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, Ph.D.
• sriram_at_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 dont 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/jakart
  a-tomcat-5_0_30.zip
• Extract inside Tutorial directory
• Set the environment variable CATALINA_HOME
• Control Panel -gt System -gt Advanced

5
Download Opal

• Download and Extract Opal
• http//nbcr.net/services/downloads/tutorial/opal-w
  s-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

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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//localhost8080/axis/happyaxis.jsp
• Watch for error messages, warnings are OK

7
Edit Opal properties

• Using Wordpad, open opal-ws-1.0RC1\etc\opal.prope
  rties
• 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

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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 this is required since Java
can't figure out the IP address if there
are multiple network interfaces
tomcat.urlhttp//localhost8080 database
information database.usefalse
database.urljdbcpostgresql//localhost/app_db
database.userapp_user database.passwdapp_p
asswd 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
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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/tutor
  ial/openbabel-2.0.0awins.zip
• Extract inside Tutorial\Babel directory
• Type babel from the above directory to ensure
  that it installed fine

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Edit Babel Config

• Using Wordpad, open opal-ws-1.0RC1\etc\babel_conf
  ig.xml
• Look over the various elements
• Change the value of the binaryLocation to point
  to your Babel executable

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Babel Config
ltappConfig xmlns"http//nbcr.sdsc.edu/opal/types"
xmlnsxsd"http//www.w3.org/2001/XMLS
chema"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 ...
gt lt/infogt lt/metadatagt
ltbinaryLocationgt/Users/sriramkrishnan/bin/babellt/b
inaryLocationgt ltdefaultArgsgtlt/defaultArgsgt
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 -f build-opal.xml deploy -DserviceNameBabelSe
  rvicePort -DappConfigetc\babel_co
  nfig.xml
• Restart Tomcat
• Type cd CATALINA_HOME\bin
• Type shutdown.bat
• Type startup.bat
• Check list of services
• http//localhost8080/axis/services

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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//localhost8080/axis/services/BabelServicePo
  rt -a "-ipdb sample.pdb -h -opdb output.pdb" -f
  etc\sample.pdb
• Replace localhost with your neighbors IP address
  to use their Babel service

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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
• We will see how to use Gemstone tomorrow

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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