ISGC’2007, Taipei, Grid Computing Program at Peking University in EUChinaGRID Project

S. Qian PKU program in EUChinaGRID project 2 ISGC’2007, Taipei, 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

S. Qian PKU program in EUChinaGRID project 3 ISGC’2007, Taipei, EUChinaGRID Project 欧中网格项目 (More details will be presented by Dr. Giuseppe ANDRONICO tomorrow)

S. Qian PKU program in EUChinaGRID project 4 ISGC’2007, Taipei, Project Banner Interconnection and Interoperability of Grids between Europe and China

S. Qian PKU program in EUChinaGRID project 5 ISGC’2007, Taipei, Timescale & Budget The official start of the project: 1st January Duration: 24 Months EU Contribution: 1,299,998 €. A total 495 Person Months (325 Funded) of effort

S. Qian PKU program in EUChinaGRID project 6 ISGC’2007, Taipei, Partners 1 Istituto Nazionale di Fisica Nucleare (IT) (coordinator) 2European Organisation for Nuclear Research (CERN) (CH) 3Università di Roma Tre, Dipartimento di Biologia – Rome (IT) 4Consortium GARR (IT) 5Greek Research & Technology Network (GR) 6Jagiellonian University, Medical College – Cracow (PL) 7School of Computer Science and Engineering – Beihang University – Beijing (CN) 8Computer Network Information Center, Chinese Academy of Sciences (CAS) – Beijing (CN) 9Institute of High Energy Physics, CAS – Beijing (CN) 10Peking University – Beijing (CN)

S. Qian PKU program in EUChinaGRID project 7 ISGC’2007, Taipei, Third Parties 1Academia Sinica Grid Computing Centre (ASGC) – Taipei 2Università di Roma Tre, Dipartimento di Fisica – Rome (IT)

S. Qian PKU program in EUChinaGRID project 8 ISGC’2007, Taipei, 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)

S. Qian PKU program in EUChinaGRID project 9 ISGC’2007, Taipei, WPs (Working Packages)

S. Qian PKU program in EUChinaGRID project 10 ISGC’2007, Taipei, Work Breakdown Structures WPName 1Project Administrative and technical management （项目行政和技术管理） 2Network planning and interoperability study （网络规划与互操作研究 ） 3Pilot 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

S. Qian PKU program in EUChinaGRID project 11 ISGC’2007, Taipei, Collaborative tools

S. Qian PKU program in EUChinaGRID project 12 ISGC’2007, Taipei, Project Web Sites and (English) (Chinese 中文 )

S. Qian PKU program in EUChinaGRID project 13 ISGC’2007, Taipei, Infrastructure 基础设施

S. Qian PKU program in EUChinaGRID project 14 ISGC’2007, Taipei, RB (Resource Broker) + BDII (Berkely Database Information Index) at CNAF (Italy) VOMS at CNAF 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

S. Qian PKU program in EUChinaGRID project 15 ISGC’2007, Taipei, Sites Map

S. Qian PKU program in EUChinaGRID project 16 ISGC’2007, Taipei, Sites Monitoring BEIJING - PKU

S. Qian PKU program in EUChinaGRID project 17 ISGC’2007, Taipei, )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 1 st Workshop in Beijing, China (done) 4)September 15-22, 2006 in Rome, Italy + Project’s 1 st 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

S. Qian PKU program in EUChinaGRID project 18 ISGC’2007, Taipei, Peking University in EUChinaGRID Project

S. Qian PKU program in EUChinaGRID project 19 ISGC’2007, Taipei, 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

S. Qian PKU program in EUChinaGRID project 20 ISGC’2007, Taipei, Biology Group

S. Qian PKU program in EUChinaGRID project 21 ISGC’2007, Taipei, Beijing N uclear M agnetic R esonance 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.

S. Qian PKU program in EUChinaGRID project 22 ISGC’2007, Taipei,  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

S. Qian PKU program in EUChinaGRID project 23 ISGC’2007, Taipei, NMR Structure Determination

S. Qian PKU program in EUChinaGRID project 24 ISGC’2007, Taipei, From Constraints to Structure Restrained molecular dynamics and simulated annealing

S. Qian PKU program in EUChinaGRID project 25 ISGC’2007, Taipei, V = E empirical + E effective with: E effective = E NOE + E torsion and E empirical = E bond + E angle + E dihedral + E vdw + E electr 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

S. Qian PKU program in EUChinaGRID project 26 ISGC’2007, Taipei, Energy Minimization

S. Qian PKU program in EUChinaGRID project 27 ISGC’2007, Taipei, Structure Calculation and Refinement Normally, 200 structures/round, > 30 rounds.

S. Qian PKU program in EUChinaGRID project 28 ISGC’2007, Taipei, Recent Structures 1Z6H 2AI6 1Z7P 2FHM 2HF6 2B9K

S. Qian PKU program in EUChinaGRID project 29 ISGC’2007, Taipei, 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.

S. Qian PKU program in EUChinaGRID project 30 ISGC’2007, Taipei, PKU-Biology Computing 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

S. Qian PKU program in EUChinaGRID project 31 ISGC’2007, Taipei, Physics Group

S. Qian PKU program in EUChinaGRID project 32 ISGC’2007, Taipei, 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:

S. Qian PKU program in EUChinaGRID project 33 ISGC’2007, Taipei, L HC C omputing G rid Model physics group regional group Tier2 Lab a Uni a Lab c Uni n Lab m Lab b Uni b Uni y Uni x Tier3 physics department    Desktop Germany Tier 1 USA UK France Italy ………. CERN Tier 1 ………. The LHC Computing Centre CERN Tier 0

S. Qian PKU program in EUChinaGRID project 34 ISGC’2007, Taipei, LCG Architecture at PKU Installed at PKU (UI) (SE) (CE) (WN) (SE) Installed at PKU (UI)

S. Qian PKU program in EUChinaGRID project 35 ISGC’2007, Taipei, 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 B 0s  J/  +  events from a DST (Data Summary Tapes) at CERN in 8/2005 Analyzed nearly 200,000 B 0s 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

S. Qian PKU program in EUChinaGRID project 36 ISGC’2007, Taipei, Procedure of Grid Application The latest procedure via the IHEP LCG Tier-2 facility: PKU’s UI gets the results from submit the jobs IHEP’s RB run the jobs, send the jobs to CE return the results to IHEP’s RB give the jobs to WN UI (User China RB (Resource China CE (Computing Italy WN (Work Italy

S. Qian PKU program in EUChinaGRID project 37 ISGC’2007, Taipei, Sample Result J/psi reconstruction efficiency as a function of PT (both muons’ |eta|<=2.4) J/  reconstruction efficiency in CMS experiment

S. Qian PKU program in EUChinaGRID project 38 ISGC’2007, Taipei, First CMS Analysis Note by Peking Univ. Group

S. Qian PKU program in EUChinaGRID project 39 ISGC’2007, Taipei, 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

S. Qian PKU program in EUChinaGRID project 40 ISGC’2007, Taipei, 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.

S. Qian PKU program in EUChinaGRID project 41 ISGC’2007, Taipei, 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)

S. Qian PKU program in EUChinaGRID project 42 ISGC’2007, Taipei, 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 Yuan/month, unlimited traffic, but disconnected every few hours if no activities Server gateway -- no interruption, but charged by bits

S. Qian PKU program in EUChinaGRID project 43 ISGC’2007, Taipei, Solutions Use the domestic gateway to connect to IHEP via VPN (V irtual P rivate N etwork ), 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.

S. Qian PKU program in EUChinaGRID project 44 ISGC’2007, Taipei, Network Topology Map The improved route (TEIN2): will upgrade to 2.5 Gbps The backup route

S. Qian PKU program in EUChinaGRID project 45 ISGC’2007, Taipei, 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.

S. Qian PKU program in EUChinaGRID project 46 ISGC’2007, Taipei, Thank you ( 謝謝 ) ！