transformation, analysis, visualization– possible worldview: dataflow-oriented (cf. signal-processing)

Scientific workflow (wf) benefits (compare w/ script-based approaches) : – wf automation – wf & component reuse – wf design, documentation– wf archival, sharing– built-in concurrency

(task-, pipeline-parallelism) – built-in provenance support– distributed & parallel exec:

Grid & cluster support – …

Page 6: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Simple Kepler analysis workflow using R …

Data source from EcoGrid(metadata-driven ingestion)

res <- lm(BARO ~ T_AIR)resplot(T_AIR, BARO)abline(res)

R processing script

Dan Higgins, NCEASDan Higgins, NCEAS

Page 7: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

… vs. “Plumbing” workflow

• to monitor, control remote supercomputer simulations …

– 50+ composite actors (subworkflows)

– 4 levels of hierarchy

– 1000+ atomic (Java) actors

43 actors, 3 levels

196 actors, 4 levels30 actors

206 actors, 4 levels

137 actors33 actors

150123 actors

66 actors12 actors

243 actors, 4 levels

Norbert Podhorszki Then: UC Davis, now: ORNL … Norbert Podhorszki Then: UC Davis, now: ORNL …

Page 8: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler: Open Source + Open Community

1. Huge diversity of domains => needs – Astrophysics, nuclear fusion research,

geoinformatics, ecology, systematics, bioinformatics, genomics, environmental monitoring, simulation, …

– Not just bioinformatics and cheminformatics …

2. A broad range of technical problems– Workflow design with a graphical UI– Sharing actors, workflows across communities– Distributed workflow execution – Data movement on the network– Integrate local apps, web services, native actors– Support a variety of computational models– Not just web service orchestration or Grid

deployment

Page 9: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

3. Many kinds of users with different backgrounds and responsibilities:

• Scientists automating and sharing their analyses of their own data or performing meta-analyses on others’ data

• Software engineers developing their own systems around Kepler• Computer scientists doing basic research in scientific workflows, data

and provenance management, distributed and collaborative computing.• Not just biologists and chemists …

4. Kepler used in many different deployment contexts• Standalone application on a scientist’s desktop computer or laptop.• Backend for web-based scientific applications.• Embedded workflow engine in larger systems.• One size (of deployment) does not fit all!

5. Kepler open to contribution and extension by anyone:• Anyone can contribute to Kepler!• Anyone can use Kepler in their own applications• Developing with Kepler doesn’t require collaboration with the “owners” …

Kepler: Open Source + Open Community

Page 10: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

COMET!

**

**

Ecology

Chemistry

Geosciences

Oceanography

Molecular Biology

Phylogenetics

Conservation Biology

Library Science

Particle Physics

Astronomy

KeplerKeplerCORECORE

KeplerKeplerCORECORE

ChIP-chip

KeplerKeplerCORECORE

KeplerKeplerCORECORE

Page 11: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler-CORE Mission

In collaboration with current and future contributors to Kepler, the Kepler/CORE team will …

– Develop and maintain the essential, interdisciplinary software components of Kepler

– Coordinate the contributions of the greater Kepler collaboration to the core (“kernel”) of the system

– Increase the role of the current and future user community in specifying requirements and priorities

Page 12: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

The Kepler-CORE Project and Team

• Kepler-CORE (sensu stricto)– 3-year, $1.7M NSF-OCI funded project

• Kepler-CORE team @ UCD,UCSB, UCSD: – UC Davis

• Bertram Ludäscher (PI@UCD), Shawn Bowers (co-PI), Tim McPhillips (co-PI & software architect), David Welker (software engineer), Sean Riddle (software engineer)

– UC Santa Barbara• Matthew Jones (PI@UCSB), Mark Schildhauer (co-PI), Aaron Schultz, Chad

Berkley (software engineer)

– UC San Diego• Ilkay Altintas (PI@SDSC), Jianwu Wang (postdoc)

• Kepler/CORE (sensu lato) – Goal: sustain long-term, beyond initial funding period – KEPLER = Kepler/Core + Kepler/X + Kepler/Y + …

• Core, X, Y, … = open community of stakeholders, contributors, users, etc.

Page 13: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler-CORE Vision

In the future we foresee Kepler…

• Satisfying the scientific workflow automation needs of– Collaborative government-funded projects– Academic research groups– Individual researchers in diverse scientific disciplines

• Enhancing the productivity of researchers by– Facilitating discovery and collaboration within and across disciplines– Being the best way for scientists to leverage developments and expertise in other

domains

• Leading to further breakthroughs and innovations in the fields of– Scientific data management– Data provenance– Collaborative scientific computing

• Shepherded by a self-sustaining effort that thrives well beyond the lifetimes of the grants that have contributed to Kepler’s development.

Kepler-CORE Duo

Page 14: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

• Kepler cannot solve everyone’s problems right out of the box– Kepler must be adaptable to different domain sciences

– Adaptation requires more than developing new actors

– Kepler is as much a development platform as an “end-user” tool

– No one group can take responsibility for supporting all the ways Kepler will be used …

• Kepler is open-source but more complex than other open source projects– Diversity of domains, users, and deployment contexts mean there can be conflicts

between the needs or priorities of contributors

– Need a way of developing and adding extensions without breaking other’s systems

– Software engineers developing code for Kepler often are not expert scientists, and cannot be the final authority on what the system should do (unlike projects like Apache, Linux, etc where the engineers are the expert users themselves and can add what they need)

– PIs and project managers on projects extending Kepler must take responsibility for knowing what needs to be done.

– It is essential that for each project employing Kepler, representatives authoritative on the scientific and technical needs of their projects participate in driving the future development of Kepler!

These differences mean that the Kepler collaboration will be unique, too

Page 15: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Stakeholders: Essential to Success of Kepler

Kepler stakeholders …– Are projects and individuals whose work depend critically on the success of

Kepler.– Are funded by a variety of sources and work in diverse fields of scientific research.– Are more likely to greatly extend Kepler and use Kepler within their own

systems than simply develop packages of actors and workflows for use with a standard distribution of Kepler.

– Need to deliver the software systems they develop to their own community of users.

– Must deliver their software systems according to their own (e.g. release) schedules as determined by their research and funding programs.

– Have different requirements that will conflict in the absence of mechanisms for enabling independent extension and deployment of Kepler-based systems.

– Require recognition for the contributions they make to Kepler as well as for their own systems based on Kepler.

– Know better than us what they need from Kepler.

Page 16: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler(-CORE) Management

• Leadership Team– 3 year terms (current members from UC + [S] + {B, D} )– Focus on

• long term viability of Kepler• strategic decisions on behalf of user community, Kepler project

• Interest Groups– Communicate, collaborate on specialized capabilities

• Development Teams– Design, develop, test specific software deliverables

• Infrastructure Teams– Identify, discuss, design, implement Kepler Framework

Page 17: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

New Kepler Build System

• Modules and suites– Develop against trunk or specific version, release– Tag, branch Kepler extensions independently of the kernel easier to share develop, share extensions svn repository (https://code.kepler-project.org/code/kepler/)

• Module Manager– New component to simplify

working with modules

David Welker et al. David Welker et al.

Page 18: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler Release Roadmap

• https://kepler-project.org/developers/teams/build/kepler-release-roadmap

• Kepler releases– based on a “standard set” of modules

• Individual module releases– Provenance– Workflow reporting– COMAD– Distributed: Master/Slave – …

• Kepler 2.0– Add modules, extensions to installed Kepler dynamically– Targeted for Summer 2009

Page 19: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

New Plone-based Web site, Forums

Page 20: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler/REAP: Workflow Run Manager

• Use case “Publication-Ready Archive”

• Archive workflow with inputs, outputs

• Tagging

• Also: Outline view– to manage browsing of

large/deeply nested workflows

Derik Barseghian et al.Derik Barseghian et al.

Page 21: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Workflow Reports (Provenance Interest Group)

Derik Barseghian et al.Derik Barseghian et al.

Page 22: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler and Scientific Workflow Research

• Scientific Workflows: – Business (workflows) as usual?

• Data-oriented, data-centric … – … as opposed to control-, task-centric

– Signal processing?– Or else …?

• Modeling scientific processes, analysis methods– Understanding is in the Mind of the Beholder!

• Example areas:– Workflow Modeling & Design– Provenance – Optimization

Page 23: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Modeling Example (ChIP-chip workflow)

Tim McPhillips et al.Tim McPhillips et al.

Page 24: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Modeling & Design: The limits of my language mean the limits of my world …

• Vanilla Process Network

• Functional Programming Dataflow Network

• XML Transformation Network

• Collection-oriented Modeling & Design framework (COMAD)

– “Look Ma: No Shims!”

Page 25: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Two different workflow designs

Page 26: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Data Provenance• Keep track of data dependencies, processing history

support interpretation, validation, reproducibility

AZG

AYG

AXG

AlignWarp Reslice Softmean Slicer Convert

AZG

AYG

AXG

AI1AH1

AI2AH2

AI4AH4

AI4AH4

RI RH

inputs

outputs

AXS

AYS

AZS

AI

AH

RI1

RH1

RI2

RH2

RI4

RH4

RI4

RH4

WP1

WP2

WP4

WP4alignWarp:4

alignWarp:3

alignWarp:2

alignWarp:1

reslice:4

reslice:3

reslice:2

reslice:1

softmean:1

slicer:1

slicer:2

slicer:3

convert:1

convert:2

convert:3

Page 27: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Kepler/pPOD: Provenance Browser

• For conventional data provenance and

• fine-grained dependencies (COMAD style)

• Navigate forward and backward in time (VCR style) in different views (collections, processes, combined)

Shawn Bowers et al.Shawn Bowers et al.

Page 28: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Collection History

• Collection and invocation view• Incrementally step through execution

history

Page 29: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

From MoCs to Models of Provenance (MoPs)

Page 30: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Fine-grained, Data & MoC-aware MoP

Manish Anand, Shawn Bowers, et al.

Manish Anand, Shawn Bowers, et al.

Page 31: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Optimization: Multi-level Workflows

Kepler

LPPN

Daniel Zinn et al. Daniel Zinn et al.

Page 32: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Modeling + Optimization: Virtual Assembly Lines (COMAD)

Page 33: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Layers in COMAD / ∆-XML Pipelines

WF Graph

Configurations(white-box)

Scientific Functions(black-boxes)

CipresRAxMLIn: DNASeq+

Thres: Float

Method: String

Out: (t:Tree, s:score)+

•Access data in XML stream•Call Scientific Functions (Services)•Put results back into stream

Daniel Zinn (UC Davis) Daniel Zinn (UC Davis)

Page 34: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Conventional vs Assembly Line / COMAD Thinking

Daniel Zinn (UC Davis) Daniel Zinn (UC Davis)

Page 35: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

More secret sauce: User vs. Optimized Dataflow

Page 36: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Conceptual Pipeline w/ Scopes & Types

Daniel Zinn (UC Davis) Daniel Zinn (UC Davis)

Page 37: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

X-CSR (“XML Scissor”): Cut-Ship-Reassemble

Daniel Zinn (UC Davis) Daniel Zinn (UC Davis)

Page 38: 8th Biennial Ptolemy Miniconference Berkeley, CA April 16, 2009 Kepler Project Overview, Status, Future Directions Bertram Ludäscher University of California,

Ptolemy Miniconference, April 16, 2009

Acknowledgments• Kepler contributors

– Many individuals: https://kepler-project.org/developers/kepler-contributors – Projects: Ptolemy, SEEK, SDM, CPES, GEON, REAP, CIPRes, ChIP2, pPOD, COMET, BAP, LTER, RAPR, ITER, …

• Funding agencies: NSF, DOE, …

• DAKS @ UC Davis Members– Research Staff

• Drs. Shawn Bowers, Timothy McPhillips, Lei Dou, Ustun Yildiz

– Developers:• Sean Riddle, David Welker, Gongjing Cao

– Students:• Manish Anand, Dave Thau, Daniel Zinn, Sven Koehler, Saumen Dey, Supriya Gulati, Faraaz Sareshwala, Xuan Li

UC DAVISDepartment ofComputer Science