Develop Reference

"The module has not been deployed. See the server log for details"

I have created Enterprise application in netbeans but whenever i run am receiving this error i uninstalled and then install the application so many times even i pointed glassfish server but i have failed. please help an new to java and netbeans. below i attached my server log and the error.
In-place deployment at \Mac\Home\Downloads\EPDAssignment\EPDAssignment-war\build\web
GlassFish Server 4.1, deploy, null, false
\\Mac\Home\Downloads\EPDAssignment\EPDAssignment-war\nbproject\build-impl.xml:1051: The module has not been deployed.
See the server log for details.
BUILD FAILED (total time: 0 seconds)
Server Log screenshot
Info: Server shutdown initiated
Info: Unregistered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl#6014a9ba from service registry.
Info: FileMonitoring shutdown
Info: JMXStartupService: Stopped JMXConnectorServer: null
Info: JMXStartupService and JMXConnectors have been shut down.
Info: JdbcRuntimeExtension, getAllSystemRAResourcesAndPools = [GlassFishConfigBean.org.glassfish.jdbc.config.JdbcResource, GlassFishConfigBean.org.glassfish.jdbc.config.JdbcResource, GlassFishConfigBean.org.glassfish.jdbc.config.JdbcResource, GlassFishConfigBean.org.glassfish.jdbc.config.JdbcConnectionPool, GlassFishConfigBean.org.glassfish.jdbc.config.JdbcConnectionPool, GlassFishConfigBean.org.glassfish.jdbc.config.JdbcConnectionPool]
Completed shutdown of Log manager service
Info: Shutdown procedure finished
Completed shutdown of GlassFish runtime
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=192m; support was removed in 8.0
Listening for transport dt_socket at address: 9009
Launching GlassFish on Felix platform
Dec 18, 2018 9:32:43 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner createBundleProvisioner
INFO: Create bundle provisioner class = class com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner.
Dec 18, 2018 9:32:43 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations
WARNING: Skipping entry because it is not an absolute URI.
Dec 18, 2018 9:32:43 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations
WARNING: Skipping entry because it is not an absolute URI.
Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishRuntime#1943da0 in service registry.
Found populator: com.sun.enterprise.v3.server.GFDomainXml
#!## LogManagerService.postConstruct : rootFolder=C:\Program Files\glassfish-4.1\glassfish
#!## LogManagerService.postConstruct : templateDir=C:\Program Files\glassfish-4.1\glassfish\lib\templates
#!## LogManagerService.postConstruct : src=C:\Program Files\glassfish-4.1\glassfish\lib\templates\logging.properties
#!## LogManagerService.postConstruct : dest=C:\Users\nurasahardid\AppData\Roaming\NetBeans\8.0.2\config\GF_4.1\domain1\config\logging.properties
Info: Running GlassFish Version: GlassFish Server Open Source Edition 4.1 (build 13)
Info: Server log file is using Formatter class: com.sun.enterprise.server.logging.ODLLogFormatter
Info: Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
Info: Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
Info: Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.
Info: Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry
Info: Authorization Service has successfully initialized.
Info: Grizzly Framework 2.3.15 started in: 31ms - bound to [/0.0.0.0:8080]
Info: Grizzly Framework 2.3.15 started in: 0ms - bound to [/0.0.0.0:8181]
Info: Grizzly Framework 2.3.15 started in: 0ms - bound to [/0.0.0.0:4848]
Info: Grizzly Framework 2.3.15 started in: 15ms - bound to [/0.0.0.0:3700]
Info: GlassFish Server Open Source Edition 4.1 (13) startup time : Felix (2,138ms), startup services(1,059ms), total(3,197ms)
Info: Grizzly Framework 2.3.15 started in: 78ms - bound to [/0.0.0.0:7676]
Info: Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl#6014a9ba as OSGi service registration: org.apache.felix.framework.ServiceRegistrationImpl#107f4980.
Info: JMXStartupService has started JMXConnector on JMXService URL service:jmx:rmi://10.211.55.3:8686/jndi/rmi://10.211.55.3:8686/jmxrmi
Info: HV000001: Hibernate Validator 5.0.0.Final
Info: Grizzly Framework 2.3.15 started in: 31ms - bound to [/0.0.0.0:8181]
Info: Grizzly Framework 2.3.15 started in: 0ms - bound to [/0.0.0.0:8080]

Netbeans 8.0.2 + Glassfish server 4.1

Whenever I run my project from Netbeans, I get this error:
The module has not been deployed.
See the server log for details.
BUILD FAILED (total time: 0 seconds)
Here is the log output:
Launching GlassFish on Felix platform
Oct 30, 2015 3:54:15 PM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner createBundleProvisioner
INFO: Create bundle provisioner class = class com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner.
Oct 30, 2015 3:54:15 PM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations
WARNING: Skipping entry because it is not an absolute URI.
Oct 30, 2015 3:54:15 PM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations
WARNING: Skipping entry because it is not an absolute URI.
Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishRuntime#2b936ab9 in service registry.
Found populator: com.sun.enterprise.v3.server.GFDomainXml
#!## LogManagerService.postConstruct : rootFolder=C: \Program Files\glassfish-4.1\glassfish
#!## LogManagerService.postConstruct : templateDir=C: \Program Files\glassfish-4.1\glassfish\lib\templates
#!## LogManagerService.postConstruct : src=C: \Program Files\glassfish-4.1\glassfish\lib\templates\logging.properties
#!## LogManagerService.postConstruct : dest=C: \Users\Jimmyzz\personal_domain1\config\logging.properties
Info: Running GlassFish Version: GlassFish Server Open Source Edition 4.1 (build 13)
Info: Server log file is using Formatter class: com.sun.enterprise.server.logging.ODLLogFormatter
Info: Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
Info: Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
Info: Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.
Info: Authorization Service has successfully initialized.
Info: Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry
Info: Grizzly Framework 2.3.15 started in: 58ms - bound to [/0.0.0.0:8080]
Info: Grizzly Framework 2.3.15 started in: 5ms - bound to [/0.0.0.0:8181]
Info: Grizzly Framework 2.3.15 started in: 7ms - bound to [/0.0.0.0:4848]
Info: Grizzly Framework 2.3.15 started in: 5ms - bound to [/0.0.0.0:3700]
Info: GlassFish Server Open Source Edition 4.1 (13) startup time : Felix (1,408ms), startup services(571ms), total(1,979ms)
Info: Grizzly Framework 2.3.15 started in: Ems - bound to [/0.0.0.0:7676]
Info: Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl#55f8669d as 0511 service registration: org.apache.felix.framework.ServiceRegistrationImpl#769d513.
Info: JMXStartupService has started JMXConnector on 3MXService URL service:jmx:rmi://100.75.255.36:8686/jndi/rmi://100.75.255.36:8686/jmxrmi
Info: HV000001: Hibernate Validator 5.0.0.Fina1
Info: Grizzly Framework 2.3.15 started in: 8ms - bound to [/0.0.0.0:8181]
Info: Grizzly Framework 2.3.15 started in: 9ms - bound to [/0.0.0.0:8080]I

For anyone who has a similar problem mine got fixed by renaming my project folder,
without spaces or symbols (eg. instead of 'Netbeans project & beans' to NetbeansProjectNBeans).

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.

can't start neo4j service after moving directory

I have a windows 7 x64 machine. I installed neo4j which went very smoothly. I then managed to install neo4django and neo4j-embedded and that was fine too.
However I decided to change the directory it was in, so I stopped the neo4j service in powershell and moved it to a different spot. Since then I haven't been able to restart the service, though if I run the console it starts neo4j in a java.exe window (I think) and thus it works (localhost:7474 accessible, able to run the neo4j-embedded example script, etc) until I close that java.exe window.
Here is the output I got in PowerShell:
PS G:\dev files\neo4j\bin> .\neo4j start
[SC] StartService FAILED 1053:
The service did not respond to the start or control request in a timely fashion.
PS G:\dev files\neo4j\bin> .\neo4j console
25/06/13 9:36:57 PM org.neo4j.server.AbstractNeoServer INFO: Setting startup timeout to: 120000ms based on -1
Detected incorrectly shut down database, performing recovery..
25/06/13 9:36:59 PM org.neo4j.server.database.Database INFO: Loaded neo4j tuning properties from conf/neo4j.properties
25/06/13 9:37:01 PM org.neo4j.server.database.Database INFO: Successfully started database
25/06/13 9:37:02 PM org.neo4j.server.AbstractNeoServer INFO: Starting Neo Server on port [7474] with [80] threads available
25/06/13 9:37:02 PM org.neo4j.server.AbstractNeoServer INFO: Enabling HTTPS on port [7473]
25/06/13 9:37:03 PM org.neo4j.server.modules.DiscoveryModule INFO: Mounted discovery module at [/]
25/06/13 9:37:03 PM org.neo4j.server.modules.RESTApiModule INFO: Mounted REST API at [/db/data/]
25/06/13 9:37:03 PM org.neo4j.server.modules.ManagementApiModule INFO: Mounted management API at [/db/manage/]
25/06/13 9:37:03 PM org.neo4j.server.modules.WebAdminModule INFO: Mounted webadmin at [/webadmin]
21:37:03.260 [main] INFO org.mortbay.log - Logging to Logger[org.mortbay.log] via org.mortbay.log.Slf4jLog
25/06/13 9:37:03 PM org.neo4j.server.web.Jetty6WebServer INFO: Mounting static content at [/webadmin] from [webadmin-html]
21:37:03.366 [main] INFO org.mortbay.log - jetty-6.1.25
21:37:03.548 [main] INFO org.mortbay.log - NO JSP Support for /webadmin, did not find org.apache.jasper.servlet.JspServlet
21:37:06.088 [main] INFO org.mortbay.log - Started SelectChannelConnector#localhost:7474
I'd be most appreciative of your help. Cheers.

When you create a service in Windows you typically bind a location for the executable that the operating system can find. Because you moved the directory your Neo4J service is no longer valid. What you must do is delete the old service, recreate the service with the new directory, and then launch it.
Code to get and delete service in PowerShell:
$service = Get-WmiObject -Class Win32_Service -Filter "Name='servicename'"
$service.delete()
taken from here

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!