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

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

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

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

  2. 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

  3. Before we get started • Should have JAVA and ANT already installed • And environment variables JAVA_HOME and ANT_HOME set correctly • Make sure that these can be accessed from the command prompt • Type “java” • Type “ant” • Watch for error messages • Ask for help if these don’t work

  4. Download Software Prerequisites • Might want to create a new folder called “Tutorial” on your Desktop • Download and Extract Axis • http://nbcr.net/services/downloads/tutorial/axis-1_2_1.zip • Extract inside Tutorial directory • Download and Extract Tomcat • http://nbcr.net/services/downloads/tutorial/jakarta-tomcat-5_0_30.zip • Extract inside Tutorial directory • Set the environment variable CATALINA_HOME • Control Panel -> System -> Advanced

  5. Download Opal • Download and Extract Opal • http://nbcr.net/services/downloads/tutorial/opal-ws-1.0RC1.zip • Extract inside Tutorial directory • Compile the sources • On the command prompt, cd to the above location • Type “ant -f build-opal.xml compile” • Watch for error messages • Ask for help if you see any

  6. Deploy Axis inside Tomcat • Copy “axis” directory inside “axis-1_2_1\webapps” into “%CATALINA_HOME%\webapps” • Copy “activation-1_0_2.jar” and “mailapi-1_3_1.jar” from “opal-ws-1.0RC1\lib” into “%CATALINA_HOME%\common\lib” • Start Tomcat from the command prompt • Type “cd %CATALINA_HOME%\bin” • Type “startup.bat” • Test the Axis deployment • http://localhost:8080/axis/happyaxis.jsp • Watch for error messages, warnings are OK

  7. Edit Opal properties • Using Wordpad, open “opal-ws-1.0RC1\etc\opal.properties” • Look over the various properties being set • Modify the property “tomcat.url” by replacing “localhost” with the the IP address of your machine • Type “ipconfig /all” to get 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 # this is required since Java can't figure out the IP # address if there are multiple network interfaces 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 # 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. Download Scientific Application • We will use the application OpenBabel • Designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data • http://openbabel.sourceforge.net/ • Download: http://nbcr.net/services/downloads/tutorial/openbabel-2.0.0awins.zip • Extract inside “Tutorial\Babel” directory • Type “babel” from the above directory to ensure that it installed fine

  10. Edit Babel Config • Using Wordpad, open “opal-ws-1.0RC1\etc\babel_config.xml” • Look over the various elements • Change the value of the “binaryLocation” to point to your Babel executable

  11. 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 ... ]]> </info> </metadata> <binaryLocation>/Users/sriramkrishnan/bin/babel</binaryLocation> <defaultArgs></defaultArgs> <parallel>false</parallel> </appConfig>

  12. Deploy application using Ant • On the command prompt, cd to your Opal installation • To deploy application, type the following: • ant -f build-opal.xml deploy -DserviceName=BabelServicePort -DappConfig=etc\babel_config.xml • Restart Tomcat • Type “cd %CATALINA_HOME%\bin” • Type “shutdown.bat” • Type “startup.bat” • Check list of services • http://localhost:8080/axis/services

  13. Run command line client • On the command prompt, cd to your Opal installation • Set classpath by typing “classpath.bat” • To run the client, type the following: • java edu.sdsc.nbcr.opal.GenericServiceClient -l http://localhost:8080/axis/services/BabelServicePort -a "-ipdb sample.pdb -h -opdb output.pdb" -f etc\sample.pdb • Replace localhost with your neighbor’s IP address to use their Babel service

  14. 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 • We will see how to use Gemstone tomorrow

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

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