A g USE submitter for Mo SGrid Molecular

A g. USE submitter for Mo. SGrid (Molecular Simulation Grid) Sandra Gesing sandra. gesing@uni-tuebingen. de Eberhard-Karls-Universität Tübingen 27. 08. 2010

Outline • Molecular simulations • Users • Mo. SGrid architecture • g. USE submitter • Future work Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 1

Molecular simulations • Computational techniques • Predicting many useful functional properties of chemicals and materials • Thermodynamic properties • Thermochemical properties • Spectroscopic properties • Mechanical properties • Transport properties • Morphological information • Diverse fields of applications, e. g. drug design Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 2

Molecular simulations http: //www. nmr. chem. uu. nl/haddock 2. 0/movies/cg 1. html Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 3

Users • Sophisticated tools and algorithms available • Scientists with different computational background • Need of self-explanatory and intuitive user interfaces ⇒ Portals Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 4

Unifying diversity 12181 12241 12301 12361 12421 12481 12541 12601 12661 12721 12781 acatttctac cagtctttta gaccatccta gactaattat taggtgactt aggagctatt ttcttataag tggttaagta tggcattaag atccaatacc taacccattt caacagtgga aattttaacc atagatacac gttgagcttg gcctgttttt tatatattct tctgtggttt tacatgacat tacatccaca cattaagctg tctgtctcta tgaggttgtt tttagagaag agtggtgtct ttaccattta ttttaattgg ggatacaagt ttatattaat aaaacggatt atattgtgca tcactcccca tggatttgcc ggtctatgtt agtcatacag cactgtgatt gacaacttca gatcttaatt tctttatcag gtttttattg atcttaacca actatcacca atctcccatt tgttctggat ctcaccaaat tcaatagcct ttaatttgca ttagagaagt tttttaaatt atacacagtt atgactgttt ttttaaaatg ctatcatact ttcccacccc attcatatta ttggtgttgt tttttagctt ttttcctgct gtctaatatt attgatttgt tgtgactatt tttacaattg taaaattcga ccaaaagggc tgacaatcaa atagaatcaa Slide copied from: Stuart Owen „Workflows with Taverna“ Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 5

Mo. SGrid Molecular Simulation Grid (D-Grid project) Goal • Providing users with Grid services for molecular simulation tools and docking via a portal • Implementation of high-performance computing • Workflows • Annotations of results • Data mining • Use of the D-Grid-infrastructure 6

Mo. SGrid - Partners • Universität zu Köln • Eberhard-Karls-Universität Tübingen • Universität Paderborn • Konrad-Zuse-Zentrum für Informationstechnik Berlin • Technische Universität Dresden • Bayer Technology Services Gmb. H, Leverkusen • Origines Gmb. H, Martinsried • GETLIG&TAR, Falkensee • Bio. Solve. IT, Sankt Augustin • COSMOlogic Gmb. H&Co. KG, Leverkusen Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 7

Mo. SGrid - Community 1. Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie 2. International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn 3. Center of Bioinformatics Saar, Universität des Saarlandes 4. Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig 5. Bremen Center for Computational Materials Science, Universität Bremen 6. Universität Münster, Organisch-Chemisches Institut 7. Max-Planck-Institut für biophysikalische Chemie, Göttingen 8. Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel 9. Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Anorganische und Analytische Chemie 10. Department Chemie, Fakultät für Naturwissenschaften, Universität Paderborn 11. Technische Universität Braunschweig, Institut für Organische Chemie 12. Institut für Pharmazeutische Chemie, Universität Marburg 13. Universität Karlsruhe (TH), Institut für Physikalische Chemie 14. Albert-Ludwigs-Universität Freiburg, Institut für Anorganische und Analytische Chemie 15. Max-Planck-Institut für Informatik, Saarbrücken 16. Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum 17. Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn 18. Lehrstuhl für Theoretische Chemie, Universität Bonn 19. Institut für Physikalische und Theoretische Chemie, Universität Tübingen 20. Zentrum für Bioinformatik, Universität Hamburg 21. Lehrstuhl für Biophysik, Ruhr-Universität Bochum 22. Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn 23. Johann Wolfgang Goethe Universität, Fachbereich Chemie 24. Universität Rostock, Institut für Chemie, Abteilung für Anorganische Chemie 25. Humboldt Universität zu Berlin, Institut für Chemie 26. Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg 27. Technische Universität Braunschweig, Institut für Anorganische und Analytische Chemie 28. Zentrum für Bioinformatik, Universität Hamburg 29. Department Chemie, Universität Hamburg 30. Fachbereich Chemie - Theoretische Chemie, Technische Universität Kaiserslautern 31. Fachbereich Angewandte Naturwissenschaften, Fachhochschule Gelsenkirchen 32. Ludwig-Maximilians-Universität München, Department Chemie und Biochemie Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 8

Mo. SGrid Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 9

Mo. SGrid Components • survey about molecular simulation tools ⇒ Gaussian, Gromacs, Flex. X (to start with) • evaluation about portals ⇒ Liferay, WS-PGRADE • evaluation about workflow engines ⇒ UNICORE, WS-PGRADE • evaluation about Grid middlewares ⇒ UNICORE (D-Grid infrastructure GT 4, g. Lite, UNICORE) Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 10

Mo. SGrid Architecture WS-PGRADE portal (integrated workflow editor) Workflow engine Grid middleware Workflow engine (UNICORE 6) Services Batch system Repository Hardware Repository (Xtreem. FS) (local, internet or integrated in a Grid or Cloud infrastructure) Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 11

g. USE submitter Installation of WS-PGRADE portal in Tübingen • added own VO bw. GRi. D • submission to GT 4 ⇒ extension of existing documentation Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 12

g. USE submitter Available information at the beginning • József’s presentation about experiences with implementing a g. USE submitter • source code of the BES interface for P-GRADE in G 3 Bridge • source code of a BES submitter for g. USE (not working) • WS-PGRADE installation (without source code) ⇒ Start to implement BES submitter Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 13

g. USE submitter In order to test your submitter, you need 1. jdk 1. 6 [on the testing machine] 2. tomcat [on the testing machine] 3. g. USE jar files for submitter [on the testing machine] 4. your own developed submitter jar file [on the testing machine] 5. appropriate configuration of your submitter [on the testing machine] 6. accessing an existing and running g. USE/WS-PGRADE 7. configuring g. USE/WS-PGRADE to use your submitter For getting 1: download it from java. sun. com For getting 2, 3, 5: g. USE developers can provide a prepared “submitter package”, only a few parameters must be configured by yourself For getting 6: get an account from the portal operators For getting 7: ask the portal operators to add your submitter to g. USE Slide copied from József‘s presentation Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 14

g. USE submitter Creation of the environment under pgportal/tomcat/webapps/submitter_BES • copy submitter_local • edit of - server-config. wsdd - web. xml - service. properties - service. xml - init. jsp • Grid. Service interface • Job. Config class • implement Grid_BES Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 15

Grid. Service interface package hu. sztaki. lpds. submitter. grids. inf; public interface Grid. Service { public void action. Job. Submit(String p. Path, Job. Config p. JC, Submitter. Portal. Client p. Proxy); public void action. Job. Abort(); public void action. Job. Output(); public int action. Job. Status(); public String action. Job. Resource(); public void action. Set. Job. Status(int p. Value); public void action. Set. Job. Resource(String p. Value); public void set. Runner. Id(String p. Value); } Slide copied from József‘s presentation Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 16

Job. Config class • Job. Config stores 3 hash tables – “Job”, “Input” and “Output” properties • Job properties table stores property-value pairs, where – “property” is one of the job properties – “value” is a string associated to the property – “property” “value” • e. g. : “params” ”-i input 1. inp -o out 1” • e. g. : “resource” “ares 02. cyf-kr. edu. pl” • Input and Output tables store key-property-value triples, where – – “key” is the name of a job port “property” is the name the property “value” is a string associated to the property (“key”, ”property”) (“value”) • e. g. : (“INPORT 1”, ”intname”) (”input 1. inp”) • e. g. : (“OUTPORT 1”, ”intname”) (”out 1”) • The list of properties can be found at: http: //wiki. sztaki. hu/lpds/index. php/T%C 3%A 1 tolt_adatok Slide copied from József‘s presentation Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 17

g. USE submitter Use of source code of the provided BES submitter • source code of Grid. Service and Job. Config included • first compilations of Grid_BES with the result of null pointer exceptions ⇒ Grid. Service and Job. Config not up-to-date any more ⇒ import both classes from the WS-PGRADE installation as jar-files Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 18

g. USE submitter Use of source code of the provided BES interface for P-GRADE • in G 3 Bridge much more information included than the certificate, e. g. ftp user • using similar methods for BES submitter but different protocol (BFT) ⇒ need to know: The list of properties can be found at: http: //wiki. sztaki. hu/lpds/index. php/T%C 3%A 1 tolt_adatok (Hungarian comments but with examples) Java doc (Hungarian) Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 19

g. USE submitter Some drawbacks occured… • my portal server was moved and not reachable for three days • needed four days to get access to a working UNICORE 6 installation • bug in the BES-UNICORE-interface for other protocols than ftp ⇒ started to implement submitter_unicore • Job. Config. class in WS-PGRADE installation not up-to-date ⇒ needed source code of Job. Config. java Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 20

g. USE submitter_unicore Current version • setup security (at the moment my certificate) • create UNICORE registry client • find an appropriate target system • create the job and submit it to the target system • upload executable and input files into the job directory (Uspace) • start the job • download output files (Uspace) Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 21

g. USE submitter_unicore Current status • jobs can be started • UNICORE returns status SUCCESSFUL • output is empty Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 22

g. USE submitter_unicore Next steps • fix the bug with the output • add SAML security • add generator availability • add possibility to submit UNICORE workflows Last but not least • English Java doc • English manual Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 23

Future work • user-friendly parameter-sweeps • choosing of executables without uploading • reporting of intermediate results • input / output masks for executables • data management (upload, local, global) • repository of molecules and recipes • restrictions on distributing tasks (dependent on location of the data) • conversion of UNICORE workflows to WSPGRADE workflows Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 24

Mo. SGrid timeline 13. -14. 09. 2010 Mo. SGrid Meeting (presentation of submitter) 07. -09. 11. 2010 6. German Conference on Chemoinformatics http: //www. gdch. de/vas/tagungen/tg/5412__e. htm (Mo. SGrid will be introduced with link to a demonstration of the portal; later the link will redirect to the „real“ portal) 01. 12. 2010 Portal-Prototype with workflow infrastructure for user community 01. 05. 2011 Portal-Prototype with access to molecule data repository (beta-tester) 01. 12. 2011 Portal-Prototype with data repository and workflow infrastructure for user community 01. 06. 2012 Portal will be released 30. 08. 2012 End of project Mo. SGrid Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 25

Thank you for your attention. Sandra Gesing - A g. USE submitter for Mo. SGrid – 27. 08. 2010 26