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

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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

Rapid Prototyping environmentProof of Concept environment

Telescience Medical Application Bio ASP

Virtual Lab.rapid prototyping

(interactive simulation)

Additional Grid Services

(OGSA services)

VL-e environments

Source: Prof. Bob Hertzberger (University of Amsterdam)

Outline

• Infrastructure for the Rapid Prototyping groupo Based on DAS (Distributed ASCI Supercomputer)o SURFnet-6 optical network (Gigaport-NG) & DAS-3

• Distributed supercomputing (Ibis)• Visualization• Interactive problem solving environments • Management of optical networks (StarPlane)

DAS-1 (1997 - 2002)

• Geographically distributed cluster-based systemo 4 clusters with 200 nodes in total

• Homogeneous system:same processors, network, OSo Eases collaboration, software exchange,

systems management, experimentation

• Shared test bed of the ASCI research school

• For experimental Computer Science research,not for production use

DAS-1

VU (128) Amsterdam (24)

Leiden (24) Delft (24)

6 Mb/sATM

Configuration

200 MHz Pentium ProMyrinet LANRedhat Linux

DAS-2 (2002)

VU (72) Amsterdam (32)

Leiden (32) Delft (32)

SURFnet1 Gb/s

Utrecht (32)

Node configuration

two 1 GHz Pentium-3s>= 1 GB memory20-80 GB disk

Myrinet LANRedhat Enterprise LinuxGlobus 3.2, SGE

Some DAS highlights

• 200 users in total• Used for over 20 Ph.D. theses• Used for many publications, including 11 in

ACM/IEEE journals and 1 in Nature• Used to solve Awari

(3500-year old game)

DAS-3

• Next generation grid in the Netherlands (2006)• Partners:

o NWO & NCF (Dutch science foundation)o ASCIo Gigaport-NG/SURFnet: DWDM computer backplane

(dedicated optical group of up to 8 lambdas)o VL-e and MultimediaN BSIK projects

DAS-3C

PU

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Outline

• Infrastructure for the Rapid Prototyping groupo Based on DAS (Distributed ASCI Supercomputer)o SURFnet-6 optical network (Gigaport-NG) & DAS-3

• Distributed supercomputing (Ibis)• Visualization• Interactive problem solving environments • Management of optical networks (StarPlane)

Distributed supercomputing (parallel computing on grids)

• Can grids be used for High-Performance Computing applications that are not trivially parallel?

• Key: grids usually are hierarchicalo Collections of clusters, supercomputerso Fast local links, slow wide-area links

• Can optimize algorithms to exploit this hierarchyo Message combining + latency hiding on wide-area linkso Optimized collective communication operations (broadcast etc.)o Often gives latency-insensitive, throughput-bound algorithms

HPC on a grid?

Ibis: a Java-centric grid programming environment

• Written in pure Java, runs on heterogeneous gridso “Write once, run everywhere ”

• Many applications:o Automated protein identification (VL-e, AMOLF)o Grammar learning (VL-e, UvA)o Cellular automaton (VL-e, UvA)o N-body simulationso SAT-solvero Raytracero Jem3D Electromagnetic simulation (with ProActive)

Available from www.cs.vu.nl/ibis

Performance on wide-area DAS-2

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single cluster of 64 machines 4 clusters of 16 machines

GridLab

• Latencies:o 9-200 ms (daytime),

9-66 ms (night)

• Bandwidths:o 9-4000 KB/s

• Machines come and go• Succeeded in doing

real experimentswith real speedups

Configuration

Type OS CPU Location CPUs

Cluster Linux Pentium-3 Amsterdam 8 1

SMP Solaris Sparc Amsterdam 1 2

Cluster Linux Xeon Brno 4 2

SMP Linux Pentium-3 Cardiff 1 2

Origin 3000 Irix MIPS ZIB Berlin 1 16

SMP Unix Alpha Lecce 1 4

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

Visualization on the Grid

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

StarPlane project

• Application-specific management of optical networks• Future applications can:

o dynamically allocate light paths, of 10 Gbit/sec eacho control topology through the Network Operations Center

• Gives flexible, dynamic, high-bandwidth links• Research questions:

o How to provide this flexibility (across domains)?o How to integrate optical networks with applications?

• Joint project with Cees de Laat (Univ. of Amsterdam), funded by NWO

DAS-3C

PU

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Summary

• VL-e (Virtual Laboratory for e-Science) studies entire e-Science chain, including applications, middleware and grids

• Organized into 2 environments:o Proof of Concept (for applications)o Rapid Prototyping (computer science research)

• New state-of-the-art Grid infrastructure planned for 2006 using optical networking

More information: http://www.vl-e.nl