Transcript Using Opal to deploy a real scientific application as a

Using Opal to deploy a real scientific application as a
Web service
Sriram Krishnan
[email protected]
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
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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
• 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
• Create a new directory called “Tutorial”
• Download and Extract Tomcat
– http://nbcr.net/services/downloads/tutorial/jakarta-tomcat5_0_30.zip
– Extract inside Tutorial directory
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
• 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
# 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
• 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
• 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
• 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
<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
• 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
• 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?
• 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
• 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
• 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