[xwiki-users] Installation problem

26 May 2011

      Hi all,

I need help with installation...

I'm trying to get xwiki running on:
RHEL 6  x64...
JDK 6 latest...
Mysql 5.1.52...
Tomcat 7.0.14

I've followed the admin guide as near as possible... The deviations I've 
made are..

created my db as 'testxwiki' instead of just xwiki...
modified xwiki.db=testxwiki (this was just a stab in the dark - not sure 
I need to change this)
made appropriate modifications to the jdbc url in hibernate.cfg.xml...

I've varified that I can connect to the database using:
mysql -uxwiki -psome_password testxwiki

and show tables returns the empty set...  xwiki / hibernate is supposed 
to create the initial schema on startup right (less indexes)?

A more complete catalina.out snip is below but essentially I'm getting...

FATAL store.DBCPConnectionProvider    - Could not create a DBCP pool. 
There is an error in the hibernate configuration file, please review it.

Unfortunately I have been through this file many many times... and I 
just don't see anything wrong with it...

I also get some interesting results when I stop tomcat after attempting 
to browse the xwiki site...

SEVERE: The web application [/xwiki] 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
clearReferencesThreads
SEVERE: The web application [/xwiki] appears to have started a thread 
named [EvictionTimer-0] but has failed to stop it. This is very likely 
to create a memory leak.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
clearReferencesThreads
SEVERE: The web application [/xwiki] appears to have started a thread 
named [EvictionTimer-1] but has failed to stop it. This is very likely 
to create a memory leak.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value [{}]) 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value 
[{url=http://neil.nmc.edu:8080/xwiki/bin/view/Main/}]) 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value 
[{url=http://neil.nmc.edu:8080/xwiki/bin/view/Main/}]) 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.

Here's the gory details of everything I did (as well as I can remember)...

====

Installed the 64bit jdk from oracle..

java -version
java version "1.6.0_25"
Java(TM) SE Runtime Environment (build 1.6.0_25-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.0-b11, mixed mode)

====

Downloaded tomcat and installed it...
tar -zxvf apache-tomcat-7.0.14.tar.gz

Modified the server.xml file and added:
  deployOnStartup="true" to the Host node

Modified catalina.sh and added:
JAVA_HOME=/usr/local/jdk160_25
JAVA_OPTS="-Xmx512m -XX:MaxPermSize=128m"

Removed examples, host-manager, and manager from 'webapps'... I prefer 
not to leave them...

====

Started tomcat - at that point I could get to the ROOT application and 
browse the tomcat docs...

====

Installed mysql from RPM packages... Configured a few parameters in 
my.cnf...

default-storage-engine=INNODB
innodb_file_per_table

skip-external-locking
max_connections=200
read_buffer_size=1M
sort_buffer_size=1M

key_buffer_size=128M

max_allowed_packet=32M

innodb_data_file_path = ibdata1:100M:autoextend

innodb_buffer_pool_size=256M
innodb_additional_mem_pool_size=20M

innodb_log_file_size=64M
innodb_log_buffer_size=8M

innodb_flush_log_at_trx_commit=1

====

Created the database and the user...

create database testxwiki default character set utf8;
grant all privileges on testxwiki.* to xwiki@localhost identified by 
'some_password';
flush privileges;

====

Extracted the war file to 'xwiki' inside of webapps...

Added mysql-connector-java-5.1.16-bin.jar to   xwiki/WEB-INF/lib

====

Changed hibernate.cfg.xml by:

commenting out the hsqldb section...
moved the comment tag for the mysql section up under the reference to 
xwiki-1945 Leaving the property and mapping nodes uncommented:

<property 
name="connection.url">jdbc:mysql://localhost/testxwiki?useServerPrepStmts=false&useUnicode=true&characterEncoding=UTF-8&sessionVariables=sql_mode=''</property>
<property name="connection.username">xwiki</property>
<property name="connection.password">some_password</property>
<property name="connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="dialect">org.hibernate.dialect.MySQLDialect</property>
<property 
name="connection.provider_class">com.xpn.xwiki.store.DBCPConnectionProvider</property>
<property name="connection.pool_size">2</property>
<property name="statement_cache.size">2</property>
<mapping resource="xwiki.hbm.xml"/>
<mapping resource="feeds.hbm.xml"/>
<mapping resource="activitystream.hbm.xml"/>

====

changed xwiki.cfg as follows:

  diff xwiki.original xwiki.cfg
82c82
< # xwiki.store.hibernate.path=/WEB-INF/hibernate.cfg.xml
---
...
xwiki.store.hibernate.path=/WEB-INF/hibernate.cfg.xml
104c104
< # xwiki.db=xwiki

...
xwiki.db=testxwiki
DO I NEED TO CHANGE THE XWIKI.DB PROPERTY???

====

When I start tomcat and go to the xwiki site I get the following in 
catalina.out

STARTING TOMCAT...

May 26, 2011 2:02:57 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/local/jdk160_25/jre/lib/amd64/server:/usr/local/jdk160_25/jre/lib/amd64:/usr/local/jdk160_25/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
May 26, 2011 2:02:57 AM org.apache.coyote.AbstractProtocolHandler init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
May 26, 2011 2:02:57 AM org.apache.coyote.AbstractProtocolHandler init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
May 26, 2011 2:02:57 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1213 ms
May 26, 2011 2:02:57 AM org.apache.catalina.core.StandardService 
startInternal
INFO: Starting service Catalina
May 26, 2011 2:02:57 AM org.apache.catalina.core.StandardEngine 
startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.14
May 26, 2011 2:02:57 AM org.apache.catalina.startup.HostConfig 
deployDirectory
INFO: Deploying web application directory xwiki
May 26, 2011 2:02:59 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/struts/tags-html-1.0.2 
is already defined
May 26, 2011 2:02:59 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/struts/tags-bean-1.0.2 
is already defined
May 26, 2011 2:02:59 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: 
http://jakarta.apache.org/struts/tags-logic-1.0.2 is already defined
May 26, 2011 2:03:09 AM org.apache.catalina.startup.HostConfig 
deployDirectory
INFO: Deploying web application directory docs
May 26, 2011 2:03:09 AM org.apache.catalina.startup.HostConfig 
deployDirectory
INFO: Deploying web application directory ROOT
May 26, 2011 2:03:09 AM org.apache.coyote.AbstractProtocolHandler start
INFO: Starting ProtocolHandler ["http-bio-8080"]
May 26, 2011 2:03:09 AM org.apache.coyote.AbstractProtocolHandler start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
May 26, 2011 2:03:09 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 12410 ms

BROWSE TO THE XWIKI APP....

2011-05-26 02:03:29,868 [/xwiki/bin/view/Main/] FATAL 
store.DBCPConnectionProvider    - Could not create a DBCP pool. There is 
an error in the hibernate configuration file, please review it.
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Unexpected exception encountered during query.)
     at 
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
     at 
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
     at 
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
     at 
com.xpn.xwiki.store.DBCPConnectionProvider.configure(DBCPConnectionProvider.java:193)
     at 
org.hibernate.connection.ConnectionProviderFactory.newConnectionProvider(ConnectionProviderFactory.java:124)
     at 
org.hibernate.connection.ConnectionProviderFactory.newConnectionProvider(ConnectionProviderFactory.java:56)
     at 
org.hibernate.cfg.SettingsFactory.createConnectionProvider(SettingsFactory.java:414)
     at 
org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:62)
     at 
org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2073)
     at 
org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1298)
     at 
com.xpn.xwiki.store.XWikiHibernateBaseStore.initHibernate(XWikiHibernateBaseStore.java:166)
     at 
com.xpn.xwiki.store.XWikiHibernateBaseStore.checkHibernate(XWikiHibernateBaseStore.java:560)
     at 
com.xpn.xwiki.store.XWikiHibernateBaseStore.execute(XWikiHibernateBaseStore.java:1073)
     at 
com.xpn.xwiki.store.XWikiHibernateBaseStore.executeRead(XWikiHibernateBaseStore.java:1117)
     at 
com.xpn.xwiki.store.migration.hibernate.XWikiHibernateMigrationManager.getDBVersion(XWikiHibernateMigrationManager.java:68)
     at 
com.xpn.xwiki.store.migration.AbstractXWikiMigrationManager.<init>(AbstractXWikiMigrationManager.java:68)
     at 
com.xpn.xwiki.store.migration.hibernate.XWikiHibernateMigrationManager.<init>(XWikiHibernateMigrationManager.java:51)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
     at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
     at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
     at com.xpn.xwiki.XWiki.createClassFromConfig(XWiki.java:1132)
     at com.xpn.xwiki.XWiki.initXWiki(XWiki.java:813)
     at com.xpn.xwiki.XWiki.<init>(XWiki.java:756)
     at com.xpn.xwiki.XWiki.getMainXWiki(XWiki.java:408)
     at com.xpn.xwiki.XWiki.getXWiki(XWiki.java:496)
     at com.xpn.xwiki.web.XWikiAction.execute(XWikiAction.java:137)
     at com.xpn.xwiki.web.XWikiAction.execute(XWikiAction.java:117)
     at 
org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:431)
     at 
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:236)
     at 
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1196)
     at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:304)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at com.xpn.xwiki.web.ActionFilter.doFilter(ActionFilter.java:129)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at 
org.xwiki.wysiwyg.server.filter.ConversionFilter.doFilter(ConversionFilter.java:152)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at 
com.xpn.xwiki.plugin.webdav.XWikiDavFilter.doFilter(XWikiDavFilter.java:68)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at 
org.xwiki.container.servlet.filters.internal.SavedRequestRestorerFilter.doFilter(SavedRequestRestorerFilter.java:218)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at 
org.xwiki.container.servlet.filters.internal.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:112)
     at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:240)
     at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:164)
     at 
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:462)
     at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:164)
     at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
     at 
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:563)
     at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
     at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:399)
     at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:317)
     at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:204)
     at 
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:311)
     at 
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
     at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
     at java.lang.Thread.run(Thread.java:662)
Caused by: java.sql.SQLException: Unexpected exception encountered 
during query.
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
     at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2665)
     at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1698)
     at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1617)
     at 
com.mysql.jdbc.ConnectionImpl.setSessionVariables(ConnectionImpl.java:5210)
     at 
com.mysql.jdbc.ConnectionImpl.initializePropsFromServer(ConnectionImpl.java:3375)
     at 
com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2385)
     at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2154)
     at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:792)
     at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)
     at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
     at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
     at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
     at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
     at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:381)
     at 
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
     at 
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
     at 
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
     at 
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
     at 
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
     ... 64 more
Caused by: java.lang.NullPointerException
     at 
com.mysql.jdbc.ConnectionImpl.getServerCharacterEncoding(ConnectionImpl.java:3100)
     at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2095)
     at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2619)
     ... 83 more
2011-05-26 02:03:29,876 [/xwiki/bin/view/Main/] WARN  
action.RequestProcessor         - Unhandled Exception thrown: class 
com.xpn.xwiki.XWikiException
May 26, 2011 2:22:34 AM org.apache.catalina.core.StandardServer await

WHEN STOPPING TOMCAT....

INFO: A valid shutdown command was received via the shutdown port. 
Stopping the Server instance.
May 26, 2011 2:22:34 AM org.apache.coyote.AbstractProtocolHandler pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
May 26, 2011 2:22:35 AM org.apache.coyote.AbstractProtocolHandler pause
INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
May 26, 2011 2:22:36 AM org.apache.catalina.core.StandardService 
stopInternal
INFO: Stopping service Catalina
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
clearReferencesJdbc
SEVERE: The web application [/xwiki] 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
clearReferencesThreads
SEVERE: The web application [/xwiki] appears to have started a thread 
named [EvictionTimer-0] but has failed to stop it. This is very likely 
to create a memory leak.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
clearReferencesThreads
SEVERE: The web application [/xwiki] appears to have started a thread 
named [EvictionTimer-1] but has failed to stop it. This is very likely 
to create a memory leak.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value [{}]) 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value 
[{url=http://neil.nmc.edu:8080/xwiki/bin/view/Main/}]) 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.
May 26, 2011 2:22:37 AM org.apache.catalina.loader.WebappClassLoader 
checkThreadLocalMapForLeaks
SEVERE: The web application [/xwiki] created a ThreadLocal with key of 
type [org.apache.log4j.helpers.ThreadLocalMap] (value 
[org.apache.log4j.helpers.ThreadLocalMap@2a717ef5]) and a value of type 
[java.util.Hashtable] (value 
[{url=http://neil.nmc.edu:8080/xwiki/bin/view/Main/}]) 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.
May 26, 2011 2:22:37 AM org.apache.coyote.AbstractProtocolHandler stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
May 26, 2011 2:22:37 AM org.apache.coyote.AbstractProtocolHandler stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]

Neil Streeter

Caleb James DeLisle

Neil Streeter

Sergiu Dumitriu

tags

participants (3)