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Tomcat Server stopping when executing Vaadin webapp

I developed a webapp with Vaadin and kept it running on an embedded Jetty Server. Now, in order to deploy it on the productive server, I need it to run on a Tomcat v7 server.
I took the WAR-file (built with Maven) and deployed it to Tomcat.
Now, when I call the Tomcat URL in the browser, the webapp starts and shows the Vaadin loading circle. After a few seconds, the circle disappears and Tomcat stops.
The Catalina Logfile says the following:
Nov 17, 2015 11:37:55 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 5830 ms
Nov 17, 2015 11:37:59 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Nov 17, 2015 11:37:59 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
Nov 17, 2015 11:37:59 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
Nov 17, 2015 11:38:01 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SCHWERWIEGEND: The web application [/myWebapp] is still processing a request that has yet to finish. This is very likely to create memory leak. You can control the time allowed for requests to finish by using the unloadDelay attribute of the standard Context implementation.
Nov 17, 2015 11:38:01 AM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SCHWERWIEGEND: The web application [/myWebapp] created a ThreadLocal with key of type [com.vaadin.util.CurrentInstance$1] (value [com.vaadin.util.CurrentInstance$1#d8b2a4cd]) and a value of type [java.util.HashMap] (value [{interface com.vaadin.server.VaadinRequest=com.vaadin.util.CurrentInstance#d59e9a8b, class com.vaadin.server.VaadinSession=com.vaadin.util.CurrentInstance#bb1b7c4b, class com.vaadin.server.VaadinService=com.vaadin.util.CurrentInstance#5b5dec40, interface com.vaadin.server.VaadinResponse=com.vaadin.util.CurrentInstance#ea949e2b, class com.vaadin.ui.UI=com.vaadin.util.CurrentInstance#174bb6a7}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Nov 17, 2015 11:38:01 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Which fault is likely to cause this behaviour? Do I need to perform certain steps in order to deploy a Jetty webapp on Tomcat?

Server is not connected. Deploy is not available. IntelliJ 13 and Tomcat 7

Trying to run my app with IntelliJ 13 and Apache tomcat 7.0.42. JDK1.6
Always getting the error Artifact app:war exploded: Server is not connected. Deploy is not available.
But when I deploy through terminal with catalina.sh start it works perfectly fine.
I referred this link for setup: http://confluence.jetbrains.com/display/IntelliJIDEA/Application+Servers
Any idea what am I missing?
Here is the Tomcat Catalina log:
Dec 29, 2014 11:43:29 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: .:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java
Dec 29, 2014 11:43:29 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 29, 2014 11:43:29 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 29, 2014 11:43:29 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 614 ms
Dec 29, 2014 11:43:29 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 29, 2014 11:43:29 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.42
Dec 29, 2014 11:43:29 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 29, 2014 11:43:29 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Dec 29, 2014 11:43:29 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 44 ms
Dec 29, 2014 11:43:39 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /Users/yesuagg/apache-tomcat-7.0.42/webapps/manager
Exception in Event log
4:58:40 PM Compilation completed successfully with 104 warnings in 6 sec
4:58:42 PM Application Server was not connected before run configuration stop, reason:
java.io.IOException: Failed to retrieve RMIServer stub: javax.naming.ServiceUnavailableException [Root exception is java.rmi.ConnectException: Connection refused to host: localhost; nested exception is:
java.net.ConnectException: Connection refused]

Please check this answer posted by Christian and also read that thread.
Tomcat deployment issue via IntelliJ
Simply try removing setenv.sh in $CATALINA_HOME/bin

I had this issue today and it wasn't due to setenv.sh as discussed on the other thread. In the end it was an issue with $CATALINA_BASE/conf/server.xml.
For some reason in our server.xml we were using a custom engine name for example
<Engine name="custom-value" defaultHost="localhost">
I tried again with a clean server.xml from tomcat 7.0.57 and the artifact deployed perfectly. After trial and error it came down to this one line.
Changing engine name to 'Catalina' as shown below value fixed our issue and allowed our exploded artifact to deploy using our customised server.xml
<Engine name="Catalina" defaultHost="localhost">
If you are seeing this issue try a clean server.xml and work backwards from there.

tomcat-7.0-doc RUNNING
(3.2) Set JRE_HOME or JAVA_HOME (required)
These variables are used to specify location of a Java Runtime
Environment or of a Java Development Kit that is used to start Tomcat.
The JRE_HOME variable is used to specify location of a JRE. The JAVA_HOME
variable is used to specify location of a JDK.
Using JAVA_HOME provides access to certain additional startup options that
are not allowed when JRE_HOME is used.
If both JRE_HOME and JAVA_HOME are specified, JRE_HOME is used.

In my case, Intellij IDEA doesn't support run tomcat8 installed from linux repositories.
/usr/share/tomcat/bin/catalina.sh start (not support)
/usr/share/tomcat/bin/catalina.sh run (supported)
Only tomcat8 installed from official website. I tried with distribution downloaded from http://tomcat.apache.org/download-80.cgi. So I got successful results.
The reason is in the catalina.sh file from linux distribution, where there isn't "run" command. But in the tomcat downloaded there is "run" command. catalina.sh_InstalledFromLinuxRepository

Do you set JAVA_OPTS anywhere in Tomcat bat/sh files?
If you do, make sure to keep previous values also - IDEA seems to use those to specify some connection options to Tomcat.
E.g. in .sh files do
JAVA_OPTS="<your new stuff> $JAVA_OPTS"
instead of just
JAVA_OPTS=<your new stuff>
P.S. Same answer as this actually: https://stackoverflow.com/a/28867346/307295

Getting error "Tomcat was unable to start within 45 seconds." [duplicate]

This question already has answers here:
Setting property 'source' to 'org.eclipse.jst.jee.server:JSFTut' did not find a matching property
(8 answers)
Closed 7 years ago.
I am getting an error while running apache tomcat server in ecllipse and the error description is"Server apache-tomcat-7.0.54 at localhost was unable to start within 45 seconds. If the server requires more time, try increasing the timeout in the server editor".
After getting this message i have increased the time for server to start but the same message i am getting again.
Console prints error is
Jun 23, 2014 11:05:20 AM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'source' to 'org.eclipse.jst.jee.server:example' did not find a matching property.
Jun 23, 2014 11:05:20 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Jun 23, 2014 11:05:20 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Jun 23, 2014 11:05:20 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 868 ms
Jun 23, 2014 11:05:20 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jun 23, 2014 11:05:20 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Jun 23, 2014 11:05:21 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Jun 23, 2014 11:05:21 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Jun 23, 2014 11:05:21 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 458 ms

Eclipse has a timeout for starting and stopping Tomcat. You can change it, by opening 'Servers' view, double clicking the server name. As I can see form your logs your server did start in 458ms. But this problem might also be caused by components running lazily after server startup, f.e. servlets having a load-on-startup value greater than 0.
First check if your server really starts up completly. This is when the green 'play' icon ('Start server') turns into a red 'stop' icon and the message 'starting server...' dissapears in the 'Progress' view. If that is not working increase the startup time, as mentioned before. If even that is not working check your servlets for endless slopes or connection attempts to a webservice or a database.

Liferay installed but localhost:8080 return "No data received"

I have downloaded liferay bundle with tomcat.
I unpack it to my mac Applications/Administrating/liferay....
I have run ./startup.sh
And at the exnd I get: INFO: Server startup in 47781 ms
But when I open localhost:8080 in browser I get "No data received" like there is no site installed.
This is whole log:
Using CATALINA_BASE: /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40
Using CATALINA_HOME: /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40
Using CATALINA_TMPDIR: /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/temp
Using JRE_HOME: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Using CLASSPATH: /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/bin/bootstrap.jar:/Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/bin/tomcat-juli.jar
STSiMacVVU:bin vladimirvucetic$ tail -f ../logs/catalina.out
Oct 21, 2013 2:30:04 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Oct 21, 2013 2:30:04 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 665 ms
Oct 21, 2013 2:30:04 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 21, 2013 2:30:04 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.40
Oct 21, 2013 2:30:04 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/conf/Catalina/localhost/ROOT.xml
Loading jar:file:/Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/ROOT/WEB-INF/lib/portal-impl.jar!/system.properties
Loading jar:file:/Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/ROOT/WEB-INF/lib/portal-impl.jar!/portal.properties
Oct 21, 2013 2:30:16 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
14:30:21,037 INFO [localhost-startStop-1][DialectDetector:71] Determine dialect for HSQL Database Engine 2
14:30:21,040 WARN [localhost-startStop-1][DialectDetector:86] Liferay is configured to use Hypersonic as its database. Do NOT use Hypersonic in production. Hypersonic is an embedded database useful for development and demo'ing purposes. The database settings can be changed in portal-ext.properties.
14:30:21,084 INFO [localhost-startStop-1][DialectDetector:136] Found dialect org.hibernate.dialect.HSQLDialect
14:30:36,629 WARN [localhost-startStop-1][PDFProcessorImpl:235] Liferay is not configured to use ImageMagick. For better quality document and image previews, install ImageMagick and enable it in portal-ext.properties or in the Server Administration control panel at: http://<server>/group/control_panel/manage/-/server/external-services
Starting Liferay Portal Community Edition 6.1.2 CE (Paton / Build 6102 / August 2, 2013)
14:30:41,605 INFO [localhost-startStop-1][BaseDB:478] Database supports case sensitive queries
14:30:42,056 INFO [localhost-startStop-1][ServerDetector:169] Server supports hot deploy
14:30:42,064 INFO [localhost-startStop-1][PluginPackageUtil:1046] Reading plugin package for the root context
14:30:44,914 INFO [localhost-startStop-1][AutoDeployDir:144] Auto deploy scanner started for /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/deploy
Oct 21, 2013 2:30:48 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'Remoting Servlet'
Oct 21, 2013 2:30:49 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/marketplace-portlet
Oct 21, 2013 2:30:50 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/portal-compat-hook
Oct 21, 2013 2:30:51 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/resources-importer-web
Oct 21, 2013 2:30:51 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /Applications/Administrating/liferay-portal-6.1.2-ce-ga3/tomcat-7.0.40/webapps/welcome-theme
Oct 21, 2013 2:30:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Oct 21, 2013 2:30:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 47781 ms
What am I missing here?

A good starting point is to check if tomcat is receiving requests on port 8080 ; in your command-line type:
telnet localhost 8080
If you get a black/empty screen then tomcat is indeed listening on that port, otherwise you get a connection failure, then you need to doublecheck you tomcat configuration.

It looks like Liferay started up normally (but add more information - catalina.out or others, as gamerson requested in a comment)
Also:
Check Firewall settings (8080 might be blocked)
Your lsof output lists IPV6 (it's been long since I interpreted lsof
output and commandline - this might be normal, or not. You don't say
if you attempt an IPV4 connection)
Try to connect with a browser from that server. If it's a shell-only
server, use w3m or lynx on http://localhost:8080/
#user nobody;
worker_processes 1;
events {
worker_connections 1024;
}
http {
passenger_root /var/lib/gems/1.9.1/gems/passenger-4.0.5;
passenger_ruby /usr/bin/ruby1.9.1;
passenger_max_pool_size 10;
include mime.types;
default_type application/octet-stream;
sendfile on;
keepalive_timeout 65;
gzip on;
server {
listen 80;
server_name localhost;
access_log /var/www/access.log;
error_log /var/www/error.log;
location / {
root /var/www/demo/public;
passenger_enabled on;
rails_env production;
}
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root html;
}
}

You haven't configured a connector port 8080 so you won't get a response. The only connector you have configured is for AJP on port 8009 as can be seen from the logs.
Oct 21, 2013 2:30:04 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]

If you're running the server from Eclipse, Go to Servers -> ports and set 8080 for HTTP/1.1
If you're running a standalone Tomcat, go and edit tomcat/conf/server.xml and set
<Connector URIEncoding="UTF-8" connectionTimeout="20000" port="8080" protocol="HTTP/1.1" redirectPort="8443"/>
Make sure that the port 8080 is allowed from the server, and it's not used from another application
When the Server start, you should be able to read in the log this :
org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]

My expectation would be to find this in the log:
24.10.2013 13:43:14 org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
24.10.2013 13:43:14 org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
this would indicate the protocol handler for 8080 to start.
My advice to find the root cause of your problem is:
Access localhost:8080 before you start Liferay. This might give you the same result, indicating that there's some other software running on port 8080.
If this didn't help: Download a Liferay tomcat bundle again, unzip unchanged to a new location, run that one unchanged as well - if this one works, compare both directories, especially tomcat's /conf/ directory.
If that doesn't work, check if your environment defines any of the variables CATALINA_HOME, CATALINA_BASE, LIFERAY_HOME.
You'll be able to see more of the logs that you posted by running just a single command like ./bin/catalina.sh run. This will run tomcat in the foreground, showing the logs from the beginning without the chance to miss something because the tail command came too late

There is probably some other process using port 8080. Check it with this command:
sudo netstat -lnp | grep ':8080'
Kill that running process
sudo kill -9 {PID}
For example
sudo kill -9 1234
Restart Tomcat (if installed as service)
service tomcat7 restart

I mistakenly had a environment variable for CATALINA_HOME setup a few months back pointing to a different tomcat setup this caused the port 8080 to be invoked by that older setup and thus getting reserved before its used by Liferay. Make sure your CATALINA_HOME variable is configured to point at the tomcat bundled with Liferay.

Severe Tomcat crash has me stumped

I'm pretty used to crashing my tomcat server. But I don't think I made any changes at all and seem to have broken it completely. Was working one min then not the next.
I really hope someone can help here is the Catalina.out:
Dec 20, 2012 1:35:56 AM org.apache.catalina.startup.Embedded initDirs
SEVERE: Cannot find specified temporary folder at
Dec 20, 2012 1:35:57 AM org.apache.catalina.core.AprLifecycleListener init
INFO: Loaded APR based Apache Tomcat Native library 1.1.23.
Dec 20, 2012 1:35:57 AM org.apache.catalina.core.AprLifecycleListener init
INFO: APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
Dec 20, 2012 1:35:57 AM org.apache.coyote.http11.Http11AprProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8040
Dec 20, 2012 1:35:57 AM org.apache.coyote.ajp.AjpAprProtocol init
INFO: Initializing Coyote AJP/1.3 on ajp-8042
Dec 20, 2012 1:35:57 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 587 ms
Dec 20, 2012 1:35:57 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Dec 20, 2012 1:35:57 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.33
Dec 20, 2012 1:35:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory docs
Dec 20, 2012 1:35:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory ROOT
Dec 20, 2012 1:35:57 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory myApp
Dec 20, 2012 1:35:57 AM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/lhome/me/tomcat6/webapps/myApp/WEB-INF/lib/javax.servlet.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Dec 20, 2012 1:35:58 AM org.apache.coyote.http11.Http11AprProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8040
Dec 20, 2012 1:35:58 AM org.apache.coyote.ajp.AjpAprProtocol start
INFO: Starting Coyote AJP/1.3 on ajp-8042
Dec 20, 2012 1:35:58 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 880 ms
Error Reading TLE line 1: java.lang.Exception: TLE line 1 not valid first line
Error Creating SGP4 Satellite
Dec 20, 2012 1:36:26 AM org.apache.coyote.http11.Http11AprProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8040
Dec 20, 2012 1:36:26 AM org.apache.coyote.ajp.AjpAprProtocol pause
INFO: Pausing Coyote AJP/1.3 on ajp-8042
Dec 20, 2012 1:36:27 AM org.apache.catalina.core.StandardService stop
INFO: Stopping service Catalina
Dec 20, 2012 1:36:30 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/myApp] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Dec 20, 2012 1:36:30 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myApp] is still processing a request that has yet to finish. This is very likely to create a memory leak. You can control the time allowed for requests to finish by using the unloadDelay attribute of the standard Context implementation.
Dec 20, 2012 1:36:30 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myApp] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Dec 20, 2012 1:36:30 AM org.apache.coyote.http11.Http11AprProtocol destroy
INFO: Stopping Coyote HTTP/1.1 on http-8040
Dec 20, 2012 1:36:30 AM org.apache.coyote.ajp.AjpAprProtocol destroy
INFO: Stopping Coyote AJP/1.3 on ajp-8042
Dec 20, 2012 1:37:12 AM org.apache.catalina.startup.Catalina stopServer
SEVERE: Catalina.stop:
java.net.ConnectException: Connection refused
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:391)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:208)
at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:422)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:338)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:416)
And I have a new log that has been created, I've never seen it before but it seems to think its something severe. A long one but here it is:
Massive Error Log I've never seen before

Your JVM's got SIGBUS. This is either a hardware problem, or a low-level JVM code bug.
siginfo:si_signo=SIGBUS: si_errno=0,
si_code=2 (BUS_ADRERR), si_addr=0x00007f0a9bb06fe5
One suspicious entry is -Djava.io.tmpdir= in your startup (i.e. temp dir is empty string). Could do funny things to JVM, though I did not test it. May be it is OK to have it like that.
jvm_args: -Dcatalina.base=/lhome/me/tomcat6
-Dcatalina.home=/usr/share/tomcat6
-Djava.endorsed.dirs=
-Djava.io.tmpdir=
-Djava.util.logging.config.file=/lhome/me/tomcat6/conf/logging.properties
-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
Bottom line: I believe your hardware goes down. Backup everything.

The bomb seems to have occurred in the native method java.util.zip.ZipFile.getZipMessage() which is called by getEntry(). ZipFile had experienced an error and was trying to construct an exception message. This occurs while stopping the running webapp as part of reload.
Did you move the .war file? That can cause the problem.
These kinds of problems are hard to diagnose and fix. However, the problem is very likely to be java.io.tmpdir not being set properly. http://efod.se/blog/archive/2011/05/02/java-sigbus is a similar issue.
If that doesn't work, use apt-get to upgrade zlib and OpenJDK, and force ZipFile.getEntry() to be interpreted:
-X:CompileCommand=exclude,java/util/zip/ZipFile,getEntry
As OSB Stats said, don't trust your hardware (although it's not likely a hardware problem).

Thanks to all who gave help here.
However I fell I should answer my own question. Although I still don't fully understand why it caused such a severe exception. The problem seemed to lie with me having dropped a table on my database that the program was reading. This table was full of data that the program used to compile other data. Once I re-populated this table it was fine.
I don't know why something so simple caused such a lot of errors and never showed up in the logs as a table not found error. However I can only assume that the program was trying to run with blank data and this someone caused a severe error.
So thanks again to those who offered help!