Celebrating 10 Years -...
Transcript of 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
Celebrating 10 Years
Congratulations and Thank You
• Eight SEAIP and PRAGMA Institute
Celebrating 10 Years
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
Celebrating 10 Years
Every Talk is an Invitation to a Collaboration
Celebrating 10 Years
If you want to travel fast, travel alone; if you want to travel far, travel together
African Proverb
Celebrating 10 Years
Celebrating 10 Years
Enabling the Long-Tail of Science through Scientific Expeditions and Infrastructure Experiments
for Pacific Rim Institutions and Researchers
PRAGMA Members
and Affiliates
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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
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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
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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
Celebrating 10 Years
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
Celebrating 10 Years
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)
Celebrating 10 Years
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)
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)
Celebrating 10 Years
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)
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Scalable instrumentation and cyberfrastructure is critical
We can do this scale now http://lakemetabolism.org Source: T Kratz
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Problematic, but possible with today’s cyberinfrastructure
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Scale needed to answer regional/continental questions
Not currently possible
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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
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
Celebrating 10 Years
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
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Building Communities • Biodiversity
– New interactions
• Environmental Observing Communities – Training & new deployments
• Mini-PRAGMA Indonesia – New activities – New workshops!
Celebrating 10 Years
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
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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
Celebrating 10 Years
Enabling the Long Tail of Team Science
Trust Envelop
Virtual Scientific Expeditions
PRAGMA Students PRAGMA Member Sites PRAGMA Community
Celebrating 10 Years
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