27.08.2010 Sandra Gesing Eberhard-Karls-Universität Tübingen A gUSE submitter for MoSGrid (Molecular Simulation Grid)

Präsentation zum Thema: "27.08.2010 Sandra Gesing Eberhard-Karls-Universität Tübingen A gUSE submitter for MoSGrid (Molecular Simulation Grid)"—  Präsentation transkript:

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

2 Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 1 Outline Molecular simulations Users MoSGrid MoSGrid architecture gUSE submitter Future work

3 2 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 for MoSGrid – 27.08.2010

4 3 Molecular simulations http://www.nmr.chem.uu.nl/haddock2.0/movies/cg1.html Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

5 4 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 for MoSGrid – 27.08.2010

6 5 Unifying diversity 12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa Slide copied from: Stuart Owen „Workflows with Taverna“ Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

7 6 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 7 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 for MoSGrid – 27.08.2010

9 8 MoSGrid - 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 gUSE submitter for MoSGrid – 27.08.2010

10 9 MoSGrid Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

11 10 MoSGrid Components Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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)

12 11 MoSGrid Architecture WS-PGRADE portal (integrated workflow editor) Hardware (local, internet or integrated in a Grid or Cloud infrastructure) Grid middleware Workflow engine (UNICORE 6) Repository (XtreemFS) Services Batch system Workflow engine Repository Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

13 12 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 Installation of WS-PGRADE portal in Tübingen added own VO bwGRiD submission to GT 4 ⇒ extension of existing documentation

14 13 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

15 14 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 In order to test your submitter, you need 1.jdk 1.6 [on the testing machine] 2.tomcat [on the testing machine] 3.gUSE 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 gUSE/WS-PGRADE 7.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

16 15 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

17 16 GridService interface Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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 int actionJobStatus(); public String actionJobResource(); public void actionSetJobStatus(int pValue); public void actionSetJobResource(String pValue); public void setRunnerId(String pValue); } Slide copied from József‘s presentation

18 17 JobConfig class Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

19 18 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

20 19 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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)

21 20 gUSE submitter Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

22 21 gUSE submitter_unicore Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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)

23 22 gUSE submitter_unicore Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 Current status jobs can be started UNICORE returns status SUCCESSFUL output is empty

24 23 gUSE submitter_unicore Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

25 24 Future work Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 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

26 25 MoSGrid timeline Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 13.-14.09.2010MoSGrid Meeting (presentation of submitter) 07.-09.11.20106. 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) 01.12.2010Portal-Prototype with workflow infrastructure for user community 01.05.2011Portal-Prototype with access to molecule data repository (beta-tester) 01.12.2011Portal-Prototype with data repository and workflow infrastructure for user community 01.06.2012Portal will be released 30.08.2012End of project MoSGrid

27 26 Thank you for your attention. Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010