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

1
Using Opal to deploy a real scientific
application as a Web service

• Sriram Krishnan
• sriram_at_sdsc.edu

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/jakart
  a-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/jakart
  a-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

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Opal Properties
parallel parameters num.procs1
mpi.run/Users/sriramkrishnan/Misc/mpich-1.2.7/bin
/mpirun the base URL for the tomcat
installation tomcat.urlhttp//localhost8080
database information
database.usefalse database.urljdbcpostgresq
l//localhost/app_db database.userapp_user
database.passwdapp_passwd drmma
information drmaa.usefalse
drmaa.pempich globus information
globus.usefalse globus.gatekeeperlocalhost2
119/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//localhost8080/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
ltappConfig xmlns"http//nbcr.sdsc.edu/opal/types
" xmlnsxsd"http//www.w3.org/2001/XML
Schema"gt ltmetadatagt ltusagegtlt!CDATA./babel
-iltinput-typegt ltnamegt -oltoutput-typegt
ltnamegtgtlt/usagegt ltinfo xsdtype"xsdstring"gt
lt!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 ... gt lt/infogt
lt/metadatagt ltbinaryLocationgt/Users/sriramkrishna
n/bin/babellt/binaryLocationgt ltdefaultArgsgtlt/defa
ultArgsgt ltparallelgtfalselt/parallelgt lt/appConfiggt
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Deploy application using Ant

• On the command prompt, cd to your Opal
  installation
• To deploy application, type the following
• ant deploy -DserviceNameBabelServicePort
  
  -DappConfigconfigs/babel_config.xml
• Check list of services
• http//localhost8080/opal/services

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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//localhost8080/opal/services/BabelServi
  cePort
• -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//localhost8080/opal/services/BabelServi
  cePort
• -r queryStatus -j ltjob_idgt

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Whats Next?

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

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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

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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