Virtual Laboratory for
e-Science (VL-e)
Henri Bal
Department of Computer Science
Vrije Universiteit Amsterdam
bal@cs.vu.nl
vrije Universiteit
e-Science
• Web is about exchanging information
• Grid is about sharing resources
o Computers, data bases, instruments, services
• e-Science supports experimental science by
providing a virtual laboratory on top of Grids
Virtual Laboratories
Distributed
computing
Application
Specific
Part
Potential Generic
Visualization & part
Management
collaboration of comm. &
computing
Knowledge
Data &
information
Application
Specific
Part
Potential Generic
part
Virtual
Laboratory
Management
of comm.
& services
Application
oriented
computing
Application
Specific
Part
Potential Generic
part
Management
of comm. &
computing
Grid
Harness multi-domain distributed resources
Virtual Laboratory for e-Science
Interactive
PSE
Adaptive
information
disclosure
High-performance
distributed computing
User Interfaces &
Virtual reality
based visualization
Security & Generic
AAA
Collaborative
information
Management
Virtual lab. &
System integration
Optical Networking
The VL-e project
• 40 M€ (20 M€ BSIK funding)
• 2004 - 2008
vrije Universiteit
• 20 partners
• Academic - Industrial
VL-e environments
Application
specific
service
Application
Potential
Generic service
&
Virtual
Lab. services
Grid
&
Network
Services
Telescience
Medical
Application
Bio ASP
Virtual Laboratory
Virtual Lab.
rapid prototyping
(interactive simulation)
Grid Middleware
Additional
Grid Services
(OGSA services)
Gigaport
Proof of Concept environment
Network Service
(lambda networking)
Rapid Prototyping
environment
Source: Prof. Bob Hertzberger (University of Amsterdam)
Outline
• Infrastructure for the Rapid Prototyping group
o 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 system
o 4 clusters with 200 nodes in total
• Homogeneous system:
same processors, network, OS
o 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)
Configuration
200 MHz Pentium Pro
Myrinet LAN
Redhat Linux
6 Mb/s
ATM
Leiden (24)
Delft (24)
Node configuration
DAS-2 (2002)
two 1 GHz Pentium-3s
>= 1 GB memory
20-80 GB disk
VU (72)
Myrinet LAN
Redhat Enterprise Linux
Globus 3.2, SGE
Amsterdam (32)
SURFnet
1 Gb/s
Leiden (32)
Utrecht (32)
Delft (32)
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 ASCI
o Gigaport-NG/SURFnet: DWDM computer backplane
(dedicated optical group of up to 8 lambdas)
o VL-e and MultimediaN BSIK projects
DAS-3
NOC
Outline
• Infrastructure for the Rapid Prototyping group
o 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)
HPC on a grid?
• Can grids be used for High-Performance Computing
applications that are not trivially parallel?
• Key: grids usually are hierarchical
o Collections of clusters, supercomputers
o Fast local links, slow wide-area links
• Can optimize algorithms to exploit this hierarchy
o Message combining + latency hiding on wide-area links
o Optimized collective communication operations (broadcast etc.)
o Often gives latency-insensitive, throughput-bound algorithms
Ibis: a Java-centric grid
programming environment
• Written in pure Java, runs on heterogeneous grids
o “Write once, run everywhere ”
• Many applications:
o
o
o
o
o
o
o
Automated protein identification (VL-e, AMOLF)
Grammar learning (VL-e, UvA)
Cellular automaton (VL-e, UvA)
N-body simulations
SAT-solver
Raytracer
Jem3D Electromagnetic simulation (with ProActive)
Available from www.cs.vu.nl/ibis
Performance on wide-area DAS-2
70.0
60.0
40.0
30.0
20.0
10.0
single cluster of 64 machines
P
TS
K
N
e
qu
ee
Pr
im
ns
e
fa
ct
or
s
Ra
yt
ra
ce
r
N
ch
oo
s
ac
k
ID
A*
Kn
ap
s
Fi
bo
na
ive
cc
in
i
te
gr
at
i
Se on
tc
Fi
ov
b.
er
th
re
sh
ol
d
0.0
Ad
ap
t
speedup
50.0
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 experiments
with 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
SMP
Linux
Pentium-3 Cardiff
12
Origin 3000
Irix
MIPS
ZIB Berlin
1  16
SMP
Unix
Alpha
Lecce
14
42
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
Interactive Problem Solving Environments
From Medical Image Acquisition to Interactive Virtual
Visualization…
MRI, PET
Patient at MRI
scanner
MR image
MR image
Segmentation
Cave, Wall, PC,
PDA
Virtual Node
navigation
Bypass creation
Simulated
blood flow
Shear stress, velocities
ce (e.g., Valencia)
se (e.g., Leiden)
MD login and Grid
Proxy creation
Monolith, Cluster
LB mesh
generation
Job submission
ce (e.g., Bratislava)
Job
monitoring
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
Simulated
Blood Flow
StarPlane project
• Application-specific management of optical networks
• Future applications can:
o dynamically allocate light paths, of 10 Gbit/sec each
o 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-3
NOC
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