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Grid Computing Program at Peking University in EUChinaGRID Project

Grid Computing Program at Peking University in EUChinaGRID Project. 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

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Grid Computing Program at Peking University in EUChinaGRID Project

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  1. Grid Computing Program at Peking University in EUChinaGRID Project

  2. 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. 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. Project Banner Interconnection and Interoperability of Grids between Europe and China S. Qian PKU program in EUChinaGRID project

  5. 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 S. Qian PKU program in EUChinaGRID project

  6. Partners S. Qian PKU program in EUChinaGRID project

  7. Third Parties S. Qian PKU program in EUChinaGRID project

  8. 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. WPs (Working Packages) S. Qian PKU program in EUChinaGRID project

  10. Work Breakdown Structures S. Qian PKU program in EUChinaGRID project

  11. Collaborative tools S. Qian PKU program in EUChinaGRID project

  12. Project Web Sites www.euchinagrid.eu and www.euchinagrid.cn (English) (Chinese中文) S. Qian PKU program in EUChinaGRID project

  13. Infrastructure基础设施 S. Qian PKU program in EUChinaGRID project

  14. What we have already done • 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) S. Qian PKU program in EUChinaGRID project

  15. Sites Map S. Qian PKU program in EUChinaGRID project

  16. Sites Monitoring BEIJING - PKU S. Qian PKU program in EUChinaGRID project

  17. Training Program • April 3-7, 2006 in Beijing, China (done) • April 18-21, 2006 in Rome, Italy (done) • June 12-16, 2006 at IHEP + Project’s 1st Workshop in Beijing, China (done) • September 15-22, 2006 in Rome, Italy + Project’s 1st Conference (done) • November 25-26, 2006 at Peking University (done). All Chinese tutors in first time. • April 16-20, 2007 at CNIC, Beijing, China S. Qian PKU program in EUChinaGRID project

  18. Peking University in EUChinaGRID Project S. Qian PKU program in EUChinaGRID project

  19. 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 inWP5 S. Qian PKU program in EUChinaGRID project

  20. Biology Group S. Qian PKU program in EUChinaGRID project

  21. 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. S. Qian PKU program in EUChinaGRID project

  22. NMR Spectroscopy • 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 S. Qian PKU program in EUChinaGRID project

  23. NMR Structure Determination S. Qian PKU program in EUChinaGRID project

  24. From Constraints to Structure Restrained molecular dynamics and simulated annealing S. Qian PKU program in EUChinaGRID project

  25. Force Field 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. S. Qian PKU program in EUChinaGRID project

  26. Energy Minimization S. Qian PKU program in EUChinaGRID project

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

  28. 2AI6 1Z6H 1Z7P 2B9K 2HF6 2FHM Recent Structures S. Qian PKU program in EUChinaGRID project

  29. 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. 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. Physics Group S. Qian PKU program in EUChinaGRID project

  32. 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 LHC completion date: 2007.11 27 km circumference S. Qian PKU program in EUChinaGRID project

  33. Lab m Uni x regional group CERN Tier 1 Uni a UK USA Lab a France The LHC Computing Centre Tier 1 Tier3 physics department Uni n Tier2 ………. Italy CERN Tier 0 Desktop Lab b Germany ………. Lab c  Uni y Uni b physics group   LHCComputingGrid Model les.robertson@cern.ch S. Qian PKU program in EUChinaGRID project

  34. LCG Architecture at PKU Installed at PKU Installed at PKU (SE) (SE) (UI) (CE) (UI) (CE) @IHEP (WN) S. Qian PKU program in EUChinaGRID project

  35. Working History • Single J/y  m+m-generation (without background) and reconstruction by using local computers in 6/2005 • Single J/y study with min-biased background in 7/2005 • Analyzed 500 B0s J/y + f events from a DST (Data Summary Tapes) at CERN in 8/2005 • Analyzed nearly 200,000 B0sevents from a DST stored in Italy by using Computing Grid tools from 9/2005 and going on • Preparing the massive (> 2 millions J/y events) Monte-Carlo simulation S. Qian PKU program in EUChinaGRID project

  36. 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 Interface)@PKU, China RB (Resource Broker)@IHEP, China CE (Computing Element)@CNAF, Italy WN (Work Nodes)@CNAF, Italy S. Qian PKU program in EUChinaGRID project

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

  38. First CMS Analysis Note by Peking Univ. Group S. Qian PKU program in EUChinaGRID project

  39. 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. 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/y 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. Main Problems • Availability of biological software (Amber) • Licensing • Stability of CMS software (CMSSW) • the suitable J/y 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. 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 S. Qian PKU program in EUChinaGRID project

  43. 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. S. Qian PKU program in EUChinaGRID project

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

  45. 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. Thank you (謝謝)！ S. Qian PKU program in EUChinaGRID project

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