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Contents

This page is intended to provide a ready-reference for LexBIG system administrators and candidate material for inclusion in the next release of the LexBIG Administration Guide.

As primary reference, see the Installation and Administration Guide which is downloadable from the FIles tab of the GForge project..

Building the LexBIG Installer from GForge CVS

Some text.

JBoss Memory Settings

JBoss tends to run out of memory while running with the default settings of JBoss. To fix the problem, modify the run.conf file under JBOSS_home/bin to change the memory setting and how frequently the rmi garbage collector runs, by editing the JAVA_OPTS line as follows:

if [[ "x$JAVA_OPTS" = "x" ]; then
   JAVA_OPTS="-server -XX:!MaxPermSize=128m -Xms256m -Xmx2000m -Dsun.rmi.dgc.client.gcInterval=120000 -Dsun.rmi.dgc.server.gcInterval=120000"
fi

Improving Performance on MySQL/Windows

MySQL can be passed a jdbc option for the Windows local environment that may improve perfomance 30 to 50%.

Try the following values in the config.props file for the DB_URL:

SINGLE_DB_MODE=true
 DB_URL=jdbc:mysql:///<dbname>?socketFactory=com.mysql.jdbc.NamedPipeSocketFactory
 DB_DRIVER=org.gjt.mm.mysql.Driver
 DB_USER=root
 DB_PASSWORD=
 DB_PREFIX=lb
 DB_PARAM=

This uses Windows Named Pipe function and avoids use of the TCP/IP protocol. It only works when connecting with a local iteration of the MySQL database on Windows.

Error Connecting to MySQL

LexBIG is distributed with an older version of the Java MySQL driver due to licensing concerns. If LexBIG reports an error concerning establishing a connection to the MySQL server yet the MySQL CLI is able to connect, a new version of Connector/J may be required.

The latest version of Connector/J is available from MySQL.org. The new jar should be placed in the LexGrid/LexBIG/2.0.0/runtime/sqlDrivers/ directory. Remove the existing mm.mysql-2.0.6.jar to ensure that the class loader does not incorrectly load the older driver file.

Configuring Manifest Files

Here

Generating RRF Files from UMLS

When generating source RRF files from the Metathesaurus, the UMLS Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations in any RRF subset to be loaded to LexGrid. Failing to do so will create an incomplete database leaving the association and concept tables empty.

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