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bq. Invocation of init method failed; nested exception is Unable to create logging directory /usr/share/tomcat6/.aduna/openrdf-sesame/logs
then this indicates that Tomcat does not have write permission to its data directory (where it stores configuration, logs, and actual repository data). To fix this, log in as root to the server machine and do the following:
To use custom rule files, GraphDB must be running in a JVM that has access to the Java compiler. The easiest way to do this is to use the Java runtime from a Java Development Kit (JDK).

h5. I am getting SocketTimout when uploading large files

This might be caused because the import is taking longer than the configured timeout for your application server. In the case of tomcat you can change/add a connectionTimeout  parameter in the Connector element like this:
{code} <Connector executor="tomcatThreadPool"
port="8080" protocol="HTTP/1.1"
redirectPort="8443" />{code}
or disable upload timeouts by setting the&nbsp;*disableUploadTimeout* to false. More information can be found in tomcat's documentation&nbsp;[here|]

h1. Backup/restore/import/export

bq. Parser has reached the entity expansion limit "64,000" set by the Application.
when it generates more than a specified number of 'entities'. The default limit for the built-in Java XML parser is 64,000, however it can be configured by using a Java system property. To increase the limit, pass the following to the JVM in which GraphDB/Sesame is running. Note that the actual value can be increased as necessary. Don't forget that if running in Tomcat then this must be passed to the Tomcat instance using the CATALINA_OPTS environment variable.