Ya-ning Arthur Chen, Feng-chien Chung Computing Centre, Academia Sinica 11 April, ISGC 2008
ISGC’2007, Taipei, 28-3-2007 Grid Computing Program at Peking University in EUChinaGRID Project.
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Transcript of ISGC’2007, Taipei, 28-3-2007 Grid Computing Program at Peking University in EUChinaGRID Project.
ISGC’2007, Taipei, 28-3-2007
Grid Computing Program at Peking University
in EUChinaGRID Project
S. Qian PKU program in EUChinaGRID project 2
ISGC’2007, Taipei, 28-3-2007
Outline• EUChinaGRID project and PKU group
• Grid infrastructure at PKU (School of Physics)
• WP4 (for Grid application) activities at PKU – Biology subgroup: Protein structure analysis
– Physics subgroup: CMS Monte-Carlo simulation and physics analysis
• Main problems and solutions– Networking
– Software installation at Grid sites
• Summary
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EUChinaGRID Project
欧中网格项目(More details will be presented by
Dr. Giuseppe ANDRONICO tomorrow)
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Project Banner
Interconnection and
Interoperability of Grids
between Europe and
China
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Timescale & Budget
• The official start of the project: 1st January 2006.
• Duration: 24 Months
• EU Contribution: 1,299,998 €.
• A total 495 Person Months (325 Funded) of effort
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Partners1 Istituto Nazionale di Fisica Nucleare (IT) (coordinator)2 European Organisation for Nuclear Research (CERN) (CH)
3 Università di Roma Tre, Dipartimento di Biologia – Rome (IT)
4 Consortium GARR (IT)
5 Greek Research & Technology Network (GR)
6 Jagiellonian University, Medical College – Cracow (PL)
7 School of Computer Science and Engineering – Beihang University – Beijing (CN)
8 Computer Network Information Center, Chinese Academy of Sciences (CAS) – Beijing (CN)
9 Institute of High Energy Physics, CAS – Beijing (CN)
10 Peking University – Beijing (CN)
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Third Parties
1 Academia Sinica Grid Computing Centre (ASGC) – Taipei
2 Università di Roma Tre, Dipartimento di Fisica – Rome (IT)
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Targets of the Project
• To foster the creation of a intercontinental eScience community– Training people– Supporting existing and new applications
• To support interoperable infrastructure for grid operations between Europe (EGEE) and China (CNGRID)
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WPs (Working Packages)
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Work Breakdown Structures
WP Name
1 Project Administrative and technical management (项目行政和技术管理)
2 Network planning and interoperability study (网络规划与互操作研究 )
3 Pilot infrastructure operational support (示范基础设施的运作支持 )
PKU
4 Applications (应用) PKU
5 Dissemination (宣传推广) PKU
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Collaborative tools
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Project Web Siteswww.euchinagrid.eu and
www.euchinagrid.cn
(English) (Chinese 中文 )
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Infrastructure基础设施
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• RB (Resource Broker) + BDII (Berkely Database Information Index) at CNAF (Italy)
• VOMS at CNAF https://voms2.cnaf.infn.it:8443/voms/euchina/
• GridIce ( Grid sites monitoring ) at CNAF• Sites linked:
– Roma 3 (Italy)– CNAF (Italy)– Catania (Italy)– Athens (Greece)– 3 sites in Beijing (CNIC, IHEP and PKU)
What we have already done
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Sites Map
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Sites Monitoring
BEIJING - PKU
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1) April 3-7, 2006 in Beijing, China (done)
2) April 18-21, 2006 in Rome, Italy (done)
3) June 12-16, 2006 at IHEP + Project’s 1st Workshop in Beijing, China (done)
4) September 15-22, 2006 in Rome, Italy + Project’s 1st Conference (done)
5) November 25-26, 2006 at Peking University (done). All Chinese tutors in first time.
6) April 16-20, 2007 at CNIC, Beijing, China
Training Program
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Peking University in
EUChinaGRID Project
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Subgroups & Personnel
• Biological Research – Protein structure study with NMR (led by Prof. B. XIA ,夏滨 )– C. JIN, Y. FENG, W. GONG, X. GUO, T. WANG.
– To participate in WP4 (4.3)
• High Energy Physics Research – CMS experiment on LHC at CERN (led by Prof. S. QIAN ,钱思进 )– Z. YANG, L. ZHAO, D. MU, S. ZHU, K. KANG
– To participate in WP4 (4.1) and WP3
• Also, both groups are working in WP5
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Biology Group
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Beijing NuclearMagneticResonance Center
Sponsored by Ministry of Science and Technology, Ministry of Education, Chinese Academy of Science, Chinese Academy of Military Medical Sciences, Managed by Peking University.
National NMR facility established on Nov. 4th, 2002 For research and training in bio-molecular NMR
studies We need to use computer for processing and
analyzing NMR data, for solution structure calculation, and for molecular dynamic simulation.
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Key method for obtaining high resolution structure
-----in addition to X-ray Structure
Physiological temperature and condition -----closer to native functional state
Time consuming for structure calculation -----multiple structures and multiple rounds
NMR Spectroscopy
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NMR Structure Determination
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From Constraints to Structure
Restrained molecular dynamics and simulated annealing
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V = Eempirical + Eeffective
with:
Eeffective = ENOE + Etorsion
and Eempirical = Ebond + Eangle + Edihedral + Evdw + Eelectr
• Empirical energy contains all information about the primary structure of the protein and also data about topology and bonds in proteins in general.
• Empirical energy are from experimental data.
Force Field
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Energy Minimization
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Structure Calculation and Refinement
Normally, 200 structures/round, > 30 rounds.
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Recent Structures
1Z6H 2AI61Z7P
2FHM 2HF6 2B9K
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Analysis Software
• Protein structure analysis software: Amber.
• Licenses are needed to be granted on all computers involved.
• University Rome III has procured the license and is testing it, hopefully it can be available for use in near future.
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PKU-BiologyComputing Need
• By using the Intel 2.4 GHz Xeon CPU
• Each structure needs 4 hours
• Each time to compute 200 structures
• Each protein needs to be computed for 10 times
• Totally 10 proteins to be analyzed
~ 80,000 hours (> 9 years) CPU time > 1TB storage space
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Physics Group
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Physics Data Analysis for CMS Experiment
CMS group in the Physics School of Peking University has started to use Grid tools to analyze physics data of CMS experiments on LHC at CERN since 9/2005
Huge amount of Monte-Carlo data (from now on) and real data (collected from the end of 2007) shall await for us to analyze
27 km
circumference
LHC completion
date: 2007.11
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LHCComputingGrid Model
les.
rob
ert
son
@ce
rn.c
h
physics group
regional group
Tier2
Lab aUni a
Lab c
Uni n
Lab m
Lab b
Uni bUni y
Uni x
Tier3physics
department
Desktop
Germany
Tier 1
USAUK
France
Italy
……….
CERN Tier 1
……….
The LHC Computing
Centre CERN Tier 0
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LCG Architecture at PKU
Installed at PKU
(UI)
(SE)
(CE)
(WN)
(SE)
Installed at PKU
(UI) (CE)
@IHEP
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Working History• Single J/generation (without background) and reconstruction
by using local computers in 6/2005
• Single J/ study with min-biased background in 7/2005
• Analyzed 500 B0s J/ + events from a DST (Data Summary Tapes)
at CERN in 8/2005
• Analyzed nearly 200,000 B0s events from a DST stored in Italy by using Computing Grid tools from 9/2005 and going on
• Preparing the massive (> 2 millions J/ events) Monte-Carlo simulation
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Procedure of Grid Application
The latest procedure via the IHEP LCG Tier-2 facility:
PKU’s UI getsthe results from submit the jobsIHEP’s RB
run the jobs, send the jobs to CEreturn the results to
IHEP’s RB give the jobs to WN
UI (User Interface)@PKU, China
RB (Resource Broker)@IHEP, China
CE (Computing Element)@CNAF, Italy
WN (Work Nodes)@CNAF, Italy
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Sample Result
J/psi reconstruction efficiency as a function of PT (both muons’ |eta|<=2.4)
J/
reconstruction efficiency in
CMS
experiment
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First CMS Analysis Note by Peking Univ. Group
CMS Analysis Note 2006-094
J μ μ Reconstruction in CMS
Zongchang YANG, Sijin QIANPeking University, China
April 2006 (Revised in November 2006)
AbstractIn this note the J/ψ → μ μ reconstruction was studied in details by using Bs J/ μ μ KK events. The reconstruction efficiencies of J/ψ and decayed di-muons were obtained at various PT and pseudo-rapidity . We also preliminari ly studied the muon trigger efficiency and the J/ψ reconstruction with default L1 and HLT. It was observed that the muon reconstruction efficiency decreases in the case of two decayed muonswith a small or large 3D angu lar separation, which further affect the J/ψ reconstruction efficiency . In an earlier study with the s imple J/ψ even ts, we obtained the upper limits of efficiency and mass resolution for J /ψ offl ine reconstruction in CMS.
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PKU-Physics Computing Need
• In 2007, we would wish to generate > 2 million events each for prompt J/Psi and Upsilon + 40% of background events
• For each 1 million events, it needs about 24,000 hours (or 1000 days) of CPU time (for
one P4 Xeon 1.5GHz computer), and about 1.1 TB of storage space.
• In result, we would need ~5600 days (i.e. ~ 18 years) of CPU time & ~6 TB of storage space
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Summary of WP3 & WP4 Activities at PKU
• Established a LCG (LHC Computing Grid) Tier-3 site for getting access to the LCG system;
• Used the above system to have analysed a large MC dataset stored at CNAF in Italy, and have produced some analysis results;
• Provided configuration files for CMS collaboration in order to generate >2 million prompt J/ events;
• Installed the CMSSW on EUChinaGrid system (Catania site);
• Preparing the protein structure analysis in Biology group;
• Has estimated the computer and storage resources needed to handle the millions of events for Physics group and to analysis the protein structure in Biology group.
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Main Problems
• Availability of biological software (Amber)– Licensing
• Stability of CMS software (CMSSW)– the suitable J/ event generator is still being tested
by CMS collaboration before to be put in production
– HLT (High Level Trigger) software
• Networking– Bandwidth (international traffic is charged by bits)
– University policy (3 levels of gateway)
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Networking in PKU
• 3 levels of gateway
– Campus network: no charge, only within campus
– Domestic gateway: minor monthly charge, unlimited traffic
– International gateways:
• Monthly package -- 90 Yuan/month, unlimited traffic, but disconnected every few hours if no activities
• Server gateway -- no interruption, but charged by bits
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Solutions
• Use the domestic gateway to connect to IHEP via VPN (Virtual Private Network), then to reach the world through the IHEP’s trunk line.
• Applied and installed the CERNET’s special link to TEIN2. The special cabling was done in 1/2007.
– No charge by bits
– No periodical interruption.
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Network Topology Map
The improved route (TEIN2): will upgrade to 2.5 Gbps
The backup route
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Summary
• PKU group has set up a very basic Grid site for getting access to the LCG system and for preparing the massive biological protein structure analysis.
• By using this system, we have engaged in some CMS physics study and got some encouraging results.
• Some long standing problems of networking have been finally solved with the TEIN2 connection.
• Much more works are to be done, we must– start the protein structure analysis as soon as the software licence
is granted;
– be fully prepared for the CMS data analysis when LHC’s first proton beam collision at the end of 2007.
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Thank you ( 謝謝 ) !