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Starting Tomcat produces heapdumps and errors in log file


vinay kumar nukala (4236572) | asked Apr 07 '14, 7:48 a.m.
edited Apr 08 '14, 2:34 a.m. by Krzysztof Kaźmierczyk (7.4k35198)
And Some Heap files are created at the location C:\Program files\IBM\JazzTeamServer\Server. I am attaching the screen shot in this, please have a look and help us to resolve the issue.

Each heap file is about 300MB. Below is the tomcat log file:


7 Apr, 2014 10:56:05 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-9080"]
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-9443"]
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-9009"]
7 Apr, 2014 10:56:05 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-9080"]
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-9443"]
7 Apr, 2014 10:56:05 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-9009"]
7 Apr, 2014 10:56:26 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: C:\Program Files\IBM\JazzTeamServer\server\jre\bin;C:\Windows\system32;C:\Windows;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program Files\IBM\RationalSDLC\ClearCase\bin;C:\Program Files\IBM\RationalSDLC\common;C:\Program Files\System Center Operations Manager 2007\;C:\Program Files\Windows Imaging\;.
7 Apr, 2014 10:56:26 AM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Server/Service/Engine/Realm} Setting property 'debug' to '99' did not find a matching property.
7 Apr, 2014 10:56:26 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-9080"]
7 Apr, 2014 10:56:26 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-9443"]
7 Apr, 2014 10:56:27 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-9009"]
7 Apr, 2014 10:56:27 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1713 ms
7 Apr, 2014 10:56:27 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
7 Apr, 2014 10:56:27 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.25
7 Apr, 2014 10:56:32 AM org.apache.catalina.realm.JNDIRealm open
WARNING: Exception performing authentication
Throwable occurred: javax.naming.CommunicationException: iichyd:389 [Root exception is java.net.SocketTimeoutException: connect timed out]
    at com.sun.jndi.ldap.Connection.<init>(Connection.java:211)
    at com.sun.jndi.ldap.LdapClient.<init>(LdapClient.java:128)
    at com.sun.jndi.ldap.LdapClient.getInstance(LdapClient.java:1592)
    at com.sun.jndi.ldap.LdapCtx.connect(LdapCtx.java:2690)
    at com.sun.jndi.ldap.LdapCtx.<init>(LdapCtx.java:308)
    at com.sun.jndi.ldap.LdapCtxFactory.getUsingURL(LdapCtxFactory.java:187)
    at com.sun.jndi.ldap.LdapCtxFactory.getUsingURLs(LdapCtxFactory.java:205)
    at com.sun.jndi.ldap.LdapCtxFactory.getLdapCtxInstance(LdapCtxFactory.java:148)
    at com.sun.jndi.ldap.LdapCtxFactory.getInitialContext(LdapCtxFactory.java:78)
    at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:247)
    at javax.naming.InitialContext.initializeDefaultInitCtx(InitialContext.java:318)
    at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:348)
    at javax.naming.InitialContext.internalInit(InitialContext.java:286)
    at javax.naming.InitialContext.<init>(InitialContext.java:211)
    at org.apache.catalina.realm.JNDIRealm.open(JNDIRealm.java:2107)
    at org.apache.catalina.realm.JNDIRealm.startInternal(JNDIRealm.java:2198)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:1116)
    at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:293)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.StandardService.startInternal(StandardService.java:443)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:727)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:646)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:322)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:450)
Caused by: java.net.SocketTimeoutException: connect timed out
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:381)
    at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:243)
    at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:230)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:377)
    at java.net.Socket.connect(Socket.java:539)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at com.sun.jndi.ldap.Connection.createSocket(Connection.java:350)
    at com.sun.jndi.ldap.Connection.<init>(Connection.java:198)
    ... 30 more
7 Apr, 2014 10:56:33 AM org.apache.catalina.startup.Catalina start
SEVERE: Catalina.start:
Throwable occurred: org.apache.catalina.LifecycleException: Failed to start component [StandardServer[9005]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:646)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:322)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:450)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardService[Catalina]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:727)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 7 more
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.StandardService.startInternal(StandardService.java:443)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 9 more
Caused by: org.apache.catalina.LifecycleException: Failed to start component [Realm[JNDIRealm]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:1116)
    at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:293)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 11 more
Caused by: org.apache.catalina.LifecycleException: Exception opening directory server connection
    at org.apache.catalina.realm.JNDIRealm.startInternal(JNDIRealm.java:2200)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 14 more
Caused by: javax.naming.CommunicationException: localhost:389 [Root exception is java.net.ConnectException: Connection refused: connect]
    at com.sun.jndi.ldap.Connection.<init>(Connection.java:211)
    at com.sun.jndi.ldap.LdapClient.<init>(LdapClient.java:128)
    at com.sun.jndi.ldap.LdapClient.getInstance(LdapClient.java:1592)
    at com.sun.jndi.ldap.LdapCtx.connect(LdapCtx.java:2690)
    at com.sun.jndi.ldap.LdapCtx.<init>(LdapCtx.java:308)
    at com.sun.jndi.ldap.LdapCtxFactory.getInitialContext(LdapCtxFactory.java:65)
    at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:247)
    at javax.naming.InitialContext.initializeDefaultInitCtx(InitialContext.java:318)
    at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:348)
    at javax.naming.InitialContext.internalInit(InitialContext.java:286)
    at javax.naming.InitialContext.<init>(InitialContext.java:211)
    at org.apache.catalina.realm.JNDIRealm.open(JNDIRealm.java:2117)
    at org.apache.catalina.realm.JNDIRealm.startInternal(JNDIRealm.java:2198)
    ... 15 more
Caused by: java.net.ConnectException: Connection refused: connect
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:381)
    at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:243)
    at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:230)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:377)
    at java.net.Socket.connect(Socket.java:539)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
    at java.lang.reflect.Method.invoke(Method.java:611)
    at com.sun.jndi.ldap.Connection.createSocket(Connection.java:350)
    at com.sun.jndi.ldap.Connection.<init>(Connection.java:198)
    ... 27 more
7 Apr, 2014 10:56:33 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 6421 ms
7 Apr, 2014 11:02:16 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-9080"]
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-9443"]
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["ajp-bio-9009"]
7 Apr, 2014 11:02:16 AM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service Catalina
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-9080"]
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-9443"]
7 Apr, 2014 11:02:16 AM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["ajp-bio-9009"]

Please help us!

Comments
Krzysztof Kaźmierczyk commented Apr 08 '14, 2:32 a.m.

Hi Vinay,
You asked further question. The answer on that question is available on
https://jazz.net/forum/questions/147884/deleting-heapdump-files-from-the-server?page=1&focusedAnswerId=147888#147888

Accepted answer


permanent link
Alex Fitzpatrick (5583716) | answered Apr 07 '14, 10:04 a.m.
JAZZ DEVELOPER
Those log entries show it's timing out trying to connect to your LDAP server, you should verify the LDAP settings in server.xml and teamserver.properties with your LDAP administrator.

The heap dump can be analyzed with free tools from IBM: Heap Analyzer (download is a link at the bottom of the page), however given the size I suspect that it won't show anything interesting.
vinay kumar nukala selected this answer as the correct answer

Comments
vinay kumar nukala commented Apr 09 '14, 2:54 a.m.

Hi Alex,
             Thank you for your support, we have resolved the issue. The issue was they have changed the hostname of the LDAP server due to shift of location.

Anyway Thanks.


Alex Fitzpatrick commented Apr 09 '14, 10:17 a.m.
JAZZ DEVELOPER

That's good to hear, thanks for the feedback. 

Your answer


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