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From Christopher Schultz <ch...@christopherschultz.net>
Subject Re: troubleshoot tomcat database connection
Date Mon, 03 Nov 2014 19:52:42 GMT
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Mark,

On 11/3/14 2:41 PM, Mark Maciolek wrote:
> 
> On 11/3/2014 2:29 PM, Daniel Mikusa wrote:
>> On Mon, Nov 3, 2014 at 1:58 PM, Mark Maciolek <mlm@sr.unh.edu>
>> wrote:
>> 
>>> hi,
>>> 
>>> system is running Scientific Linux release 6.5 rpm installed
>>> 
>>> tomcat6-servlet-2.5-api-6.0.24-78.el6_5.noarch 
>>> tomcat6-javadoc-6.0.24-78.el6_5.noarch 
>>> tomcat6-lib-6.0.24-78.el6_5.noarch 
>>> tomcat-native-1.1.30-1.el6.x86_64 
>>> tomcat6-el-2.1-api-6.0.24-78.el6_5.noarch 
>>> tomcat6-admin-webapps-6.0.24-78.el6_5.noarch 
>>> apache-tomcat-apis-0.1-1.el6.noarch 
>>> tomcat6-jsp-2.1-api-6.0.24-78.el6_5.noarch 
>>> tomcat6-webapps-6.0.24-78.el6_5.noarch 
>>> tomcat-servlet-3.0-api-7.0.33-4.el6.noarch 
>>> tomcat6-6.0.24-78.el6_5.noarch 
>>> tomcat6-docs-webapp-6.0.24-78.el6_5.noarch
>>> 
>> For what it's worth, 6.0.24 is pretty old.  You should strongly
>> consider upgrading to 6.0.41, or whatever is the latest at the
>> time you go to upgrade.
>> 
>> 
>>> httpd-2.2.15-31.sl6.x86_64
>>> 
>>> tomcat starts and I can reach the page on the 8080 port
>>> 
>> Good!
>> 
>> 
>>> It never starts the connection host name connection from the
>>> server.xml
>>> 
>> Hmm, not sure what you mean here.  Are you talking about virtual
>> hosting with Tomcat?
>> 
>> http://tomcat.apache.org/tomcat-6.0-doc/virtual-hosting-howto.html
>>
>
>> 
not currently just this one site on the server serving jsp file.
>>> I do a kill -3 on the tomcat pid and this is what the logs
>>> shows:
>>> 
>>> INFO: Starting Servlet Engine: Apache Tomcat/6.0.24 Nov 3, 2014
>>> 1:19:10 PM org.apache.catalina.startup.HostConfig 
>>> deployDescriptor INFO: Deploying configuration descriptor
>>> host-manager.xml Nov 3, 2014 1:19:10 PM
>>> org.apache.catalina.startup.HostConfig deployDescriptor INFO:
>>> Deploying configuration descriptor manager.xml Nov 3, 2014
>>> 1:19:10 PM org.apache.catalina.startup.HostConfig 
>>> deployDirectory INFO: Deploying web application directory ROOT 
>>> Nov 3, 2014 1:19:10 PM org.apache.catalina.startup.HostConfig 
>>> deployDirectory INFO: Deploying web application directory
>>> examples Nov 3, 2014 1:19:11 PM
>>> org.apache.catalina.startup.HostConfig deployDirectory INFO:
>>> Deploying web application directory sample Nov 3, 2014 1:19:11
>>> PM org.apache.catalina.startup.HostConfig deployDirectory INFO:
>>> Deploying web application directory docs Nov 3, 2014 1:19:11 PM
>>> org.apache.coyote.http11.Http11Protocol start INFO: Starting
>>> Coyote HTTP/1.1 on http-8080 Nov 3, 2014 1:19:11 PM
>>> org.apache.jk.common.ChannelSocket init INFO: JK: ajp13
>>> listening on /0.0.0.0:8009 Nov 3, 2014 1:19:11 PM
>>> org.apache.jk.server.JkMain start INFO: Jk running ID=0
>>> time=0/54  config=null Nov 3, 2014 1:19:11 PM
>>> org.apache.catalina.startup.Catalina start INFO: Server startup
>>> in 1307 ms 2014-11-03 13:19:37 Full thread dump OpenJDK 64-Bit
>>> Server VM (23.25-b01 mixed mode):
>>> 
>>> "TP-Monitor" daemon prio=10 tid=0x00007feca454d800 nid=0x729f
>>> in Object.wait() [0x00007feca2410000] java.lang.Thread.State:
>>> TIMED_WAITING (on object monitor) at
>>> java.lang.Object.wait(Native Method) - waiting on
>>> <0x00000000ba74ea78> (a org.apache.tomcat.util. 
>>> threads.ThreadPool$MonitorRunnable) at 
>>> org.apache.tomcat.util.threads.ThreadPool$MonitorRunnable.run( 
>>> ThreadPool.java:565) - locked <0x00000000ba74ea78> (a
>>> org.apache.tomcat.util. threads.ThreadPool$MonitorRunnable) at
>>> java.lang.Thread.run(Thread.java:701)
>>> 
>>> "TP-Processor4" daemon prio=10 tid=0x00007feca452f000
>>> nid=0x729e runnable [0x00007feca2511000] 
>>> java.lang.Thread.State: RUNNABLE at
>>> java.net.PlainSocketImpl.socketAccept(Native Method) at
>>> java.net.AbstractPlainSocketImpl.accept( 
>>> AbstractPlainSocketImpl.java:375) at
>>> java.net.ServerSocket.implAccept(ServerSocket.java:478) at
>>> java.net.ServerSocket.accept(ServerSocket.java:446) at
>>> org.apache.jk.common.ChannelSocket.accept( 
>>> ChannelSocket.java:307) at
>>> org.apache.jk.common.ChannelSocket.acceptConnections( 
>>> ChannelSocket.java:661) at
>>> org.apache.jk.common.ChannelSocket$SocketAcceptor. 
>>> runIt(ChannelSocket.java:872) at 
>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run( 
>>> ThreadPool.java:690) at java.lang.Thread.run(Thread.java:701)
>>> 
>>> "TP-Processor3" daemon prio=10 tid=0x00007feca452d000
>>> nid=0x729d in Object.wait() [0x00007feca2612000] 
>>> java.lang.Thread.State: WAITING (on object monitor) at
>>> java.lang.Object.wait(Native Method) - waiting on
>>> <0x00000000ba74e3a8> (a org.apache.tomcat.util. 
>>> threads.ThreadPool$ControlRunnable) at
>>> java.lang.Object.wait(Object.java:502) at 
>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run( 
>>> ThreadPool.java:662) - locked <0x00000000ba74e3a8> (a
>>> org.apache.tomcat.util. threads.ThreadPool$ControlRunnable) at
>>> java.lang.Thread.run(Thread.java:701)
>>> 
>>> "TP-Processor2" daemon prio=10 tid=0x00007feca4532000
>>> nid=0x729c in Object.wait() [0x00007feca2713000] 
>>> java.lang.Thread.State: WAITING (on object monitor) at
>>> java.lang.Object.wait(Native Method) - waiting on
>>> <0x00000000ba74e010> (a org.apache.tomcat.util. 
>>> threads.ThreadPool$ControlRunnable) at
>>> java.lang.Object.wait(Object.java:502) at 
>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run( 
>>> ThreadPool.java:662) - locked <0x00000000ba74e010> (a
>>> org.apache.tomcat.util. threads.ThreadPool$ControlRunnable) at
>>> java.lang.Thread.run(Thread.java:701)
>>> 
>>> "TP-Processor1" daemon prio=10 tid=0x00007feca452a000
>>> nid=0x729b in Object.wait() [0x00007feca2814000] 
>>> java.lang.Thread.State: WAITING (on object monitor) at
>>> java.lang.Object.wait(Native Method) - waiting on
>>> <0x00000000ba74dc60> (a org.apache.tomcat.util. 
>>> threads.ThreadPool$ControlRunnable) at
>>> java.lang.Object.wait(Object.java:502) at 
>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run( 
>>> ThreadPool.java:662) - locked <0x00000000ba74dc60> (a
>>> org.apache.tomcat.util. threads.ThreadPool$ControlRunnable) at
>>> java.lang.Thread.run(Thread.java:701)
>>> 
>>> "http-8080-Acceptor-0" daemon prio=10 tid=0x00007feca44fb000
>>> nid=0x7299 runnable [0x00007feca2915000] 
>>> java.lang.Thread.State: RUNNABLE at
>>> java.net.PlainSocketImpl.socketAccept(Native Method) at
>>> java.net.AbstractPlainSocketImpl.accept( 
>>> AbstractPlainSocketImpl.java:375) at
>>> java.net.ServerSocket.implAccept(ServerSocket.java:478) at
>>> java.net.ServerSocket.accept(ServerSocket.java:446) at
>>> org.apache.tomcat.util.net.DefaultServerSocketFactory. 
>>> acceptSocket(DefaultServerSocketFactory.java:61) at
>>> org.apache.tomcat.util.net.JIoEndpoint$Acceptor.run( 
>>> JIoEndpoint.java:352) at java.lang.Thread.run(Thread.java:701)
>>> 
>>> "ContainerBackgroundProcessor[StandardEngine[Catalina]]" daemon
>>> prio=10 tid=0x00007feca4501000 nid=0x7298 waiting on condition 
>>> [0x00007feca2a16000] java.lang.Thread.State: TIMED_WAITING
>>> (sleeping) at java.lang.Thread.sleep(Native Method) at
>>> org.apache.catalina.core.ContainerBase$ 
>>> ContainerBackgroundProcessor.run(ContainerBase.java:1579) at
>>> java.lang.Thread.run(Thread.java:701)
>>> 
>>> "GC Daemon" daemon prio=10 tid=0x00007feca440e800 nid=0x7297
>>> in Object.wait() [0x00007feca2d2d000] java.lang.Thread.State:
>>> TIMED_WAITING (on object monitor) at
>>> java.lang.Object.wait(Native Method) - waiting on
>>> <0x00000000cdd49190> (a sun.misc.GC$LatencyLock) at
>>> sun.misc.GC$Daemon.run(GC.java:117) - locked
>>> <0x00000000cdd49190> (a sun.misc.GC$LatencyLock)
>>> 
>>> "Low Memory Detector" daemon prio=10 tid=0x00007feca40f0000
>>> nid=0x7295 runnable [0x0000000000000000] 
>>> java.lang.Thread.State: RUNNABLE
>>> 
>>> "C2 CompilerThread1" daemon prio=10 tid=0x00007feca40ed800
>>> nid=0x7294 waiting on condition [0x0000000000000000] 
>>> java.lang.Thread.State: RUNNABLE
>>> 
>>> "C2 CompilerThread0" daemon prio=10 tid=0x00007feca40eb000
>>> nid=0x7293 waiting on condition [0x0000000000000000] 
>>> java.lang.Thread.State: RUNNABLE
>>> 
>>> "Signal Dispatcher" daemon prio=10 tid=0x00007feca40e9000
>>> nid=0x7292 waiting on condition [0x0000000000000000] 
>>> java.lang.Thread.State: RUNNABLE
>>> 
>>> "Finalizer" daemon prio=10 tid=0x00007feca409a800 nid=0x7291
>>> in Object.wait() [0x00007feca3c65000] java.lang.Thread.State:
>>> WAITING (on object monitor) at java.lang.Object.wait(Native
>>> Method) - waiting on <0x00000000cdb55a98> (a 
>>> java.lang.ref.ReferenceQueue$ Lock) at
>>> java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:133) -
>>> locked <0x00000000cdb55a98> (a java.lang.ref.ReferenceQueue$ 
>>> Lock) at
>>> java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:149) 
>>> at 
>>> java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:189)
>>>
>>>
>>> 
"Reference Handler" daemon prio=10 tid=0x00007feca4098800 nid=0x7290 in
>>> Object.wait() [0x00007feca3d66000] java.lang.Thread.State:
>>> WAITING (on object monitor) at java.lang.Object.wait(Native
>>> Method) - waiting on <0x00000000cdb557c8> (a 
>>> java.lang.ref.Reference$Lock) at
>>> java.lang.Object.wait(Object.java:502) at
>>> java.lang.ref.Reference$ReferenceHandler.run( 
>>> Reference.java:133) - locked <0x00000000cdb557c8> (a
>>> java.lang.ref.Reference$Lock)
>>> 
>>> "main" prio=10 tid=0x00007feca4009000 nid=0x728d runnable 
>>> [0x00007fecabf19000] java.lang.Thread.State: RUNNABLE at
>>> java.net.PlainSocketImpl.socketAccept(Native Method) at
>>> java.net.AbstractPlainSocketImpl.accept( 
>>> AbstractPlainSocketImpl.java:375) at
>>> java.net.ServerSocket.implAccept(ServerSocket.java:478) at
>>> java.net.ServerSocket.accept(ServerSocket.java:446) at
>>> org.apache.catalina.core.StandardServer.await( 
>>> StandardServer.java:389) at 
>>> org.apache.catalina.startup.Catalina.await(Catalina.java:657) 
>>> at 
>>> org.apache.catalina.startup.Catalina.start(Catalina.java:617) 
>>> 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:622) at 
>>> org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
>>>
>>> 
at
>>> org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
>>> 
>>> "VM Thread" prio=10 tid=0x00007feca4089800 nid=0x728f runnable
>>> 
>>> "VM Periodic Task Thread" prio=10 tid=0x00007feca40fb000
>>> nid=0x7296 waiting on condition
>>> 
>>> JNI global references: 231
>>> 
>>> Heap def new generation   total 18432K, used 13769K
>>> [0x00000000b9c00000, 0x00000000bb000000, 0x00000000cdb50000) 
>>> eden space 16384K,  74% used [0x00000000b9c00000,
>>> 0x00000000ba7f1588, 0x00000000bac00000) from space 2048K,  75%
>>> used [0x00000000bae00000, 0x00000000baf81118, 
>>> 0x00000000bb000000) to   space 2048K,   0% used
>>> [0x00000000bac00000, 0x00000000bac00000, 0x00000000bae00000) 
>>> tenured generation   total 40896K, used 2039K
>>> [0x00000000cdb50000, 0x00000000d0340000, 0x00000000f5a00000) 
>>> the space 40896K,   4% used [0x00000000cdb50000,
>>> 0x00000000cdd4df20, 0x00000000cdd4e000, 0x00000000d0340000) 
>>> compacting perm gen  total 21248K, used 12267K
>>> [0x00000000f5a00000, 0x00000000f6ec0000, 0x0000000100000000) 
>>> the space 21248K,  57% used [0x00000000f5a00000,
>>> 0x00000000f65faf88, 0x00000000f65fb000, 0x00000000f6ec0000) No
>>> shared spaces configured.
>>> 
>>> 
>>> Is the issue with the No shared spaces configured or is it
>>> more likely the java code being called to make the startup
>>> connection?
>>> 
>>> Any pointers in how to troubleshoot this problem would be
>>> greatly appreciated.
>>> 
>> It's not really clear what's failing here.  Can you be more
>> specific about what isn't working?  Perhaps provide an example of
>> what fails and what you expect should happen.
>> 
>> Dan
>> 
> 
> On a working server with similar setup this is what shows in the 
> catalina.out log
> 
> 2014-11-03 11:34:59  Config Instatiated: {OS_OWNER=ag, 
> TOMCAT_GROUP=tomcat, DB_USER=dbuser, SUPPORT_PHONE=603-862-0348, 
> BASE_PATH=/data1/picturepost, TOMCAT_HOME=/usr/share/tomcat6, 
> MAP_FILE=/data1/picturepost/cgi-bin/modis.map,
> CONVERT=/usr/bin/convert, DB_PORT=5432, 
> GOOGLE_MAPS_KEY=ABQIAAAAXLtB9cZEiOZ_WJC3vUyI2RQG0VXM1isChuPqZL77qjLf3s1C-hSFtmTt8t6XLAWqQA-40gXr1h4CJg,
>
> 
PICTURE_DIR=/data1/picturepost/data/pictures, APACHE_GROUP=apache,
> MAX_FILE_UPLOAD_SIZE=10485760, MAX_DB_CONNECTION_TIME=120, 
> PICTURE_DIR_URL=/images/pictures, 
> APACHE_SERVER_NAME=picturepost.unh.edu, 
> SUPPORT_EMAIL=picturepostsupport@picturepost.unh.edu, 
> HOST=/data1/picturepost/logs/picturepost.log, 
> DOCUMENT_ROOT_DIR=/data1/picturepost/webapps/ROOT,
> DB_PASSWORD=n0rMal1, DB_ADMIN_USER=postgres, MODE=live,
> NUM_DB_CONNECTIONS=20, URL=http://picturepost.unh.edu,
> NAME=picturepost, LOG=/data1/picturepost/logs/picturepost.log, 
> RECAPTCHA_PUBLIC_KEY=6Lckb8USAAAAAPU_hxR1X6lmNXO1goLP_vLPGlnF, 
> DB_HOST_IP=127.0.0.1, 
> LAYERS_FILE=/data1/picturepost/cgi-bin/modis_layers.map, 
> DATABASE=picturepost, PHPBB_PTA_SECRET=PAGoJcPsNJuN0GsjuOZpB, 
> DB_ADMIN_PASSWORD=, 
> RECAPTCHA_PRIVATE_KEY=6Lckb8USAAAAAAPOLqa9bls_ss80YStO5PyPseVK, 
> OS_GROUP=users, APACHE_ADDR_PORT=*:80, 
> CONFIG_FILE=/data1/picturepost/config/picturepost.cfg, 
> EMAIL_COMMAND=/usr/sbin/sendmail -oi -t}

I've never seen anything like that ever before. Is that some custom
component that is generating that logging?

> So on the server that is not working I never see the Config
> Instatiated
> 
> <Host name="centaur.sr.unh.edu" appBase="/web/opal/webapps"> 
> <Context docBase="ROOT" path="" allowLinking="true"> <Parameter
> name="BASE_PATH" value="/web/opal"/> </Context>

The above is probably going to double-deploy your web application or
otherwise do something weird. Don't put your <Context> in server.xml.
Instead, declare the <Context> element in your web application's
META-INF/context.xml file, where you can put things like your
BASE_PATH parameter.

> </Host>
> 
> We leaning towards something wrong in the StartupCooa.java file
> but since I never see the attempt to startup the config in the
> catalina.out file I suspect some else might be wrong.

I've never heard of StartupCooa.java.

- -chris
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