Transcript GRID projects for the Mediterranean and China

EUChinaGRID
&
EUMEDGRID
+
ArchaeoGrid
Federico Ruggieri – INFN
Riunione Referee
Bologna 29 Agosto 2007
EGEE and collaborating projects
SEEGRID-SCP
Obiettivi Generali
• Estensione di EGEE fuori Europa.
• Disseminazione della Tecnologia Grid gLite.
• Interoperabilità con Middleware di Grid di
altre Regioni.
• Supporto a comunità applicative già
presenti in EGEE: esperimenti LHC,
BioMedici.
• Allargamento a nuove applicazioni e
comunità: Scienza della Terra, Archeologia,
Medicina, Genetica, Geofisica, Vulcanologia,
Sismologia, ecc.
Specific Support Actions
Project
Start Date
Duration
EU contribution
Sedi INFN
coinvolte
1 Jan 2006
1 Jan 2006
27 Months (esteso al
31 Marzo 2008)
24 Months
~ 1.3 M€
1.645 M€
Catania, CNAF, Roma3
Catania, CNAF, Roma3
(Firenze)
Continuazione dei progetti
• Richieste per 3 mesi di prolungamento di
EUChinaGRID nel 2008.
• Attività dei nuovi progetti: EUMEDGRID-2 ed
EUChinaGRID-2 che verranno sommessi alla
call che scade il 20 Settembre 2007.
• Spese di gestione delle attività che non sono
rendicontabili o che eccedono il budget
(principalmente dedicato al personale).
Richieste EUMED + EUChina
Persone
FTE
Missioni
Interne
CT
4
2,6
15
15
15
10
55
CNAF
2
2,0
5
7
5
10
27
FI
3
1,2
2
5
1
RM3
16
8,6
10,0
30
10
10
60
Totale
25
14,4
32
57
31
30
150
Sito
Missioni
Consumo Inventariabile
Estere
Totale
sito
8
Participants
Partners
Nuovi Partners
INFN (Italy) Coordinator
CNRS (FR)
CERN (CH)
Consorzio COMETA (IT)
Università di Roma Tre - Dip.
CYFRONET (PL)
di Biologia - (IT)
Consortium GARR (IT)
Bejing Genomics Institute (CN)
GRNET (GR)
Shandong University (CN)
Jagiellonian University - MC The Institute of Hydrogeology and
Cracow (PL)
Environmental Geology (CN)
Beihang
(CN)
University
Beijing Shanghai Institute of Materia Medica
(CN)
CNIC-CAS – Beijing (CN)
IHEP-CAS - Beijing (CN)
Peking
(CN)
University
–
Beijing
Xian Jiaotong Institute (CN)
Infrastructure
gLite - GOS gateway
Scheduler
Extended GOS
forwards batch
job to gateway
Thread Pool
Idle thread pool
used in scheduler
Batch job
Batch job
WMProxy
GOS
Batch job
Pipeline for GOS to GLite
Batch job
Extended
LCG-CE
GOS
Extended
LCG-CE
forwards
batch jobs to
gateway
Pipeline for GLite to GOS
Thread Pool
Scheduler executes stage in
pipeline using idle thread
from thread pool
Different colors in pipeline stand for different
stages (StageIn, StageOut, … )
Scheduler
Each pipeline has corresponding thread pool
and scheduler
New Architecture for Interoperability
(Logical) Super
Broker
Unified Portal
edg glite-UI
JDL
Super Gateway
Multi/Single MWare
JDL
Brokers
Components of
Super Broker can
stay on different
machines
JSDL
(x2)
Portal or WS-Client
JSDL
Other GRID Portal
??DL
gLite WMS RB
MM Library
GOS
Computing
GT4
Resource
RSL
Selection
Other MW’s Broker
Interoperable
Information and
Monitoring
System
Inf. Index
Interoperable
Data Mgmt
System
RSL
CE
WN WN WN
GOS Node
CROWN Node Other’s Node
(Even) Multi Middleware Nodes
IPv6 compatibility of Grid middleware
 A specific task was started in order to investigate if
libraries, software and other third-party elements
used in gLite and GOS are IPv6 compliant.
 A compatibility list is available and constantly
enlarged and updated.
 IPv6 Test-bed set up
ARGO-YBJ Data Mover
 Reliable Data
Transfer from
Yangbajing
 2 Data Repositories
(CNAF & IHEP)
synchronized via LFC
and FTS + custom
scripts.
YBJ:
User Interface
SRM (DPM)
local DB
User Interface
SRM (DPM)
FTS
LFC
local DB
User Interface
SRM (DPM)
FTS
LFC
local DB
Figure 5 - ARGO Data Transfer Schema
Biological applications
 Generate “never born protein” sequences database
 Port protein structure prediction software on grid
 Develop web tools for non grid trained users
KWCWPFASHNDLKVQSQ
WYVEPPDTIPPYNKYGTN
FIKHCQYIAHMQGDTHFF
NRVRMHQLWKIIVDCAY
Rosetta
Early/Late Stage
New Biological Applications
 Applications should be used by scientists both in Europe and
China
• Particular interest for applications proposed by chinese partners
 4 potential applications
•
•
•
•
Molecular epidemiology on emerging diseases
Joint in silico drug discovery on CNGrid and EUChinaGRID
Telemedecine
Bioinformatics grid services for the Human Cancer Genome
Project
 Development of a new tool
EUChinaGrid II – Proposed UROM3 contribution
 Function recognition and the structural genomics challenge
•
•
•
•
•
Gene sequencing proceeds currently with an exponential rate
Experimental structure determination requires more time, more effort and
more money
In structural genomics initiatives genes are selected for protein structure
determination for their involvement in functional pathways (cancer and other
pathologies) or for their functional role in pathogens but often without
knowledge of their precise catalytic activity
In silico structural genomics can give valuable structural informations
– GRID computing coupled with modeling software (Rosetta in our case)
allows the prediction of the protein structure of entire genomes
Function recognition software tools can help to identify the catalytic activity
and provide a starting point for drug design
– Identification of the function of modelled structures
– Tool for experimental structural genomics initiatives
FP6−2004−Infrastructures−6-SSA-026024
Participants
Partners
Nuovi Partners:
Bibliotheca Alexandrina (Egypt)
CIEHAM-MAIB (Italy)
JUNet (Jordan)
INFN (Italy) Coordinator
CERN (Switzerland)
CYNET (Cyprus)
DANTE (UK)
GARR (Italy)
GRNET (Greece)
RED.ES (Spain)
CIEMAT
University of Malta (Malta)
CERIST (Algeria)
CNRST (Morocco)
EUN (Egypt)
HIAST (Syria)
MRSTDC (Tunisia)
TUBITAK-ULAKBIM (Turkey)
University of Tunis
FP6−2004−Infrastructures−6-SSA-026024
The EUMEDGRID e-Infrastructure
INFN - CNAF
INFN -Roma3
CYNET
INFN -Catania
MA-GRID
ULAKBIM
Un. of Tunis
GRNET
Un. of Malta
ERI
IUCC
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Monitoring
The “spread” of Knowledge:
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geo-distribution of training
events
2
2
2
1
2
1
2
1
1
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Already Deployed
Applications
 CODESA-3D (Earth Science)
• It is a three-dimensional finite element simulator for
coupled flow and density dependent transport in
variably saturated porous media.
• Requires data from: Geology, Topography,
Meteorology, Water extraction, Aquifer properties, Soil
maps, Land use.
 ArchaeoGrid (Multi-disciplinar)
• Paleoclimate simulation (with modern tools like MM5)
• Aims at studying the origin of the City in the
Mediterranean Region between X-VIII Centuries B.C.
Grid-enabled Subsurface
Hydrology application in the
Mediterranean area
FP6−2004−Infrastructures−6-SSA-026024
 Sustainable management of groundwater exploitation using
Monte Carlo simulation of seawater intrusion in the Korba
aquifer (Tunisia).
 Seawater intrusion in the aquifer is a very severe problem in
some of the coastal zones of the Med Area.
 Data requirement
Geology
 Topography
 Meteorology
 Water extraction by the farmer
 Aquifer properties
 Soil maps
 Land use

A
A'
Korba
FP6−2004−Infrastructures−6-SSA-026024
New activities
 Usage of sensors (from GRIDCC)
 Earth Science applications for:
• Atmospheric and Oceanic Fluid Dynamics and Climate
Change
• Solid Earth Physics
 Usage of Grids and sensors for Agriculture and Water
Management (CIAHAM-MAIB) Ist. Agron. Medit. Bari
 Interoperability of gLite with other MW used in the area.
FP6−2004−Infrastructures−6-SSA-026024
BioMed Applications
 EUMEDGRID supported the WISDOM data
challenge on it’s infrastructure.
 WISDOM is an initiative for Grid-enabled drug
discovery against neglected and emergent
diseases, using GRIDs for in Silico Drug
discovery.
 Simulation of docking of compounds on
proteins.
[Empowering eScience across the Mediterranean]
Archaeology on EUMEDGRID:
the ArchaeoGRID project
ArchaeoGRID Group in Florence
Roberto Cecchini, INFN, Florence
Giuliano Pelfer, CSDC, University of Florence
Pier Giovanni Pelfer, University of Florence and INFN
Antonio Politi , CSDS, University of Florence and ISC-CNR, Florence
Alessandro Torcini, CSDS, University of Florence, ISC-CNR and INFN, Florence
FP6−2004−Infrastructures−6-SSA-026024
General Questions and
Goals of the Modern
Archaeology
FP6−2004−Infrastructures−6-SSA-026024
Modern Archaeology is requested to answer at new
general questions and to achieve new goals
• It is a common and well founded opinion between scientists that at least
during Holocene, the last 10000 years, the human-environment systems
have been intimately linked
• Current earth system changes, strongly associated with the present and past
changes in the coupled human-environment system, make the integration of
archaeology and earth system history an important step in understanding the
factors leading to global change.
• The past is the only one laboratory we have to test our hypotesis and models
• A new goal of the Archaeology is therefore to understand the origin, growth
and collapse processes of past societies and how the interactions of the
environmental and human processes over the last ten millennia have
contributed to determine such human and environmental dynamics.
25
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Archaeology of the
Mediterranean Region
 The Mediterranean is one of the most studied regions on Earth.
Over some 10,000 years, environmental, archaeological, written
historical and instrumental data testify to the complex
interactions between the atmosphere, the geosphere, the
biosphere and a range of successive societies.
 The basin has been studied at different scales, from the local to
the sub–regional to the regional, and by researchers in
disciplines ranging from atmospheric studies to tectonics,
geomorphology, biology, economics, and various social
sciences to history and geography.
 Moreover, the area has been the theater of the emergence as
well as the collapse of a number of social systems of various
sizes and forms. It is therefore an ideal area to do a case study
based on multi-scalar, multi-disciplinary different kinds of data.
26
FP6−2004−Infrastructures−6-SSA-026024
The Mediterranean Region at the end of Urban Revolution
The Mediterranean Basin, between 3100 and 2700 Years B.P., started as a Global Trade and
Market Area. PHOENICIANS for the first, ETRUSCANS, GREEKS for the last promoted this change.
Urban Centers grew and previous spread Villages disappeared in few tenths of years.
27
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The ArchaeoGRID System
a Laboratory of Past
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FP6−2004−Infrastructures−6-SSA-026024
ArchaeoGRID Objectives
 The structure of ArchaeoGRID Laboratory of the
Past is set up for the following objectives:
• RECONSTRUCTION OF SOCIAL, ECOLOGICAL AND
ECONOMICAL LANDSCAPE of crucial historical periods
and for
large geographical regions,
using
archaeological, geological, biological and ecological and
any other useful and available data.
• SIMULATION WITH MODELS FROM THE THEORY OF
COMPLEXITY of social, ecological and economical
processes dynamics.
• VALIDATION
of
the
simulated
processes
by
reconstructed landscape in a holistic top to bottom
approach
• NARRATION by the realization of a FINAL DIGITAL
DOCUMENT with a DIGITAL LIBRARY
29
FP6−2004−Infrastructures−6-SSA-026024
Applications on EUMEDGRID:
Paleoclimate
 Paleoclimate Evaluation by Community Climate Models:
MM5/WRF and Stochastic Weather Generators
8 km
Climate Evaluation by MM5 Mesoscale Model
30
CCSM,
FP6−2004−Infrastructures−6-SSA-026024
Applications on EUMEDGRID:
Paleoenvironment
 Paleoenvironment (DTM, Hydrology, Land Cover, etc)
Map
of Erosion Classes on the DTM for Geomorphological Evolution Study
31
FP6−2004−Infrastructures−6-SSA-026024
Applications
on EUMEDGRID:
Archaeological Land
Evaluation
 Archaeological
Land Evaluation
(Soils, Crops,
Agriculture
Techniques, etc.)
by following the
rules of the FAO
applied to Ancient
Land.
Soils Suitability Map for Cereals Cultivation
32
FP6−2004−Infrastructures−6-SSA-026024
Applications on EUMEDGRID:
ArchaeoGIS
 ArchaeoGIS (ArchaeoGIS Portal: Aerial and Satellite Images,
Cartographic Base, Historical Maps, Written Sources, etc)
QGIS/GRASS
GIS
QGIS/GRASS GIS
Web-Based
Mapserver
Mapserver
Making data accessible
via Web Services.
Fully Integrated
Open-Source
ArchaeoGIS
ArchaeoGIS Portal
R-Statistics
GMT
Adding the analytical
tools for Statistical
and Spatial Analysis
33
DBMI
PostgreSQL
Oracle
MySQL
Adding DataBase access
Fusion of Aerial/Satellite Data with
Geophysical Maps
FP6−2004−Infrastructures−6-SSA-026024
ArchaeoGRID Community in
EUMEDGrid
 Present ArchaeoGRID Community in EUMEDGRID-2:
• GREECE: IMS-FORTH, Crete;
• ITALY: INFN-Florence; ISC-CNR-Florence; CSDCUniversity of Florence;
• MALTA: University of Malta;
• MOROCCO: CNRST, Rabat;
• PALESTINE: An-najah University, Nablus;
• SPAIN: UPM, Madrid; USAL, Salamanca;
• TURKEY: ITU and TAY, Instanbul
34
Conclusioni
• EUChinaGRID e EUMEDGRID stanno promuovendo
l’uso di Grid nelle aree geografiche di interesse.
• EUChinaGRID ha un peso tecnico maggiore (IPv6,
Interoperabilità).
• EUMEDGRID è molto focalizzato sulla diffusione della
tecnologia, la creazione di infrastrutture nazionali e
nella collaborazione scientifica nell’area
mediterranea.
• EUChinaGRID ed EUMEDGRID proporranno una
continuazione nella call del 20 settembre.
• Il campo delle applicazioni si sta allargando.