Virtual Laboratory fore-Science (VL-e)

Henri Bal

Department of Computer ScienceVrije Universiteit Amsterdam

bal@cs.vu.nl

vrije Universiteit

e-Science

• Web is about exchanging information

• Grid is about sharing resourceso Computers, data bases, instruments, services

• e-Science supports experimental science by providing a virtual laboratory on top of Grids

Managementof comm. & computing

Managementof comm. & computing

Managementof comm. & computing

Potential Genericpart Potential Generic

partPotential Generic

part

ApplicationSpecific

Part

ApplicationSpecific

Part

ApplicationSpecific

Part

Virtual Laboratory Application oriented services

GridHarness multi-domain distributed resources

Virtual LaboratoriesDistributed computing

Visualization & collaboration

Knowledge

Data & information

Optical NetworkingHigh-performance

distributed computingSecurity & Generic

AAA

Virtual lab. &System integration

Interactive PSE

Collaborative information Management

Adaptive information

disclosure

User Interfaces & Virtual reality

based visualization

Bio

-div

ers

ity

Bio

-In

form

ati

cs

Te

les

cie

nc

e

Da

ta I

nte

ns

ive

Sc

ien

ce

Fo

od

In

form

ati

cs

Me

dic

al

dia

gn

os

is &

im

ag

ing

Virtual Laboratory for e-Science

The VL-e project• 40 M€ (20 M€ BSIK funding)• 2004 - 2008

vrije Universiteit

• 20 partners• Academic - Industrial

Grid Middleware

Gigaport Network Service (lambda networking)

Application specificservice

Application Potential

Generic service &

Virtual Lab. services

Grid &

NetworkServices

Virtual Laboratory

VL-E Experimental Environment

VL-E Proof of concept Environment

Telescience Medical Application Bio ASP

Virtual Lab.rapid prototyping

(interactive simulation)

Additional Grid Services

(OGSA services)

VL-e environments

VL-e workshop

Optical NetworkingHigh-performance

distributed computingSecurity

Virtual labi PSE CIMA.I.D. Visualization

Bio

-div

Bio

-In

f

Te

les

cie

nc

e

Da

ta

Inte

ns

ie

Fo

od

Me

dic

al

ima

gin

g

demo

P4

: S

calin

g u

p

Jansen

Belleman Marshall, Breit Konijnenburg

Bouwhuis

MRI, PET Monolith, Cluster Cave, Wall, PC, PDA

From Medical Image Acquisition to Interactive Virtual Visualization…

MD login and Grid Proxy creation

Bypass creation LB mesh generation

Job submission Job monitoring

Virtual Node navigation Simulated

Blood Flow

Patient at MRI scanner

MR image MR image Segmentation

Shear stress, velocitiesSimulated blood flow

se (e.g., Leiden)ce (e.g., Valencia) ce (e.g., Bratislava)

ui (VRE)

P.M.A. Sloot, A.G. Hoekstra, R.G. Belleman, A. Tirado-Ramos, E.V. Zudilova, D.P. Shamonin, R.M. Shulakov, A.M. Artoli , L. Abrahamyan

Interactive Problem Solving Environments

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

High-PerformanceDistributed Computing

• Ibis: a Java-centric grid programming environmento Remote Method Invocation (RMI), group communication,

divide&conquer parallelism, object migration (ProActive)

• Written in pure Java, runs on heterogeneous gridso “Write once, run everywhere ” o Use bytecode rewriting for optimizations (e.g. serialization)o Use native code as special-case optimization (e.g. Myrinet)

Experiences with Ibis

• Distributed supercomputing applicationso Electromagnetic simulation (Jem3D)o Automated protein identification (AMOLF)o N-body simulations, SAT-solver, raytracer

• Successful grid experimentso On DAS-2 (homogeneous Dutch grid)o On GridLab (European grid)

• Need co-allocation mechanisms

More info + distribution at www.cs.vu.nl/ibis

Optical networking• Formally part of GigaPort-NG BSIK project • Studies optical networking technology in a grid

context (e.g., bandwidth-on-demand)• Useful for many VL-e applications

o Data-intensive sciences, visualization,HPDC, etc.

CP

U’s

R

CPU’sR

CPU’s

R

CP

U’s

R

CPU’s

R

NOC

Workshop program

• 14:15 - 14:45 Workflow and data integration in e-bioscience: Some user requirements (Scot Marshall)

• 14:45 - 15:15 The Knowledge Grid and Adaptive Information Disclosure (Machiel Jansen)

• 15:15 - 15:45 Data management in the Proof-of-Concept environment of VL-e (Maurice

Bouwhuis)• 15:45 - 16:00 Presentation of the Demos• 16:00 - 16:30 Break & Demo at the LightHouse (SARA+UvA)• 16:30 - 17:00 Medical Application (Robert Belleman)• 17:00 - 17:30 Bioinformatics (Timo Breit)• 17:30 - 18:00 Dutch Tele-science Lab (Marco Konijnenburg)