MTA SzTAKI - 27.08.2010 (pdf) - Universität Tübingen

A gUSE submitter for 

MoSGrid 

(Molecular Simulation Grid) 

Sandra Gesing 

sandra.gesing@uni-tuebingen.de 

Eberhard-Karls-Universität Tübingen 

27.08.2010

Outline 

• Molecular simulations 

• Users 

• MoSGrid 

• MoSGrid architecture 

• gUSE submitter 

• Future work 

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

2

Molecular simulations 


http://www.nmr.chem.uu.nl/haddock2.0/movies/cg1.html 

3

Users 

• Sophisticated tools and algorithms available 

• Scientists with different computational 

background 

• Need of self-explanatory and intuitive user 

interfaces 

⇒ Portals 


4

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“ 

5

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 

6

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 


7

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 


8

MoSGrid 


9

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) 


10

MoSGrid Architecture 

Grid middleware 

Workflow engine 

(UNICORE 6) 

Batch system 

WS-PGRADE portal 

(integrated workflow editor) 

Workflow engine Repository 

Services 

Hardware 

(local, internet or 

integrated in a Grid or Cloud infrastructure) 


Repository 

(XtreemFS) 

11

gUSE submitter 

Installation of WS-PGRADE portal in Tübingen 

• added own VO bwGRiD 

• submission to GT 4 

⇒ extension of existing documentation 


12


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 


13


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 

14


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 


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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 int actionJobStatus(); 

public String actionJobResource(); 

} 

public void actionSetJobStatus(int pValue); 

public void actionSetJobResource(String pValue); 

public void setRunnerId(String pValue); 



16

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 



17


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 


18


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) 


19


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 


20

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) 


21


Current status 

• jobs can be started 

• UNICORE returns status SUCCESSFUL 

• output is empty 


22


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 


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 WS- 

PGRADE workflows 


24

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 


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Thank you for your attention. 


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MTA SzTAKI - 27.08.2010 (pdf) - Universität Tübingen

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