celebrating 10 years -...

Celebrating 10 Years

PRAGMA: a Pacific-Rim collaborative for cyberinfrastructure research in support of

scientific expeditions and building community

On behalf of and with input from PRAGMA members

Peter Arzberger


Congratulations and Thank You

• Eight SEAIP and PRAGMA Institute


SEAIP Contributes to PRAGMA

• Meet New People and Institutions – Philippines – ASTI

– Vietnam – IOIT, HUST

– Indonesia – UI

– Malaysia – UTM

• Generate New Ideas – Scientific Expeditions

• Start New Collaborations – Biodiversity Expedition

• Travel to Taiwan – People

– Scenery

– Food

– Culture

• Thank you – NCHC and NARL

– NSC

– Partipants

Celebrating 10 Years NCHC Contributions to PRAGMA and the

Community

• Ecological Observing – GLEON

• Visualization and modeling – collaboration on GEO Grid

• Technology of Virtualization – work on PRAGMA migration – used in response to Tsunami

• SARS: intervention of technologies

• Engagement with researchers from Southeast Asia


Every Talk is an Invitation to a Collaboration


If you want to travel fast, travel alone; if you want to travel far, travel together

African Proverb


Enabling the Long-Tail of Science through Scientific Expeditions and Infrastructure Experiments

for Pacific Rim Institutions and Researchers

PRAGMA Members

and Affiliates


Accomplishments

• Advanced scientific understanding

• Developed, tested, improved, shared approaches and software

• Created PRAGMA cloud

• Built communities

• Trained students

• Evolved with technology and needs: Grid to Cloud

• Encouraged trust, idea sharing, partner participation

Ezilla: Developed NCHC GNU General Public License

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From Scientific Expedition to Community Building on NCHC Ecogrid

8 Months: Concept to Deployment

• Wireless Infrastructure (2004)

• Science

• Need more than one lake to understand processes

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Precipitation8 Years Later

NCHC SARS Task Force

http://antisars.nchc.gov.tw/

Developers at the NCHC Access Grid node test the SARS Grid network links

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PRAGMA 4 Program

Committee / request for help

(16, May, Fri)

Suggest in PRAGMA

4 Draft Agenda to

help SARS relief…(15,

Apr)

1st Hospital Outbreak (Taipei

Municipal Ho-Pin Hospital)

Chang Gung Hospital

outbreak (South)

PRAGMA 4

2 AG nodes + H.323

X-ray image interface +

medical information +

high speed network

2 AG nodes + …

14, May:SARS AG\Task Force

Source: Fang-Pang Lin


March 2011:Tohoku Earthquake and Tsunami

• GEO Grid Disaster Task Force migrated services to other sites, including – NARL|NCHC|NSPO – UCSD|SDSC – OCC, Orkney, ERSDAC, NTT-

data-CCS, CTC, Univ. Lille, and ITT

• Used aspects of virtualization porting and distributed resources at NCHC and SDSC

Machine Room AIST

GEO Grid Disaster Response Task Force http://disaster-e.geogrid.org

http://disaster-e.geogrid.org/




PRAGMA’s Overarching Activities to Enable Long Tail of (Team) Science

• Foster international scientific expeditions

• Develop and improve a grassroots, international cyberinfrastructure

• Infuse new ideas through students and strategic partners

• Build and enhance the essential people-to-people trust fabric

Interdependence Essential

Celebrating 10 Years Grass-roots International CI:

User-defined Trust Envelop

Components

• VM image, virtual cluster porting

• Software defined overlay networks

• Data cloud & provenance

• Observing systems

Challenge: Integration

and a Plan for Trust Envelop

Using the Expeditions to Drive Development of a TRUST ENVELOPE

Importance of

Trust Envelop

• Traverse firewalls and simplify network re-configuration of application VMs

• Provide an infrastructure that initially limits access to data


PRAGMA Collaborative Overview 2013 - 2014

• Highlights

• PRAGMA Students

• Community Building

• Working Groups

• Institutions and Sponsors

Celebrating 10 Years Predicting Water Quality in Lakes

Learning Phytoplankton Rules using SDN • Indicators of water

quality controlled by phytoplankton

• Run multiple simulations to understand rules

• Using VMs to avoid challenges of different architectures

• Using IP-over-P2P (IPOP) to interconnect VMs across multiple institutions

Demo / Poster: Renato Figueiredo (U FL), Paul Hanson (U Wi), Cayelan Carey (VA Tech), Pierre St. Juste, Kyuho Jeong (U FL, Grant Langlois, Luke Winslow (U Wi), Jonathan Doubek (VA Tech)

Collecting light, temperature data

Celebrating 10 Years Biodiversity in Extreme Environments

Distribution Prediction by Sharing CI and Provenance Capture

• Mt Kinabalu: Biodiversity rich, extreme (toxic) environment

• Lifemapper software predicts spatial distribution

• Goal is to share computation data in trusted network

• Improve efficiency, portability and capture provenance

• Pushed Virtual Cluster technology, improved Lifemapper, incorporated Karma provenance

Demo: Nadya Williams (UCSD), Aimee Stewart (KU), Quan Zhou (IU)

Additional Work of Expedition • Gained remote sensing data • Expanded interactions


PRAGMA VC Sharing Automation Phase 4

• For specialized applications: “build once, run easily everywhere”

• Share a virtual machine image among multiple hypervisors (Xen and KVM, and Virtual Machine (VM) and hosting middleware (Rocks, Ezilla, OpenNebula, Amazon EC2)

• Developed pragma_boot to automate VC translation

Demo: U-chupala, Pongsakorn, Ichikawa Kohei (NAIST); Clementi Luca, Williams Nadya, Papadopoulos Philip (UCSD) Tanaka Yoshio, Ota Akihiko (AIST) Huang Weicheng (NCHC)


Lightweight Cloud Application Marketplace

• Metadata Service to bridge cloud users and available VM images Provides registration service for vm owners (storage designated by owner)

• Provides tool to convert between VM formats

• http://140.110.30.2:6242/appliance

Demo: Chi-Ming Chen, Kuo-Yang Cheng, Weicheng Huang (NCHC); Yoshio Tanaka (AIST), Luca Clementi, Nadya Williams, Philip Papadopoulos (UCSD)

http://140.110.30.2:6242/appliance

http://140.110.30.2:6242/appliance

Celebrating 10 Years ViNe: Software Defined IP Overlays

Infrastructure (VR) and Management

• ViNe (U FL): SDN establishes wide-area IP overlays (public, private networks)

• ViNe live migration of VM illustrated at PRAGMA 24

• Future: expand PRAGMA sites; user defined isolated overlays

Demo: Mauricio Tsugawa (U FL); Nadya Williams, Luca Clementi,

Phil Papadopoulos (UCSD)


OpenFlow Controller and Collaboration

• Developed OpenFlow Controller, and measured performance five sites (NAIST, Osaka, NICT, others)

• Will build in a distributed network monitoring system “OverLoad” developed by Kasetsart U team (based on PRAGMA 24 discussions)

Celebrating 10 Years Mobile Technology and Clouds:

Development, Deployment, Community Building

• OSTD Android SensorPods: Rapid deployment of sensors, data stream to cloud (http://www.dataturbine.org/)

• Prototypes of multiple pod management (Sensor Rocks) and monitoring (INCA – PRIME student)

http://www.dataturbine.org/

http://www.dataturbine.org/


Scalable instrumentation and cyberfrastructure is critical

We can do this scale now http://lakemetabolism.org Source: T Kratz


Problematic, but possible with today’s cyberinfrastructure


Scale needed to answer regional/continental questions

Not currently possible


Challenge

What is PRAGMA’s role in

cloud-mobile technology

development?

Celebrating 10 Years San Kei En Project

(Japanese Friendship Garden Haiku Hunt)

• Android-based, location-aware mobile application

• First outside use of Place Sticker technology to preserve beauty, maintain connectivity

• Fun! Haiku! Impact!

Demo: UCSD: Jason Haga, Jesus Rios (PRIME 2013); Osaka U: Shinji Shimojo;

BPOC: Vivian Haga, Wesley Hsu (PRIME 2011); ISID: Kazuhiro Toda;

Ritsumeikan U: Nobuhiko Nishio

Celebrating 10 Years PRAGMA Students: Contributions

• Workshop Shops for Students

• Poster Sessions for PRAGMA

• Distributed Seminar for PRAGMA

• Involvement in Projects and Research

Celebrating 10 Years PRAGMA Students: Benefits

• Gain professional experience interacting in an international setting

• Create lasting network of international peers through working with peers on joint efforts

• Strengthen research through engagement with mentors/advisors outside students’ home institution

• Undertake opportunities for short-term visits by undergraduate / early PhD student Opportunity to Publish


PRIME 2013: Advancing PRAGMA Activities Projects

• Extend Android SensorPod to new application

• Prototype INCA monitoring to mobile technology

• Develop Haiku Hunt and deploy Place-Sticker technology to out doors

• Implement images for virtual screening

• Use computer technology for drug discovery in infectious and other diseases

Institutions • Nara Institute of Science and

Technology (NAIST)

• National Institute for Information and Communication Technology (NICT)

• National Taiwan University (NTU)

• Osaka University

• Taiwan Forest Research Institute (TFRI)

• University of Auckland

• University of Queensland

PRAGMA can support these opportunities for our students Students build connections between PRAGMA members

Celebrating 10 Years Deployment of Virtual Clusters for Molecular

Docking Experiments on the PRAGMA Cloud

• Docking experiments are key tool in silico drug discover

• Physical grid computing can create inconsistent results - heterogeneity – Impacting results

– Demonstrated by PRIME student (2009)

• Used pragma_boot

• Long-term goal: improve virtual dock

Demo: Kohei Ichikawa (NAIST), Kevin Lam, Karen Rodriguez (PRIME 2013)

Wen-Wai Yim (PRIME 2009), Jason Haga UCSD


Building Communities • Biodiversity

– New interactions

• Environmental Observing Communities – Training & new deployments

• Mini-PRAGMA Indonesia – New activities – New workshops!


PRAGMA Special Symposium – Organized by Reed Beaman

PRAGMA Community Other WGs

(Resource/Tele-Science

Bio/Geo)

Web based Portal Service

Sharing Computing Resource

(middleware/SaaS/Cloud Computing)

Education/Research,

S/W development

Workshop/Seminar/Contest

Cyber

Learning

WG

Collaborations

Activities

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Objectives

Providing cyber education & research environments in computational science

Utilizing Computing resources & services in PRAGMA community

Promoting developing & utilizing activities through global collaborations

Development of Education open platform and education/research S/W

Establishment of international research communities and connections to higher education

Construction of collaboration channels amongst PRAGMA WG

Cyber Learning Working Group

Source: Kum Won Cho


Enabling the Long Tail of Team Science

Trust Envelop

Virtual Scientific Expeditions

PRAGMA Students PRAGMA Member Sites PRAGMA Community

http://rocks-210.sdsc.edu/wiki/index.php/File:PRAGMA_22_Student_Meeting.jpg


What Other PRAGMA Expeditions?

• Disaster Mitigation

– IT to help predict areas of floods

– IT to help migrate services

• One science issue to consider: Biology of Stress

From Benison and Stephenson (2004), Global and Planetary Change 44: 1-9.

Number of worldwide extreme climate-related events including heat, cold, wind, floods and drought.

Source: John Wingfield

Future research

Global climate change includes warming trends as well as increased frequency and intensity of storms (climate versus weather)

Some populations of animals and plants are able to cope with these events whereas others appear to be less able. Why?

What are the physiological, cellular and genetic reasons for these differences?

We must understand how different phenotypes are developed from specific genotypes in a changing environment (grand challenge)

Important for sustainability: conservation of biodiversity, natural resources, bioeconomy, biomedical insights and quality of life

Source: John Wingfield

International Collaborations Value Proposition, Lessons Learned

Science: Increasingly global, collaborative, distributed

Knowledge, Networks and Nations:

Global scientific collaboration in the 21st century.

The Royal Society. March 2011

“intellectual power [is]

becoming increasingly

evenly distributed” N. Birdsall, F. Fukuyama

• The architecture of world science is also changing, with the expansion of global networks

• The primary driver of most collaboration is the scientists themselves.

• International activities and collaboration should be embedded in national science and innovation strategies

What is the Value Proposition of International Collaboration?

• What is to be gained?

• Compete in market place of ideas

• Access to resources

• Interact with expertise

• Address problems at scale

• Your value propositions here

Value Proposition of PRAGMA

• Rapid sharing of idea • Testing software • Integration into larger infrastructure and research

enterprise • Connections and new partnerships • Opportunities for students • Entrance to larger activities • In short, access to:

– People – Ideas – Resources

Lessons Learned in Building e-Communities

• Repeated semi-structured, high-quality, face-to face interactions (workshops) to build the community

• Group focuses on enabling science outcomes • Technology builders give tutorials on capabilities • Science + Technologists work side-by-side • Culture of openness and sharing of know-how and

software • Continue to experiment: Applications, Technologies,

Meetings (structure, types), People (and students) • Baby steps; and more baby steps (Learn by doing) • Break bread together • Stay PRAGMAtic

What Makes Partnerships Work • Match between institutions

• Legitimate decision making process in a collaboration

• Limited number of partners

• Shared understanding of what a partnership will do

• Trust

• Mutual benefit

• Flexibility

• Pursue workable, achievable projects

• Put as much time into relationship as into projects

• Frequent and regular communications

• Process to deal with disagreements openly

• Recognize inequities in what people can contribute (allow for intangibles)

• Provide students and faculty guides in culture

• Need to have people charged with keeping partnership going

Notes from Meeting on Global Innovation Initiative (GII) 2013 Nov 13: Speaker Susan Buck Sutton Bryn Mawr College

Building Collaborations Takes Time

Comment to Self:

Do we have the right support mechanisms for this?

Thank You

Please Join PRAGMA 26 in Tainan 2014 April 9 - 11

celebrating 10 years -...

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