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Step :5
Deploy the Analysis Server.

Step:5.1
Copy the caintegrator-analysis-server.tar file created to the directory /local/content/caintegrator.
Step:5.2
Type the command: (color:red}tar -xvf caintegrator-analysis-server.tar
Step: 6
Go to the newly created directory /local/content/caintegrator/bin. Type the commands:
chmod u+x *.sh
dos2unix *.sh
Step :7
Start Rserve by typing:

./startRserve.sh
Rserve should now be running. The last line printed on the console should be:

"Rserv started in daemon mode."

Step:8
Go to the directory /home/caintegrator (you can do this by just typing cd).
Start the analysis server by executing the command:

./S92Rserver start

Additional post-deployment test case instructions:
1) Open the file/local/content/caintegrator/log/analysisServer.log and you should see something similar to:

a) main INFO gov.nih.nci.caintegrator.analysis.server.RThread - Done initializing Rserver connection elapsedTime=5100
b) main INFO gov.nih.nci.caintegrator.analysis.server.RThread - RThread name=Thread-0 successfully initialized R connection. 5046

2) There may be a warning:
a) main WARN gov.nih.nci.caintegrator.analysis.server.AnalysisServer - could not establish connection with...

But this is of no concern. It is because there will be no JMS MQs available until JMS message Queues have been established, running and listed in the JNDI lookup found at the location specified in the property:

3) After you deploy the application you should return to this log file and see the following:
a) main INFO gov.nih.nci.caintegrator.analysis.server.AnalysisServer - Now listening for requests...
Troubleshooting :

• "could not establish connection with provider.." when starting the Analysis Server.

This error can occur when the Java Messaging Service (JMS) provider is not running or has not fully initialized. Make sure that the JMS provider that is configured in the analysis server build file is running. If it is running but has not fully initialized the analysis server will automatically connect when it is fully initialized.

• Analysis Server appears to be running but no results are returned.

Using the jmx-console (see the JBoss documentation) application go to the jboss.mq.destination section and inspect the AnalysisResponseQueue. Make sure that the receivers count equals 1. If it is greater than 1 then there is another listener on the queue which is stealing the results from application.
Next inspect the AnalysisRequestQueue. Make sure that the receivers count is equal to the number of analysis server machines. For example if you have configured four analysis server machines then the receivers count should equal four.
If the receiver counts are not as expected then the problem may stem from network/firewall issues or from a conflicting instance of the application.

• If you are using a version of JBoss other than 4.0.2, you should replace the following jar files:

concurrent.jar
jbossmq-client.jar
jboss-common-client.jar
jboss-system-client.jar
jnp-client.jar

in the lib directory under the analysis server install directory, with the corresponding jar files from the JBoss distribution.

Steps to add a Data File:
Step:1
Click on this link https://gforge.nci.nih.gov/frs/?group_id=406^{Image Added} and you will find data files for particular application
For example:
Rembrandt:
Rembrandt_mas5.dataMatrix_275_10-15-07.Rda
Rembrandt_UnifiedGene.dataMatrix_275_10-15-07.Rda
Ispy :
newDataFile.zip
Step 2:
Copy the data file to the directory local/content/caintegrator/Rdatafiles/
Step 3: Restart the analysis server
Log in to the analysis machine
Stop the analysis server by executing the command:
./S92Rserver stop
Start the analysis server by executing the command:
./S92Rserver start

Using the Analysis Server for Development Purposes:

On caIntegrator project, for development, the developers share a common analysis server and have a dedicate JMS node for their local Jboss.

This allows us to independently develop and test queries against the analysis server.

You can setup something similar for development using our files

1) Copy StartStopNodes_develop to /home/caIntegrator and started and stopped similar to S92Rserver

./StartStopNodes_develop stop

And

./StartStopNodes_develop start

2) Copy runDeveloperNodes.sh to /local/content/caintegrator/bin/

And modify it by adding a new line for each developer using this file as an example

3) Copy & rename analysisServerDeveloper1.properties to local/content/caintegrator/bin/

And modify the ip address of the developer in this file plus the file name should match the setting in the runDeveloperNodes.sh file

Next use localhost:1099 on your server to connect to the analysis server. You do not need to start and stop the analysis server for each developer unless your going to upload a new R-binary file.

You can substitute actual developer name to identify each node