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From Mark Maciolek <...@sr.unh.edu>
Subject Re: troubleshoot tomcat database connection
Date Mon, 03 Nov 2014 19:41:24 GMT

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}

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>
      </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.

Mark
>> Mark
>>
>> --
>>
>> Mark Maciolek
>> Network Administrator
>> Morse Hall Room 339
>> 603-862-3050
>> https://www.unh.edu/research/support-units/research-computing-center
>>
>>
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>>

-- 

Mark Maciolek
Network Administrator
Morse Hall Room 339
603-862-3050
https://www.unh.edu/research/support-units/research-computing-center


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