Develop Reference

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?

OpenAM is hung and high CPU utilization by Java

I recently started working in a project which uses OpenAM for single sign on top of tomcat 7 and server running on Apache 2.4.12.
Installed Java version details:
java version "1.7.0_65"
OpenJDK Runtime Environment (rhel-2.5.1.2.el6_5-x86_64 u65-b17)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)
OpenAM 11.0.0 (2013-November-08 10:40)
Most of the time 95% of CPU utilization is by java. I can't find the reason for this high CPU utilization.
We had an issue today with OpenAM, OpenAM Tomcat processes seems to have hung in two servers out of 8 and not listening to the port 8180. After restart, the service is up and running fine with ports listening.
However, I could see below error in openAM logs, I tried to find the root cause but unfortunately I can't, could anyone please help?
Server 1:
Jul 28, 2015 8:33:36 AM com.sun.xml.ws.transport.http.servlet.WSServletContextListener contextDestroyed
INFO: WSSERVLET13: JAX-WS context listener destroyed
Jul 28, 2015 8:33:43 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/sso] appears to have started a thread named [com.google.inject.internal.util.$Finalizer] but has failed to stop it. This is very likely to create a memory leak.
Jul 28, 2015 8:33:43 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/sso] appears to have started a thread named [Monitor Provider State Updater] but has failed to stop it. This is very likely to create a memory leak.
Jul 28, 2015 8:33:43 AM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/sso] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal#4ee2edc3]) and a value of type [org.glassfish.grizzly.ThreadCache.ObjectCache] (value [org.glassfish.grizzly.ThreadCache$ObjectCache#1467c5ab]) 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.
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8180"]
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol destroy
Server 2:
Jul 28, 2015 8:34:50 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/sso] appears to have started a thread named [com.google.inject.internal.util.$Finalizer] but has failed to stop it. This is very likely to create a memory leak.
Jul 28, 2015 8:34:50 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/sso] appears to have started a thread named [Monitor Provider State Updater] but has failed to stop it. This is very likely to create a memory leak.
Jul 28, 2015 8:33:43 AM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/sso] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal#4ee2edc3]) and a value of type [org.glassfish.grizzly.ThreadCache.ObjectCache] (value [org.glassfish.grizzly.ThreadCache$ObjectCache#1467c5ab]) 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.
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8180"]
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8180"]
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["ajp-bio-8109"]
Jul 28, 2015 8:33:43 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-8109"]
Jul 28, 2015 8:33:50 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: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Jul 28, 2015 8:33:50 AM org.apache.coyote.AbstractProtocol init
Other WARNING in Server 2:
Jul 28, 2015 8:35:13 AM com.sun.jersey.server.impl.application.WebApplicationImpl newResourceClass
WARNING: A sub-resource method, public javax.ws.rs.core.Response org.forgerock.openam.forgerockrest.authn.AuthenticationRestService.getMethodNotSupported(), with URI template, "/", is treated as a resource method
Jul 28, 2015 8:35:13 AM com.sun.jersey.server.impl.application.WebApplicationImpl newResourceClass
WARNING: A sub-resource method, public javax.ws.rs.core.Response org.forgerock.openam.forgerockrest.authn.AuthenticationRestService.authenticate(javax.ws.rs.core.HttpHeaders,javax.servlet.http.HttpServletRequest,javax.servlet.http.HttpServletResponse,java.lang.String,java.lang.String,java.lang.String,java.lang.String), with URI template, "/", is treated as a resource method
Jul 28, 2015 8:35:23 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/openam/webapps/manager

WAR file being deployed on TomEE - first time deployed not as expected, subsequent restarts result in ClassNotFoundExceptions

I've successfully deployed a war file that I exported using Eclipse to a local instance of a TomEE server, but when trying to do exactly the same thing with the war file on another server, I get the following output to the console:
Jul 30, 2014 12:50:47 PM org.apache.openejb.util.JarExtractor extract
INFO: Extracting jar: C:\Apache TomEE\apache-tomee-plus-1.6.0.2\webapps\MyWar.war
Jul 30, 2014 12:50:47 PM org.apache.openejb.util.JarExtractor extract
INFO: Extracted path: C:\Apache TomEE\apache-tomee-plus-1.6.0.2\webapps\MyWar
Jul 30, 2014 12:50:48 PM org.apache.myfaces.ee6.MyFacesContainerInitializer onSt
artup
INFO: Added FacesServlet with mappings=[/faces/*, *.jsf, *.faces]
Jul 30, 2014 12:50:48 PM org.apache.tomee.myfaces.TomEEMyFacesContainerInitializ
er addListener
INFO: Installing <listener>org.apache.myfaces.webapp.StartupServletContextListen
er</listener>
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.DefaultFacesConfigurationProv
ider getStandardFacesConfig
INFO: Reading standard config META-INF/standard-faces-config.xml
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.DefaultFacesConfigurationProv
ider getClassloaderFacesConfig
INFO: Reading config : jar:file:/C:/Apache%20TomEE/apache-tomee-plus-1.6.0.2/lib
/openwebbeans-el22-1.2.1.jar!/META-INF/faces-config.xml
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.DefaultFacesConfigurationProv
ider getClassloaderFacesConfig
INFO: Reading config : jar:file:/C:/Apache%20TomEE/apache-tomee-plus-1.6.0.2/lib
/openwebbeans-jsf-1.2.1.jar!/META-INF/faces-config.xml
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.LogMetaInfUtils logArtifact
INFO: Artifact 'myfaces-api' was found in version '2.1.13' from path 'file:/C:/A
pache%20TomEE/apache-tomee-plus-1.6.0.2/lib/myfaces-api-2.1.13.jar'
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.LogMetaInfUtils logArtifact
INFO: Artifact 'myfaces-impl' was found in version '2.1.13' from path 'file:/C:/
Apache%20TomEE/apache-tomee-plus-1.6.0.2/lib/myfaces-impl-2.1.13.jar'
Jul 30, 2014 12:50:48 PM org.apache.myfaces.application.ApplicationImpl getProje
ctStage
INFO: Couldn't discover the current project stage, using Production
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.FacesConfigurator handleSeria
lFactory
INFO: Serialization provider : class org.apache.myfaces.shared_impl.util.serial.
DefaultSerialFactory
Jul 30, 2014 12:50:48 PM org.apache.myfaces.config.annotation.DefaultLifecyclePr
oviderFactory getLifecycleProvider
INFO: Using LifecycleProvider org.apache.myfaces.config.annotation.Tomcat7Annota
tionLifecycleProvider
Jul 30, 2014 12:50:48 PM org.apache.myfaces.webapp.AbstractFacesInitializer init
Faces
INFO: ServletContext initialized.
... the EJBs that are contained within the WAR are not initialised, and nothing happens.
Upon server restart, I get ClassNotFoundExceptions for all of the classes contained within my WAR (and now within WEB-INF/classes once exploded)
Can anyone help?

Guess it comes from the space, try in another folder with space maybe.

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!

Error starting TOMCAT [duplicate]

This question already has answers here:
Closed 10 years ago.
Possible Duplicate:
How to fix this Spring MVC startup exception in tomcat?
Someone knows what is happening ?
What is happening, do you guys know ? Where can I see the logs for more details ?
Here is what the console says:
02/06/2012 01:08:50 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: C:\Arquivos de programas\Java\jre6\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:/Arquivos de programas/Java/jre6/bin/client;C:/Arquivos de programas/Java/jre6/bin;C:/Arquivos de programas/Java/jre6/lib/i386;C:\Ruby193\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Arquivos de programas\Java\jdk1.6.0_25\bin;C:\apache-maven-3.0.3\bin;C:\spring-roo-1.1.3.RELEASE\bin;C:\Arquivos de programas\Android\android-sdk\tools;C:\Arquivos de programas\QuickTime\QTSystem\;C:\eclipse;;.
02/06/2012 01:08:51 org.apache.tomcat.util.digester.SetPropertiesRule begin
AVISO: [SetPropertiesRule]{Server/Service/Engine/Host/Context} Setting property 'source' to 'org.eclipse.jst.jee.server:springapp' did not find a matching property.
02/06/2012 01:08:51 org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
02/06/2012 01:08:51 org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
02/06/2012 01:08:51 org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 766 ms
02/06/2012 01:08:51 org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
02/06/2012 01:08:51 org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.27
02/06/2012 01:08:51 org.apache.catalina.util.SessionIdGenerator createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [109] milliseconds.
02/06/2012 01:08:51 org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
02/06/2012 01:08:51 org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
02/06/2012 01:08:51 org.apache.catalina.startup.Catalina start
INFO: Server startup in 522 ms

(I was hoping that you might say why you thought there was an error here, but you haven't bothered. So ...)
There is no error in that log, and it looks like Tomcat has started up successfully and is running normally. The only thing that appears slightly odd is that there are no startup messages from any webapps. Perhaps you simply haven't deployed them yet ... or you've deployed them in the wrong directory.
The INFO message about the missing APR native code is harmless. Tomcat works fine without it ... assuming that you haven't explicitly configured an APR connector in the server.xml file.
The AVISO message (strange category name ...) looks like it is telling you that you've made a mistake in the name of an attribute in some config file. Maybe, the "source" attribute whose value you've set to "org.eclipse.jst.jee.server:springapp" has the wrong name? Or it is on the wrong XML element? If the problem is in your webapp's web.xml, it might be causing your webapp to not find any servlets to start ... or something like that.

Tomcat server log usually can be found here ${catalina.home}/logs/catalina.out or ${catalina.home}/logs/tomcat.log