PeterKeynoteOct08.ppt

Transcript PeterKeynoteOct08.ppt

Grid Frontier and PRAGMA: Advances and Future

3 rd Peter Arzberger PRAGMA Institute 21 October 2008

Cyberinfrastructure: Enabling Research Compute resources for modeling, simulation, data analysis Instruments for observations Human Global Connectivity Interfaces for visualization and collaborations

M.Brown

Optical Networking Tools: Digital collections for knowledge management Bringing Remote Resources to Researchers

Living Beyond our Means Societal Relevance

March 2005

Among the outstanding problems identified by this assessment are the dire state of many of the world’s fish stocks; the intense vulnerability of the 2 billion people living in dry regions to the loss of ecosystem services, including water supply; and the growing threat to ecosystems from climate change and nutrient pollution.

In many cases, it is literally a matter of living on borrowed time. By using up supplies of fresh groundwater faster than they can be recharged, for example, we are depleting assets at the expense of our children.

Summary for Policymakers of the Synthesis Report of the IPCC Fourth Assessment Report 16 November 2007

The prosperity bug

The dengue mosquito is one of globalisation's winners

Economist 14thJuly07 US Edition, p 46 http://www.economist.com/world/asia/ displaystory.cfm?story_id=9487109 • Indonesia: • 100,000 confirmed cases, • 1,000 deaths • Cambodia: • More than 15,000 cases • More than 180 deaths • Malaysia, Vietnam, Thailand • Each over 20,000 cases • Globalization: Population move to cities • Global warming: Faster breeding

Infectious Diseases

• • •

NIV/AIDS, tuberculosis, Malaria, Avian Flu, SARS, others 1 billion people are affected by one or more neglected tropical diseases (NTDs) (one in six people affected) – Buruli ulcer, Chagas disease, cholera/epidemic diarrhoeal diseases, dengue/dengue haemorrhagic fever, dracunculiasis (guinea-worm), endemic treponematoses (yaws, pinta, endemic syphilis), human African trypanosomiasis (sleeping sickness), leishmaniasis, leprosy, lymphatic filariasis, onchocerciais, schistosomiasis, soil-transmitted helminthiasis, and trachoma.

Less than 1% of the nearly 1400 drugs registered between 1975 and 1999 were for tropical diseases.

Affect of Heart Disease in Society

+ According to the World Health Organization (WHO) : - In 2004,

Heart Disease and Stroke

kill

17 million

people a year =

1/3

of all world death + According to : - U.S. Government (Center for Disease Control and Prevention),

Heart Disease = #1 Leading Cause of Death

in U.S.A. per year.

UHVEM CCD camera controller Source: Young Chun One of slice images obtained from thick heart sections PRIME 2007 3-D surface mesh models of mitochondria in the heart

International Threats to Coral Reefs and Ocean Biology -- Urgent Need for Extensive Sensornets

Science December 14, 2007 Science February 15, 2008 Science May 14, 2007 Source L Smarr

Education: The Stakes are High

• “What nations don’t know can hurt them. The stakes involved in study abroad are that simple, that straightforward, and that important. … college graduates today must be internationally competent.” [Lincoln Report 2005]

• • • •

Ask the Right Question

Why don’t you take advantage of your location, on the Pacific Rim, and create deep collaborations by working with others in the this region? How are we, as a community, with all of our technology, addressing issues of societal relevance? What’s in the future?

How do we structure partnerships to succeed?

PRAGMA

A Practical Collaborative Framework

http://www.

pragma -grid.net

Strengthen Existing and Establish New Collaborations Work with Science Teams to Advance Grid Technologies and Improve the Underlying Infrastructure In the Pacific Rim and Globally

Working Groups: Organize Activities Resources Biosciences

H5N1 related glycan conformation analysis using M*Grid and Glyco-M*Grid Relaxed Complex Method Molecular Dynamics Simulation Data Sets & Database Virtual Screening Data Sets & Database HPC Clusters, NBCR, TeraGrid, MHPCC PRAGMA Portal My WorkSphere CSF4 Server

Virtual Directory Tree

/gfs/$USER databases applications Zinc NCIDS

Gfarm File System

NAMD AutoDock Mr. Bayes

Telescience GEO

Accomplishments

Science and Applications

NCHC SARS Task Force

Developers at the NCHC Access Grid node test the SARS Grid network links 1 st Hospital Outbreak (Taipei Municipal Ho-Pin Hospital) PRAGMA 4 Program Committee / request for help (16, May, Fri) 2 AG nodes + H.323 X-ray image interface + medical information + high speed network 100 90 80 70 60 50 40 30 20 10 0

Chang Gung Hospital outbreak (South)

Suggest in PRAGMA 4 Draft Agenda to help SARS relief…(15, Apr) 2 AG nodes + …

PRAGMA 4

S us pe cte d P roba ble ¤T ¤ë 5 ¤é ¤T ¤ë 8 ¤é ¤T ¤ë 1 1 ¤T ¤ë 1 4 ¤T ¤ë 1 7 ¤T ¤ë 2 0 ¤T ¤ë 2 3 ¤T ¤ë 2 6 ¤T ¤ë 2 9 ¥| ¤ë 1 ¤é ¥| ¤ë 4 ¤é ¥| ¤ë 7 ¤é ¥| ¤ë 1 0 ¥| ¤ë 1 3 ¥| ¤ë 1 6 ¥| ¤ë 1 9 ¥| ¤ë 2 2 ¥| ¤ë 2 5 ¥| ¤ë 2 8 ¤ ¤ë 1 ¤é ¤ ¤ë 4 ¤é ¤ ¤ë 7 ¤é ¤ ¤ë 1 0 ¤ ¤ë 1 3 ¤ ¤ë 1 6 ¤ ¤ë 1 9 ¤ ¤ë 2 2 ¤ ¤ë 2 5 ¤ ¤ë 2 8 ¤ ¤ë 3 1 ¤» ¤ë 3 ¤é

14, May:SARS AG\Task Force

Da te of ons e t

Source: Fang-Pang Lin

Savannah Burn: How tightly linked are burning, vegetation, and rainfall?

• • • PRAGMA Testbed ran CSIRO climate model called CCAM in combination with Nimrod/G tool set. Executed on a maximum of 90 processors (out of a maximum 159) across 7 PRAGMA grid resources located in Australia, Japan, Korea, Taiwan, Thailand and the U.S. David Abramson, Amanda Lynch Lynch AH., Abramson D, Görgen K, Beringer J, and Uotila P. "Influence of savanna fire on Australian monsoon season precipitation and circulation as simulated using a distributed computing environment:,

Geophys. Res. Lett., 34, L20801,

doi:10.1029/2007 GL030879. 2007. (Savannah PRAGMA Grid application)

• Avian Flu Grid – –

Avian Flu and FMO

• FMO and Grid Major infectious disease High throughput screening help identify possible targets – FMO enables first-principle calculation of proteins; accurate energy of molecules – Requires: • Approach: RCS, Autodock NBCR • • • Computers: PRAGMA Grid Scheduling: CSF4 Data handling: Gfarm • • • Web service layer: CNIC Portal: Konkuk Testing: USM – – FMO used to study reaction mechanism of enzymes (drug design); electronic structure (photosynthesis) Experiment with OSG, PRAGMA, ran Grid FMO stably 3 months 2007 oseltamivir in the binding pocket of neuraminidase: L Chang AIST, PRAGMA OSG

22 20 18 16 14

Towards a Global Lake Ecological Observatory Network

interesting times 12 22-Aug Surface 0.5 meters 1 meter 1.5 meters 2 meters 2.5 meters 3 meters Precipitation

Photo by Peter Arzberger, October 2004

6 4 10 8 20 18 16 14 12 23-Aug 24-Aug 25-Aug

Date Source: Tim Kratz

26-Aug 27-Aug 2 0 28-Aug Seasonal dynamics and regulation of lake metabolism in a subtropical humic lake: Tsai et al, Fresh Water Ecology 2008

Yuan Yang Lake, Taiwan ; photo by Matt Van de Bogert

Tele Science Extension: from GLEON to Flood Mitigation Sensor net river monitoring system found flow over crest of levee in Den-Pau Creek Flood Sensor Monitoring System was officially used in Disaster Prevention & Response Center During Typhoon KALMAEGI Premier More than hundred times of log-in Sensor Net System during Typhoon KALMAEGI

Source WF Tsai

Accomplishments

Technology Advances

PRAGMA Grid

UZH Switzerland LZU China CNIC GUCAS China JLU China KISTI Korea AIST OsakaU UTsukuba TITech Japan UoHyd India CUHK HongKong ASGC NCHC Taiwan NECTEC ThaiGrid Thailand MIMOS USM Malaysia ASTI Philippines BII IHPC NGO NTU Singapore SKU UI Indonesia MU HCMUT HUT IOIT-HCM Vietnam Australia APAC QUT Australia SDSC USA CICESE Mexico BESTGrid New Zealand UUtah USA UNAM NCSA USA Mexico CeNAT-ITCR Costa Rica UChile Chile BU USA UPRM Puerto Rico 27 institutions in 17 countries/regions , 24 compute sites ( + 14 in preparation ) Active Participation Source: Cindy Zheng

PRAGMA Grid Compute Resources http://goc.pragma-grid.net/pragma-doc/computegrid.html

PRAGMA 15 (10/24/2008)

Source: Cindy Zheng

•

Applications http://goc.pragma-grid.net/wiki/index.php/Applications

13 applications: (8 by PRIME) – Structure biology • Phaser/Nimrod (MU, Australia) – Drug analysis • EMSAM (PRIME) – Bio-medical research • Cardiac output (PRIME) • Cardial mechanics (PRIME) • Ventricular Myocyte model (PRIME) – Genomics and meta-genomics • Avian Flu Grid/CSF (SDSC/CNIC/JLU/UTsukuba/…) – Computational fluid dynamics • e-AIRS (KISTI, Korea) – Environmental Science • CSTFT/Ninf-G (UPRM, Puerto Rico) – Organic-chemistry • Enediynes (PRIME) • Virtual screen SHP-1 and SHP-2 (PRIME) • Virtual screen SSH-2 (PRIME) – Computer Science • Image Analysis (UMelb, Australia) – Nanotechnology • Nanoengineering simulation (PRIME)

PRAGMA 15 (10/24/2008)

Source: Cindy Zheng

Key Middleware Activities

PRAGMA 15 (10/24/2008)

• • • •

Validation of Cyberinfrastructure Investments by the Savannah Burn experiment

Science Resulted: The hypothesis that burning the Savannah can affect the strength and timing of the monsoon was confirmed. Testbed Exercised: The testbed operated for 170 days, and delivered over 1.25 million processor hours! Importantly, we were able to do a live upgrade of a number of the cyberinfrastructure components during the period.

– Middleware Improved: Improved Nimrod's ability to schedule computations by incorporating both data location and transport delays. Allowing it to make a better choice of resources, improving the performance of the system as well as its fault tolerance. – We also enhanced Nimrod's ability to handle faults in the Grid testbed.

Policy Impacted: The experiment shipped some 1.6TB of data across national and international networks. This exposed some interesting features of Australia’s network charging policy, and will lead to lasting improvements.

Nimrod

New Year’s Challenge: Streaming Underwater Video From Taiwan’s Kenting Reef to Calit2’s OptIPortal

Open Source DataTurbine and SAGE/Rocks-Based OptIPortals My next plan is to stream stable and quality underwater images to Calit2, hopefully by PRAGMA 14. - Fang-Pang to LS Jan. 1, 2008 March 6, 2008 Plan Accomplished!

Source L Smarr UCSD: Rajvikram Singh, Sameer Tilak, Jurgen Schulze, Tony Fountain, Peter Arzberger NCHC : Ebbe Strandell, Sun-In Lin, Yao-Tsung Wang, Fang-Pang Lin

SCMSWeb New Features

• Automatic email alert deployed and operational – According to probe failure status – 3 times a week – Email to site admins and Cindy Zheng • Bi-directional bandwidth measurements using iPerf – Deployed on 11 systems – Need to investigate problems with some sites in one direction – Need to deploy to all systems • Software catalog – Implemented for 7 software so far • Amber, APBS, AutoDock, NAMD • Ninf-G • Intel-C, Intel-Fortran – Deployed on 11 systems – Need to deploy to all systems – Add more software as needed • Prototype integration with Condor – Take advantage of SCMSWeb information

PRAGMA 15 (10/24/2008)

Source: Cindy Zheng, and SCMSWeb team

• •

PRAGMA-CA and VOMS

PRAGMA-UCSD CA ( https://goc.pragma-grid.net/ca ) – Lead by Yoshio Tanaka, Mason Katz and Cindy Zheng – Built according to the most current APGrid recommendations and guidelines – Naregi-CA developed new version – Setup at SDSC – Accredited by APGrid PMA in April, 2008 – Included in IGTF distribution in July, 2008 – Issued 10 host certs for PRAGMA grid services at SDSC • Compute clusters • GOC server • VOMS server • Condor server • Portals VOMS (http://goc.pragma-grid.net/wiki/index.php/VOMRS) – Lead by Vladimir Mencl (BeSTGrid) and Cindy Zheng – Setup VOMRS server at SDSC – Focused on group mapping to local account – Successfully tested with BeSTGrid as a client system – Documented for users and site administrators – Issues need to be discussed before wider deployment

PRAGMA 15 (10/24/2008)

Mesh Generation using e-AIRS

Flow around a NACA0012 airfoil

PRAGMA 15 (10/24/2008)

Accomplishment

Educational Models People form the core of virtual communities

PRIME Students 2008

PRIME Host and Mentor Sites

U Zurich Switzerland CNIC China Osaka U Japan U WI USA UCSD USA NCHC Taiwan UoHyd India USM Malaysia Monash U Australia U Auckland U Waikato New Zealand Currently there are 4 host sites: Osaka, NCHC, Monash, CNIC; New in 2008: USM, NTU, U Auckland, U Waikato , New 2009 U Hyderabad; And new US mentoring sites: U WI

Source Cindy Zheng

PRIME 2008

• Projects (some) – Avian Flu (CNIC, USM) – Molecular Screening (Osaka, Monash) – Quantum Chemistry (Monash) – Tile display walls (NCHC, Osaka, Monash) – Cardiac and Muscle Modeling (Monash, Auckland) – Computational materials modeling (Monash) – Environmental data infrastructure (Waikato • Mixture of new projects and continuing ones • Total number of students 21

Source: A. Altshuler, I Wu Source: C.Chang, D Goodman, M Levesque Source: L. Cheng

PRIME Projects – USM 2008

• Avian Influenza Virus H5N1 Polymerase Subunit PB2 Cap-binding Site Inhibitors,

Lihua Yang

• Avian Flu: neuraminidase,

Cindy Tran

• Comparison of AutoDock and GAMES/APBS Methods for Performing Molecular Computations on Biological Systems,

Ranmali Perera

•

PRIUS and MURPA: Based on PRIME

New Models for Building Research Capacity and Cultural Awareness

U Hyderabad

Hyderabad, India

USM Penang Malaysia

12 Oct 05

U Auckland U Waikato New Zealand

+ MURPA

31 Jul 08

Accomplishments

Community Building

GLEON Sites

September 2008 Lake Observatory + IT Development

GLEON 6, Florida February 2008 Lake Erken, GLEON 7 September 2008 T. Blenckner Telescience WG Source: Tim Kratz

Lake Sunapee, USA

Source: Tim Kratz

Typical Instrumentation •Weather •Dissolved Oxygen sensor Torrens Lake, Australia Lake Mangueira, Brazil Lake Annie, USA •Turbidity •pH •CO2 •PAR penetration Crystal Bog, USA •ADCP •etc Lake Rotorua, New Zealand Lake Erken, Sweden

Coral Reef Environmental Observatory Network (CREON)

Taiwan NOAA

CREON Integration Meeting March 2008 Kenting Taiwan Telescience WG

GBR

Source: Stuart Kininmonth, AIMS Source : Fang-Pang Lin, NCHC

UCSB http://www.coralreefeon.org/

Building Avian Flu Grid Partnership Integrate Technology and Science

Biosciences Working Group

Funding NSF, TATRC, and NIH

Virtual Directory Tree

/gfs/$USER databases applications Zinc NCIDS

Gfarm File System

NAMD AutoDock Mr. Bayes PRAGMA 12, Bangkok, Mar07 AFG, Hawaii, Aug07 Focus on Neuraminidase (Tamiflu)

Grass Roots Approach in Geosciences

• • •

Workshops: – October 2005 (PRAGMA 9) – August 2007: Training Prototype – Hyderabad – Pune, and Rajamundhry Persistence, Grassroots

Arun Agarwal U Hyderabad

PRAGMA Institutes: Building the Community

1 st PRAGMA Institute Held in conjunction with PRAGMA 13 NCSA and IACAT, U IL, USA 26 – 27 September 2007 2 nd PRAGMA Institute, Held in conjunction with the Southeast Asia Joint Institute Hsinchu and Hualien, Taiwan 3 – 7 December 2007

What is in the Future?

Virtualization and Commodity Computing

• • Virtualization: Fundamental shift in using resources: Bring your own environment Commodity Computing: Sometimes it is cheaper to rent than to own.

Two different Virtual Computers on a single physical host Network Accessible Source: P Papadopoulos

PRAGMA as a Conduit of ideas And technology

Trend: Data richness drives computation

Pipelines from acquisition to translational insights Diagnostics, optimize interventions, new drugs

Imaging Recon struction Segment Meshing Modeling Simulation

Linking the tools, models, and resources

Mesh Generation for Biomedical Applications Source Zeyun Yu

Molecular level (PDB/PQR) Cellular level (LM/EM Images) Organ level (3D CT Maps)

(mAChE tetramer: 36,638 atoms)

2um

T-tubules in mouse cardiac myocytes

(Image courtesy of Masahiko Hoshijima, UCSD)

3D CT reconstruction of human heart

(Data courtesy of Charles Taylor, Stanford) (Yu et al, J. of Mol Graphics and Modeling 2008) (Yu et al, Journal of Structural Biology 2008) (Yu et al, Finite Element Analysis & Design 2008)

Integrate Remote and Land-based Measurements Lake Rotorua in New Zealand Aster data, Source: R. Nakamura Color is surface temp, centigrade Deniz Özkundakci

• •

“I have seen the future, and it is now” Nam June Paik, Korean artist, invented video art

Chancellor Monash U, upon seeing HD Video presentation on “Multi-Scale Modeling of the Heart”, a MURPA seminar Three dimensional video teleconferencing between Osaka and NCHC – Developed algorithms and tested creating and streaming of 3D data – Used Covise

Conductor and Ensemble in different locations Monash U

Education

Is there a larger, coordinated role PRAGMA can play in education?

Coordination and expansion of PRIME, PRIUS, MURPA, PRIUSM?

These are our future leaders

What is the future conduct of science?

Future Discovery and Community Research

• • • •

High Performance Computing Data, Data Analysis, Visualization Learning & Workforce Development Virtual Organizations for Distributed Communities: – Cyberinfrastructure enables distributed knowledge communities that collaborate and communicate across disciplines, distances and cultures, …[to become] virtual organizations that transcend geographic and institutional boundaries (A.Bement)

What are the practices of successful virtual organizations?

• •

Societal Problems: Wisconsin Idea

The boundaries of the university should be the boundaries of the state, and that research conducted at the University of Wisconsin System should be applied to solve problems and improve health, quality of life, the environment and agriculture for all citizens of the state.

– UW President Charles Van Hise in 1904. Van Hise declared that he would "never be content until the beneficent influence of the university reaches every family in the state."

• • • •

Ask the Right Question

How do we structure partnerships to succeed?

• • • • • • • • • • • • • • • •

Acknowledgements

All PRAGMA members – Slides from Phil Papadopoulos, Cindy Zheng, FangPang Lin, Satoshi Sekiguchi, Jysoo Lee – Karpjoo Jeong, Yoshio Tanaka, Putchong Uthayopas, Piyawut Srichaikul G. Wienhausen, D. Abramson, Kai Nan, FP Lin, Shinji Shimojo, S.Date- PRIME Susumu Date and Shinji Shimojo, Osaka University – PRIUS Tim Kratz, U Wisconsin; Fang-Pang Lin, NCHC, David Hamilton, U Waikato – GLEON Larry Smarr – OptIPuter Wilfred Li – National Biomedical Computation Resource Tony Fountain, Tim Kratz, Ken Chiu, Rick McMullen, Sameer Tilak - Autoscaling Bill Chang, NSF for planting the seed and ongoing encouragement; Others at NSF!

NSF, Gordon and Betty Moore Foundation, TATRC, NIH PRAGMA is supported by the NSF (Grant No. INT-0216895, INT-0314015, OCI -0627026), the San Diego Supercomputer Center, and the California Institute of Telecommuncations and Information Technology , The University of California, San Diego and member institutions PRIME is Supported by the National Science Foundation under NSF INT 04007508 AutoScaling, NEON 0446802 The OptIPuter receives major funding from the National Science Foundation, cooperative agreement ANI-0225642 to UCSD GLEON, CREON: Funding in part by Gordon and Betty Moore Foundation TATRC – for funding of avian flu international collaboration NBCR – for biomedical infrastructure, funded by NIH