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Experiences integrating new applications in EGEE Roberto Barbera - - PowerPoint PPT Presentation

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Enabling Grids for E-sciencE Experiences integrating new applications in EGEE Roberto Barbera University of Catania and INFN First EGEE User Forum CERN, 01-03.03.2006 www.eu-egee.org INFSO-RI-508833 Outline Enabling Grids for E-sciencE

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INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org

Experiences integrating new applications in EGEE

Roberto Barbera University of Catania and INFN First EGEE User Forum CERN, 01-03.03.2006

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First EGEE User Forum, CERN, 01-03.03.2006 2

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Outline

  • The mission
  • The present results
  • The future
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First EGEE User Forum, CERN, 01-03.03.2006 3

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Goals of EGEE Applications Sector

  • Drive the evolution of the grid technology through

specific, challenging applications.

– pilot applications (HEP and Biomed) committed to use the large distributed infrastructure EGEE to achieve their scientific goals.

  • Demonstrate that EGEE provides a viable computing

infrastructure for research to several scientific communities.

– EGEE hosts a number of scientifically diverse applications with the help of teams of engineers funded by EGEE and the scientific communities concerned.

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Pilot Applications: HEP

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First EGEE User Forum, CERN, 01-03.03.2006 5

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How to prepare for LHC: LCG Service Challenges

SC2 SC3 LHC Service Operation

Full physics run

2005 2007 2006 2008

First physics First beams cosmics

June05 - Technical Design Report Sep05 - SC3 Service Phase May06 –SC4 Service Phase starts Sep06 – Initial LHC Service in stable operation

SC4

Apr07 – LHC Service commissioned Apr05 – SC2 Complete Jul05 – SC3 Throughput Test Apr06 – SC4 Throughput Test Dec05 – Tier-1 Network operational

preparation setup service

SC2 SC2 SC3 SC3 LHC Service Operation LHC Service Operation

Full physics run

2005 2007 2006 2008

First physics First beams cosmics Full physics run

2005 2007 2006 2008 2005 2007 2006 2008

First physics First beams cosmics

June05 - Technical Design Report Sep05 - SC3 Service Phase May06 –SC4 Service Phase starts Sep06 – Initial LHC Service in stable operation

SC4 SC4

Apr07 – LHC Service commissioned Apr05 – SC2 Complete Jul05 – SC3 Throughput Test Apr06 – SC4 Throughput Test Dec05 – Tier-1 Network operational

preparation setup service preparation setup service

  • LHC starts in 2007
  • Ramp-up with series of service

challenges to ensure key services & infrastructure in place for the experiments computing systems

  • Extremely aggressive timescale
  • Emphasis on providing a service
  • Data movement
  • Data handling
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First EGEE User Forum, CERN, 01-03.03.2006 6

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HEP success stories

  • Fundamental activity in

preparation of LHC start up

– Physics – Computing systems

  • Examples:

– LHCb: ~700 CPU/years in 2005

  • n the EGEE infrastructure

– ATLAS: over 10,000 jobs per day

Comprehensive analysis: see S.Campana et al., “Analysis of the ATLAS Rome Production experience on the EGEE Computing Grid“, e-Science 2005, Melbourne, Australia

– A lot of activity in all involved applications (including as usual a lot of activity within non-LHC experiments like BaBar, CDF and D0)

CPU used: 6,389,638 h Data Output: 77 TB

DIRAC.Barcelona.es 0.214% DIRAC.Bologna-T2.it 0.696% DIRAC.CERN.ch 0.571% DIRAC.Cambridge.uk 0.001% DIRAC.CracowAgu.pl 0.001% DIRAC.IF-UFRJ.br 0.175% DIRAC.LHCBONLINE.ch 0.779% DIRAC.Lyon.fr 2.552% DIRAC.PNPI.ru 0.000% DIRAC.Santiago.es 0.148% DIRAC.ScotGrid.uk 3.068% DIRAC.Zurich-spz.ch 0.003% DIRAC.Zurich.ch 0.756% LCG.ACAD.bg 0.106% LCG.BHAM-HEP.uk 0.705% LCG.Barcelona.es 0.281% LCG.Bari.it 1.357% LCG.Bologna.it 0.032% LCG.CERN.ch 10.960% LCG.CESGA.es 0.528% LCG.CGG.fr 0.676% LCG.CNAF-GRIDIT.it 0.012% LCG.CNAF.it 13.196% LCG.CNB.es 0.385% LCG.CPPM.fr 0.242% LCG.CSCS.ch 0.282% LCG.CY01.cy 0.103% LCG.Cagliari.it 0.515% LCG.Cambridge.uk 0.010% LCG.Catania.it 0.551% LCG.Durham.uk 0.476% LCG.Edinburgh.uk 0.031% LCG.FZK.de 1.708% LCG.Ferrara.it 0.073% LCG.Firenze.it 1.047% LCG.GR-01.gr 0.349% LCG.GR-02.gr 0.226% LCG.GR-03.gr 0.171% LCG.GR-04.gr 0.056% LCG.GRNET.gr 1.170% LCG.HPC2N.se 0.001% LCG.ICI.ro 0.088% LCG.IFCA.es 0.022% LCG.IHEP.su 1.245% LCG.IN2P3.fr 4.143% LCG.INTA.es 0.076% LCG.IPP.bg 0.033% LCG.ITEP.ru 0.792% LCG.Imperial.uk 0.891% LCG.Iowa.us 0.287% LCG.JINR.ru 0.472% LCG.KFKI.hu 1.436% LCG.Lancashire.uk 6.796% LCG.Legnaro.it 1.569% LCG.Manchester.uk 0.285% LCG.Milano.it 0.770% LCG.Montreal.ca 0.069% LCG.NIKHEF.nl 5.140% LCG.NSC.se 0.465% LCG.Napoli.it 0.175% LCG.Oxford.uk 1.214% LCG.PIC.es 2.366% LCG.PNPI.ru 0.278% LCG.Padova.it 2.041% LCG.Pisa.it 0.121% LCG.QMUL.uk 6.407% LCG.RAL-HEP.uk 0.938% LCG.RAL.uk 9.518% LCG.RHUL.uk 2.168% LCG.SARA.nl 0.675% LCG.Sheffield.uk 0.094% LCG.Torino.it 1.455% LCG.Toronto.ca 0.343% LCG.Triumf.ca 0.105% LCG.UCL-CCC.uk 1.455% LCG.USC.es 1.853% 20-6-2005, P. Jenni 4 LCG POB: ATLAS on the LCG/EGEE Grid

t o yea s a ead

ATLAS LHCb

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First EGEE User Forum, CERN, 01-03.03.2006 7

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10,000 jobs/day !

From Accounting data: ~3 million jobs in 2005 so far Sustained daily rates (per month Jan – Nov 2005): [2185, 2796, 7617, 10312, 11151, 9247, 9218, 11445, 10079, 11124, 9491] ~8.2 M kSI2K.cpu.hours >1000 cpu years

Real usage is higher as accounting data was not published from all

sites until recently

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Pilot Applications: Biomed

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Medical image processing

  • GATE: Radiotherapy planning

– CNRS – Monte Carlo simulation – Parallel execution on different seeds

  • Pharmacokinetics: contrast agent diffusion study

– UPV – Medical images registration – Distribution of registration pairs

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Bioinformatics

  • GPS@: bioinformatics portal

– http://gpsa.ibcp.fr/ web portal – Existing (but overloaded NPSA portal) – Tens of bioinformatics legacy code – Thousands of potential users – Large input databases

  • Electron-microscopic image reconstruction

– Image filtering and noise reduction – 3D structure analysis

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First biomedical data challenge: World-wide In Silico Docking On Malaria (WISDOM)

Domain distribution of Flexx run jobs

es; 5122 fr; 7580 gr; 2004 il; 263 it; 3687 nl; 3356 tw; 827 uk; 8106 bg; 597 com; 1072 de; 715 cy; 383 pl; 1877 ru; 218 ro; 337

  • Significant biological parameters

– two different molecular docking applications (Autodock and FlexX) – about one million virtual ligands selected – target proteins from the parasite responsible for malaria

  • Significant numbers

– Total of about 46 million ligands docked in 6 weeks – 1TB of data produced – Up to 1000 computers in 15 countries used simultaneously for a total of about 80 CPU years

  • Significant results

– Best hits to be re-ranked using Molecular Dynamics

New data challenge in the fall of 2006 New malaria targets Focus on other neglected diseases Enlarged collaboration (possibly including related projects)

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First EGEE User Forum, CERN, 01-03.03.2006 12

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Generic Applications

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First EGEE User Forum, CERN, 01-03.03.2006 13

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The EGEE Virtuous Cycle

NA2, NA3, N4 NA3, NA4, SA1 SA1 JRA1

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The birth of a new VO in EGEE

EGAAP NA3/NA4/SA1 (OAG) MoU

Deployment & configuration

Ask for change

Recommended VO candidate Resource allocation proposal VO requirements

  • Gen. Apps. Quest. & Prop.

New community

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The MoU’s

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The status of Generic Applications deployment

  • Applications accepted before Pisa conference

– Earth Science Research (Earth Observation, Hydrology, Climate) – Geophysics (Industry) – Computational Chemistry – Astro(particle)-physics (MAGIC and Planck collaborations) – Finance (EGRID)

  • Applications approved at last EGEE conference in Pisa

(October 2005)

– Fusion (ITER) – Archaeology – EC Projects (EELA, EUMEDGRID, EUCHINAGRID, BIOINFOGRID)

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First EGEE User Forum, CERN, 01-03.03.2006 17

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EGEE Grid

Computational Chemistry

Client side HTTP Server side MPI libraries SimGate Apache server

GEMS Programs

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First EGEE User Forum, CERN, 01-03.03.2006 18

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V e n u s : Q C T f

  • r

m a n y b

  • d

y s y s t e m s

Computational Chemistry

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First EGEE User Forum, CERN, 01-03.03.2006 19

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Earth Science Research

Ozone maps Earthquakes’ epicenter determination Climate

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FUSION: reactor confinement optimization

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FUSION: reactor confinement optimization

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MAGIC

  • Build a Grid system

with

FZK (Germany) CNAF(Italy) PIC (Spain)

  • MAGIC applied as a

generic application for EGEE

  • MAGIC got accepted

with the air shower Monte Carlo simulation based on CORSIKA

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First EGEE User Forum, CERN, 01-03.03.2006 23

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MAGIC

  • Stability is improving

– Number of failed jobs is decreasing:

  • March 2005 -

10%

  • June 2005 -

3.9%

  • September 2005 -

3.4%

  • Around 18000 jobs submitted in three data

challenges

  • A system with >90% quality level is there!
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First EGEE User Forum, CERN, 01-03.03.2006 24

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Planck on Grid

LevelS basic gridification:

UI env; WN env; Data handling.

Basic tests:

INFN production grid; LFI (22 channels);

PLANCK

Development of G-DSE in collaboration with INFN

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EGEE application sector: other numbers

  • Total effort (funded + unfunded) : 100 FTE’s for 2 years
  • Total EC funding: 3600k€, corresponding to about 30

FTE’s

  • 20 partners
  • More than 20 applications deployed on the production

infrastructure

  • The number of users in application related VO’s has

doubled from ~500 in December 2004 to ~1000 in September 2005

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EU Projects Applications

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Related EU grid projects

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EELA

  • Biomed

– GATE – WISDOM – CECALC web portal (ULA - http://www.cecalc.ula.ve/) – Protein Dynamics (UFRJ)

  • HEP

– LHC Exps.

  • Additional (EELA specific)

– Climate in the Grid Environment – Education in the Grid Environment (“gridification” started in Trieste, see further on)

  • New (not foreseen in the T.A.)

– Questionnaire finalized

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First EGEE User Forum, CERN, 01-03.03.2006 29

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The ARGO–YBJ Experiment

  • Unique High Altitude Cosmic Ray Laboratory (4300 m) Tibet,

90 km North to Lhasa. Chinese-Italian collaboration.

  • The Experiment data rate to be transferred is 250 TB/Year

requiring a steady transfer rate of the order of 100 Mbps to Beijing and from there to Italy.

EUCHINAGRID

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  • Aim: estimate sustainable

extraction scheme - improve management

  • CODESA-3D: Density-

dependent 3D coupled groundwater flow and transport simulations

  • Data requirement

– Geology – Topography – Meteorology – Water extraction by the farmer – Aquifer properties – Soil maps – Land use

6.60E+05 6.70E+05 6.80E+05 4.04E+06 4.05E+06 4.06E+06 4.07E+06

H [m.a.s.l] 160 120 80 40 20 10 5

  • 2

N

One simulated map of water levels

EUMEDGRID

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GILDA Applications

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  • 19 sites in 3 continents
  • > 3000 certificates issued, >15%

renewed at least once

  • > 100 tutorials and demos perfor-

med in 23 months

  • > 1,000,000 hits (> 50,000 unique

visits) on (of) the web site from 10’s of different countries

  • > 0.6 TB of training material

downloaded from the web site

The GILDA t-Infrastructure

(https://gilda.ct.infn.it)

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Number of trained users vs. time

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Early Diagnosis of Alzheimer Disease

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Early Diagnosis of Alzheimer Disease

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ArchaeoGrid

Laboratory Measurements DB Archaeological bibliography DB Archaeological Objects DB Images DB TextFile DB

Archaeological GIS

GeoArchaeology DB Archaeo Climatology DB Archaeo Zoology/Botanic DB Simulation/VR DB Media Tourism Archaeology Cultural Heritage Land Management

ArchaeoNet

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gLite Digital Library DILIGENT UI Visualization Narration Distributed Resources I Archaeological Digital Archives/GIS Earth Science GRID

Web Service Interface Web Service Interface

ArchaeoGrid

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Music for Science: Data Sonification on Grid

  • Data sonification is the representation of data by sound
  • signals. It can be considered as the acoustic

counterpart of data graphic visualization, a mathema- tical mapping of information from data sets to sounds.

  • Data sonification is currently used in several fields, for

different purposes: science and engineering, education and training, mainly as data analysis and interpretation tool.

  • Data sonification has been applied to geophysical data

collected by a digital seismograph placed on the Etna volcano in Italy (courtesy of INGV).

  • The hope is to learn more about eruption dynamics

from patterns in sonograms.

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Seismograms Sonification (15’ of data = 20h of CPU!)

Example of audible seismogram (just at the start of the eruption) Corresponding sonogram Spectral lines ↔ Regular patterns

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Seismograms Melodisation

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Seismograms Melodisation

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Seismograms Melodisation

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Seismograms Melodisation

Melodies can then be analized with mathematical tools to look for patterns and self-similarities

… have you ever heard a volcano playing on a piano ?

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Grid for Art: 3D Data Visualization

  • Letters in a text are associated to graphical objects

such as spheres.

  • Radii, indexes of reflection and refraction, light

diffusion properties, positions in the space are associated to the position of the letters in the english alphabet.

NA4 Generic Applications

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A new kind of cryptography is born!

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VOMS FiReMan Catalog Metadata Catalog

W N WN WN

CE

Storage Elements User GENIUS Portal Workload Management System

get Role

AMGA

gMOD

(a grid for entertainment)

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gMOD

(a grid for entertainment)

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Authenticate with X509 Certificate VOMS Proxy with Group & Role Information

A M G A S e r v e r

PostGreSQL

VOMS

(gLibraryManager gLibrarySubmitter VO user)

LFC (or Fireman) Catalog

VOMS Proxy w/Role & Group

SE SE SE

V O M S P r

  • x

y V O M S P r

  • x

y

UI

gLibrary

(multimedia contents management on the grid)

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gLibrary

(multimedia contents management on the grid)

T

  • b

e s

  • n

i n t e g r a t e d i n G E N I U S a n d a p

  • p

l i e d t

  • t

h e N A 3 c

  • l

l e c t i

  • n
  • f

p r e s e n t a t i

  • n

s

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Lessons learned

  • The first three magic words: training, training, training!
  • Identify the VO experts from the beginning so that they can

set a bridge between EGEE and their community.

  • Show to the users what is possible but also what is not so

that they can understand the current limits of the middleware.

  • For things not working look around very quickly for

replacements (remember the metadata crisis in June ’05 and the adoption of AMGA).

  • Provide users not only with the information on the single

services but with small use cases that can be expanded (e.g., gMOD, gLibrary, etc.)

  • Try to find occasions to organize dedicated meetings/

workshops to port the new applications on grid

  • The last three magic words: support, support, support!
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A very good example…

ICTP/Democritos International Grid School Trieste, 6-17 February 2006 http://cdsagenda5.ictp.trieste.it/full_display.php?ida=a05191

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Experimental result Time: 00:15:37 11:56 + 03:41 Predicted results Single AA junction Three AA junction

A very good example…

(simulations of proteins with genetic algorithms)

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A very good example…

(Grid-Torrent)

Architecture

UI QE SE SE VOMS / MYPROXY QE QE SE AMGA

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NA4 in EGEE-2

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Application sector in EGEE-II

  • Ongoing support to 2 pilot areas (High Energy Physics,

Biomedicine) with established user communities and large scale applications

  • Increased support to 4 scientific disciplines

(Astrophysics, Computational Chemistry, Earth Sciences, Fusion)

  • On-going support to GILDA, the virtual grid laboratory
  • Increased effort to foster a cohesive application

community at NA4 management level

  • Increased complexity from the wider regional distribution

and the associated projects

– 40 partners – Total effort of 150 FTEs (funded + unfunded) for 2 years

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NA4 in EGEE

NA4 geographic coverage

NA4 in EGEE-II

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Tasks involved in application development

training on grid services Consulting/collaboration

  • n application interface and

grid services Gridification Deployment On (P)PS (pilot resources) Problem resolution user support Application to gridify Grid-enabled prototype Validated grid-enabled prototype

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Tasks involved in application deployment

: Troubleshooting, Testing training on VO administration & node installation user support for Sys. Admin. & users Resource & VO expansion Validated grid-enabled prototype Initial deployment

  • n allocated

production resources Large scale Grid deployment Demonstration of Grid added value Production resources available Deployment Application Evaluation Performance Evaluation

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A citation …

Telephone, Light bulb, Telegraph, Radio, TV, Computer, Network, PC, Web, …

(in the same order as they were invented)

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… and a conclusion

  • Maybe we are not there yet with the Grid but …
  • … EGEE is surely paving the way for this and,

for the quantity and the quality of the work done, it is one of the most important key enablers of the European Research Area.