A gUSE submitter for MoSGrid (Molecular Simulation Grid)

1. A gUSE submitter forMoSGrid (Molecular Simulation Grid) Sandra Gesing sandra.gesing@uni-tuebingen.de Eberhard-Karls-Universität Tübingen 27.08.2010

2. Outline • Molecular simulations • Users • MoSGrid • MoSGrid architecture • gUSE submitter • Future work Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

3. 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 gUSE submitter forMoSGrid – 27.08.2010

4. Molecular simulations http://www.nmr.chem.uu.nl/haddock2.0/movies/cg1.html Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

5. Users • Sophisticated tools and algorithms available • Scientists with different computational background • Need of self-explanatory and intuitive user interfaces • ⇒ Portals Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

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7. MoSGrid • 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

8. MoSGrid - Partners • Universität zu Köln • Eberhard-Karls-Universität Tübingen • Universität Paderborn • Konrad-Zuse-Zentrum für Informationstechnik Berlin • Technische Universität Dresden • Bayer Technology Services GmbH, Leverkusen • Origines GmbH, Martinsried • GETLIG&TAR, Falkensee • BioSolveIT, Sankt Augustin • COSMOlogic GmbH&Co. KG, Leverkusen Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

9. MoSGrid - Community Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn Center of Bioinformatics Saar, Universität des Saarlandes Institut für Physikalische und Theoretische Chemie,Technische Universität Braunschweig Bremen Center for Computational Materials Science, Universität Bremen Universität Münster, Organisch-Chemisches Institut Max-Planck-Institut für biophysikalische Chemie,Göttingen Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel Johann Wolfgang Goethe-Universität Frankfurt am Main,Institut für Anorganische und Analytische Chemie Department Chemie, Fakultät für Naturwissenschaften,Universität Paderborn Technische Universität Braunschweig, Institut für Organische Chemie Institut für Pharmazeutische Chemie, Universität Marburg Universität Karlsruhe (TH), Institut für Physikalische Chemie Albert-Ludwigs-Universität Freiburg, Institut für Anorganische und Analytische Chemie Max-Planck-Institut für Informatik, Saarbrücken Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn Lehrstuhl für Theoretische Chemie, Universität Bonn Institut für Physikalische und Theoretische Chemie, Universität Tübingen Zentrum für Bioinformatik, Universität Hamburg Lehrstuhl für Biophysik, Ruhr-Universität Bochum Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn Johann Wolfgang Goethe Universität, Fachbereich Chemie Universität Rostock, Institut für Chemie, Abteilung für Anorganische Chemie Humboldt Universität zu Berlin, Institut für Chemie Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg Technische Universität Braunschweig, Institut für Anorganische und Analytische Chemie Zentrum für Bioinformatik, Universität Hamburg Department Chemie, Universität Hamburg Fachbereich Chemie - Theoretische Chemie, Technische Universität Kaiserslautern Fachbereich Angewandte Naturwissenschaften, Fachhochschule Gelsenkirchen Ludwig-Maximilians-Universität München, Department Chemie und Biochemie Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

10. MoSGrid Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

11. MoSGrid Components • survey about molecular simulation tools ⇒ Gaussian, Gromacs, FlexX (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, gLite, UNICORE) Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

12. MoSGrid Architecture WS-PGRADE portal (integrated workflow editor) Workflow engine Repository Grid middleware Workflow engine (UNICORE 6) Services Repository (XtreemFS) Hardware (local, internet or integrated in a Grid or Cloud infrastructure) Batch system Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

13. gUSE submitter • Installation of WS-PGRADE portal in Tübingen • added own VO bwGRiD • submission to GT 4 ⇒ extension of existing documentation Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

14. gUSE submitter • Available information at the beginning • József’s presentation about experiences with implementing a gUSE submitter • source code of the BES interface for P-GRADE in G3Bridge • source code of a BES submitter for gUSE (not working) • WS-PGRADE installation (without source code) • ⇒ Start to implement BES submitter Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

15. gUSE submitter • In order to test your submitter, you need • jdk 1.6 [on the testing machine] • tomcat [on the testing machine] • gUSE jar files for submitter [on the testing machine] • your own developed submitter jar file [on the testing machine] • appropriate configuration of your submitter [on the testing machine] • accessing an existing and running gUSE/WS-PGRADE • configuring gUSE/WS-PGRADE to use your submitter • For getting 1: download it from java.sun.com • For getting 2,3,5: gUSE 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 gUSE Slide copied from József‘s presentation Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

16. gUSE submitter • Creation of the environment under pgportal/tomcat/webapps/submitter/submitter_BES • copy submitter_local • edit of • server-config.wsdd • web.xml • service.properties • service.xml • init.jsp • GridService interface • JobConfig class • implement Grid_BES Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

17. GridService interface package hu.sztaki.lpds.submitter.grids.inf; public interface GridService { public void actionJobSubmit(String pPath,JobConfig pJC, SubmitterPortalClient pProxy); public void actionJobAbort(); public void actionJobOutput(); public intactionJobStatus(); public StringactionJobResource(); public voidactionSetJobStatus(intpValue); public voidactionSetJobResource(String pValue); public void setRunnerId(String pValue); } Slide copied from József‘s presentation Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

18. JobConfig class • JobConfig 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 input1.inp -o out1” • e.g.: “resource”  “ares02.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.: (“INPORT1”,”intname”)  (”input1.inp”) • e.g.: (“OUTPORT1”,”intname”)  (”out1”) • The list of properties can be found at: http://wiki.sztaki.hu/lpds/index.php/T%C3%A1tolt_adatok Slide copied from József‘s presentation Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

19. gUSE submitter • Use of source code of the provided BES submitter • source code of GridService and JobConfig included • first compilations of Grid_BES with the result of null pointer exceptions • ⇒ GridService and JobConfig not up-to-date any more • ⇒ import both classes from the WS-PGRADE installation as jar-files Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

20. gUSE submitter • Use of source code of the provided BES interface for P-GRADE • in G3Bridge 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%C3%A1tolt_adatok(Hungarian comments but with examples) Java doc (Hungarian) Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

21. gUSE 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 • JobConfig.class in WS-PGRADE installation not up-to-date • ⇒ needed source code of JobConfig.java Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

22. gUSE 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 gUSE submitter forMoSGrid – 27.08.2010

23. gUSE submitter_unicore • Current status • jobs can be started • UNICORE returns status SUCCESSFUL • output is empty Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

24. gUSE submitter_unicore • Next steps • fix the bug with the output • add SAML security • add generator availability • add possibility to submit UNICORE workflowsLast but not least • English Java doc • English manual Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

25. 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 WS-PGRADE workflows Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

26. MoSGrid timeline 13.-14.09.2010 MoSGrid Meeting (presentation of submitter) 07.-09.11.2010 6. German Conference on Chemoinformatics http://www.gdch.de/vas/tagungen/tg/5412__e.htm (MoSGrid 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 MoSGrid Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010

27. Thank you for your attention. Sandra Gesing - A gUSE submitter forMoSGrid – 27.08.2010