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Startup problems with VM

Hi,

I've downloaded the VM version of OpenClinica and followed the directions; it's up and running. However, the tomcat logs (catalina.out in particular) are full of startup errors. Below I've listed the first lines and the last -- I haven't been actively using the system since I brought it up, but it's not actively throwing errors. Still, those errors on initialization are worrying. Do I need to be concerned -- sorry is this is a newbie question or FAQ but I couldn't find the answer in the forum?

Thanks,
Bill

Top:


Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version: Apache Tomcat/7.0.65
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server built: Jan 6 2016 18:50:03 UTC
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server number: 7.0.65.0
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Name: Linux
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: OS Version: 2.6.32-573.18.1.el6.x86_64
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Architecture: amd64
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Java Home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.95.x86_64/jre
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Version: 1.7.0_95-mockbuild_2016_01_21_15_45-b00
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: JVM Vendor: Oracle Corporation
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_BASE: /usr/share/tomcat
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: CATALINA_HOME: /usr/share/tomcat
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.base=/usr/share/tomcat
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Dcatalina.home=/usr/share/tomcat
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.endorsed.dirs=
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.io.tmpdir=/var/cache/tomcat/temp
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.VersionLoggerListener log
INFO: Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Feb 25, 2016 9:58:13 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Feb 25, 2016 9:58:13 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Feb 25, 2016 9:58:13 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Feb 25, 2016 9:58:13 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1551 ms
Feb 25, 2016 9:58:13 PM org.apache.tomcat.util.digester.Digester fatalError
SEVERE: Parse Fatal Error at line 2 column 2: The markup in the document following the root element must be well-formed.
org.xml.sax.SAXParseException; lineNumber: 2; columnNumber: 2; The markup in the document following the root element must be well-formed.
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198)
at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
...
...

There are lots of XML parsing errors like this, but differing in their stack traces.

Bottom:


INFO: Initiating Jersey application, version 'Jersey: 1.17.1 02/28/2013 12:47 PM'
Feb 25, 2016 9:58:59 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /var/lib/tomcat/webapps/OpenClinica.war has finished in 45,913 ms
Feb 25, 2016 9:58:59 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 25, 2016 9:58:59 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Feb 25, 2016 9:58:59 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 46154 ms
The time is now 22:00:00
Feb 25, 2016 10:00:51 PM org.apache.jasper.compiler.TldLocationsCache tldScanJar
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
is ub a ldapuser??false
here
is ub a ldapuser??false
is ub a ldapuser??false
The time is now 23:00:00
The time is now 00:00:00
The time is now 01:00:00
The time is now 02:00:00
The time is now 03:00:00
The time is now 04:00:00
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