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Using Opal to deploy a real scientific application as a Web service

Sriram Krishnan sriram@sdsc.edu. Using Opal to deploy a real scientific application as a Web service. Downloads. Opal Tutorial This presentation JDK 1.5: http://java.sun.com/javase/downloads Apache Ant: http://ant.apache.org/ Apache Tomcat:

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Using Opal to deploy a real scientific application as a Web service

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  1. Sriram Krishnan sriram@sdsc.edu Using Opal to deploy a real scientific application as a Web service

  2. Downloads • Opal Tutorial • This presentation • JDK 1.5: • http://java.sun.com/javase/downloads • Apache Ant: • http://ant.apache.org/ • Apache Tomcat: • http://nbcr.net/services/downloads/tutorial/jakarta-tomcat-5_0_30.zip • Opal 1.9 Distribution • From the Opal website

  3. Goals • Start off with a clean slate • Install software prerequisites • Install the Opal toolkit • Deploy scientific application as Web service • Access service via command-line client

  4. Before we get started • Should have JAVA and ANT already installed • And environment variables JAVA_HOME and ANT_HOME set correctly • Java: http://java.sun.com/javase/downloads • Ant: http://ant.apache.org/ • Make sure that these can be accessed from the command prompt • Type “java” • Type “ant”

  5. Download Software Prerequisites • Create a new directory called “Tutorial” • Download and Extract Tomcat • http://nbcr.net/services/downloads/tutorial/jakarta-tomcat-5_0_30.zip • Extract inside Tutorial directory

  6. Download Opal • Download and extract Opal • Extract inside the Tutorial directory • Compile the sources • On the command prompt, cd to the above location • Open the “build.properties” and modify the variable “catalina.home” with the path where you installed tomcat (previous slide) • Type “ant jar” • Watch for error messages

  7. Edit Opal properties • Open the file “etc/opal.properties” inside the Opal installation • Look over the various properties being set • Modify the property “tomcat.url” by replacing “localhost” with the the IP address of your machine • Type “ifconfig -a” to figure out your IP address

  8. Opal Properties # parallel parameters num.procs=1 mpi.run=/Users/sriramkrishnan/Misc/mpich-1.2.7/bin/mpirun # the base URL for the tomcat installation tomcat.url=http://localhost:8080 # database information database.use=false database.url=jdbc:postgresql://localhost/app_db database.user=app_user database.passwd=app_passwd # drmma information drmaa.use=false drmaa.pe=mpich # globus information globus.use=false globus.gatekeeper=localhost:2119/jobmanager-sge globus.service_cert=/Users/sriramkrishnan/certs/app_service.cert.pem globus.service_privkey=/Users/sriramkrishnan/certs/app_service.privkey

  9. Deploy Opal inside Tomcat • From the Opal directory, type the following command: • “ant install” • Start Tomcat from the command prompt • Type “cd $CATALINA_HOME/bin” • Type “ chmod +x *.sh” (so this only once)‏ • Type “./startup.sh” (use this command to start the server)‏ • Test the Opal installation • http://localhost:8080/opal/happyaxis.jsp • Watch for error messages, warnings are OK • If you wanna stop the Tomcat server type “./shutdown.sh”

  10. Download Scientific Application • We will use the application OpenBabel • Designed to support molecular modeling, chemistry, and many related areas, including inter-conversion of file formats and data. • Download appropriate version from: • http://openbabel.sourceforge.net/ • Extract inside the “Tutorial/Babel” directory • Type “babel” from the above directory to ensure that it installed fine

  11. Edit Babel Config • Open the file “configs/babel_config.xml” inside the Opal installation • Look over the various elements • Change the value of the “binaryLocation” to point to your Babel executable

  12. Babel Config <appConfig xmlns="http://nbcr.sdsc.edu/opal/types" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> <metadata> <usage><![CDATA[./babel [-i<input-type>] <name> [-o<output-type>] <name>]]></usage> <info xsd:type="xsd:string"> <![CDATA[ ... Currently supported input types alc -- Alchemy file prep -- Amber PREP file ... Currently supported output types caccrt -- Cacao Cartesian file cacint -- Cacao Internal file ... Additional options : ... ]]> </info> </metadata> <binaryLocation>/Users/sriramkrishnan/bin/babel</binaryLocation> <defaultArgs></defaultArgs> <parallel>false</parallel> </appConfig>

  13. Deploy application using Ant • On the command prompt, cd to your Opal installation • To deploy application, type the following: • ant deploy -DserviceName=BabelServicePort -DappConfig=configs/babel_config.xml • Check list of services • http://localhost:8080/opal/services

  14. Run command line client • On the command prompt, cd to your Opal installation • Set classpath by typing “. etc/classpath.sh” (on Bash)‏ • To run the job, type the following: • java edu.sdsc.nbcr.opal.GenericServiceClient -l http://localhost:8080/opal/services/BabelServicePort -a ”-ipdb sample.pdb -opdb out.pdb" -f etc/sample.pdb -r launchJob • To query status, type the following: • java edu.sdsc.nbcr.opal.GenericServiceClient -l http://localhost:8080/opal/services/BabelServicePort -r queryStatus -j <job_id>

  15. What’s Next? • To add another service, you just need to add another application config • And deploy using Ant - that’s all! • You can write custom clients for your Web services • e.g. Java, Python, Perl, JavaScript

  16. Advanced Configuration • Database: • http://nbcr.net/software/opal/docs/database.html • For persisting job metadata and access logs • Scheduler: • http://nbcr.net/software/opal/docs/scheduler.html • To access local schedulers via DRMAA or GRAM • GSI Security: • http://nbcr.net/software/opal/docs/security.html • To enable GSI-based authentication and authorization

  17. More Information • http://nbcr.net/software/opal • Downloads, Papers, Presentations • More documentation • Advanced configuration like Database, Scheduler, and Security setup • Feel free to drop us a note - contacts available from our web page

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