sriram krishnan sriram@sdsc edu n.
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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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downloads
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
goals
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
before we get started
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”
download software prerequisites
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
download opal
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
edit opal properties
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
opal properties
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

deploy opal inside tomcat
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”
download scientific application
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
edit babel config
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
babel config
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>

deploy application using ant
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
run command line client
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>

what s next
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
advanced configuration
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
more information
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