Alfresco startup error post mysql re-install

[christopher]

Can anyone help me out.

I have a ubuntu system where alfresco enterprise edition3.4.5 and mysql5.5 was installed.

Mysql got corrupt and I re-installed it and started again. Iam able to log into mysql as root & as alfresco user without any issues, post reinstall…. Restarted alfresco, but it throws below error . Its a blocker for me where I'm not able to proceed.

Alfresco is started via /opt/alfresco-3.4.5/alfresco.sh

My questions are :
—————-
Should I run any script having installed mysql freshly before restart of alfresco ?
Should I clear anything from alfresco temp directory before restarting alfresco?
Am I missing something else.

S/w details:
———
x86_64 GNU/Linux Ubuntu
Alfresco - 3.4.5
Mysql - 5.5

Error Stacktrace:
————–

Apr 16, 2015 12:04:06 PM 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: /opt/alfresco-3.4.5/java/jre/lib/amd64/server:/opt/alfresco-3.4.5/java/jre/lib/amd64:/opt/alfresco-3.4.5/java/jre/../lib/amd64:/opt/alfresco-3.4.5/common/lib::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Apr 16, 2015 12:04:07 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8180
Apr 16, 2015 12:04:07 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 504 ms
Apr 16, 2015 12:04:07 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Apr 16, 2015 12:04:07 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.29
Apr 16, 2015 12:04:07 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor ROOT.xml
Apr 16, 2015 12:04:08 PM org.apache.catalina.core.StandardContext addApplicationListener
INFO: The listener "org.apache.myfaces.webapp.StartupServletContextListener" is already configured for this context. The duplicate definition has been ignored.
12:04:13,853  INFO  [alfresco.config.JndiPropertiesFactoryBean] Loading properties file from class path resource [alfresco/repository.properties]
12:04:13,857  INFO  [alfresco.config.JndiPropertiesFactoryBean] Loading properties file from class path resource [alfresco/domain/transaction.properties]
12:04:13,858  INFO  [alfresco.config.JndiPropertiesFactoryBean] Loading properties file from file [/opt/alfresco-3.4.5/tomcat/webapps/ROOT/WEB-INF/classes/alfresco/module/test/alfresco-global.properties]
12:04:13,859  INFO  [alfresco.config.JndiPropertiesFactoryBean] Loading properties file from URL [file:/opt/alfresco-3.4.5/tomcat/shared/classes/alfresco-global.properties]
12:04:13,925  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/version.properties]
12:04:13,975  INFO  [alfresco.config.JndiPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/alfresco-shared.properties]
12:04:14,023  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/domain/cache-strategies.properties]
12:04:14,573  INFO  [management.subsystems.ChildApplicationContextFactory] Starting 'sysAdmin' subsystem, ID: [sysAdmin, default]
12:04:14,600  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/version.properties]
12:04:14,600  INFO  [alfresco.config.JndiPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/alfresco-shared.properties]
12:04:14,600  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/domain/cache-strategies.properties]
12:04:14,611  INFO  [management.subsystems.ChildApplicationContextFactory] Startup of 'sysAdmin' subsystem, ID: [sysAdmin, default] complete
12:04:24,949  INFO  [extensions.webscripts.TemplateProcessorRegistry] Registered template processor Repository Template Processor for extension ftl
12:04:24,950  INFO  [extensions.webscripts.ScriptProcessorRegistry] Registered script processor Repository Script Processor for extension js
java.net.UnknownHostException: basename
   at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)
   at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
   at java.net.Socket.connect(Socket.java:529)
   at java.net.Socket.connect(Socket.java:478)
   at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
   at sun.net.NetworkClient.openServer(NetworkClient.java:118)
   at sun.net.ftp.FtpClient.openServer(FtpClient.java:488)
   at sun.net.ftp.FtpClient.openServer(FtpClient.java:475)
   at sun.net.www.protocol.ftp.FtpURLConnection.connect(FtpURLConnection.java:270)
   at sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(FtpURLConnection.java:352)
   at java.net.URL.openStream(URL.java:1010)
   at org.apache.xml.resolver.Catalog.parseCatalogFile(Unknown Source)
   at org.apache.xml.resolver.Catalog.parsePendingCatalogs(Unknown Source)
   at org.apache.xml.resolver.Catalog.parseCatalog(Unknown Source)
   at org.apache.xml.resolver.Catalog.loadSystemCatalogs(Unknown Source)
   at org.apache.xml.resolver.CatalogManager.getPrivateCatalog(Unknown Source)
   at org.apache.xml.resolver.CatalogManager.getCatalog(Unknown Source)
   at org.apache.xml.resolver.tools.CatalogResolver.initializeCatalogs(Unknown Source)
   at org.apache.xml.resolver.tools.CatalogResolver.<init>(Unknown Source)
   at org.apache.cxf.catalog.OASISCatalogManager.getResolver(OASISCatalogManager.java:69)
   at org.apache.cxf.catalog.OASISCatalogManager.<init>(OASISCatalogManager.java:58)
   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 org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:72)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:938)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:890)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:557)
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:842)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:416)
   at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:261)
   at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:192)
   at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
   at org.alfresco.web.app.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:63)
   at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4135)
   at org.apache.catalina.core.StandardContext.start(StandardContext.java:4630)
   at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
   at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
   at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
   at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
   at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
   at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
   at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
   at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
   at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
   at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
   at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
   at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
   at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
   at org.apache.catalina.core.StandardService.start(StandardService.java:519)
   at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
   at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
   at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
12:04:30,097  INFO  [domain.schema.SchemaBootstrap] Schema managed by database dialect org.hibernate.dialect.MySQLInnoDBDialect.
12:04:30,509  INFO  [domain.schema.SchemaBootstrap] No changes were made to the schema.
12:04:31,674  INFO  [management.subsystems.ChildApplicationContextFactory] Starting 'thirdparty' subsystem, ID: [thirdparty, default]
12:04:31,689  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/version.properties]
12:04:31,690  INFO  [alfresco.config.JndiPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/alfresco-shared.properties]
12:04:31,690  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/domain/cache-strategies.properties]
12:04:31,907  INFO  [management.subsystems.ChildApplicationContextFactory] Startup of 'thirdparty' subsystem, ID: [thirdparty, default] complete
12:04:31,907  INFO  [management.subsystems.ChildApplicationContextFactory] Starting 'OOoDirect' subsystem, ID: [OOoDirect, default]
12:04:31,918  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/version.properties]
12:04:31,918  INFO  [alfresco.config.JndiPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/alfresco-shared.properties]
12:04:31,918  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/domain/cache-strategies.properties]
12:04:32,256  WARN  [alfresco.util.OpenOfficeConnectionTester] An initial OpenOffice connection could not be established.
12:04:32,264  INFO  [management.subsystems.ChildApplicationContextFactory] Startup of 'OOoDirect' subsystem, ID: [OOoDirect, default] complete
12:04:32,264  INFO  [management.subsystems.ChildApplicationContextFactory] Starting 'OOoJodconverter' subsystem, ID: [OOoJodconverter, default]
12:04:32,275  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/version.properties]
12:04:32,275  INFO  [alfresco.config.JndiPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/alfresco-shared.properties]
12:04:32,276  INFO  [alfresco.config.FixedPropertyPlaceholderConfigurer] Loading properties file from class path resource [alfresco/domain/cache-strategies.properties]
12:04:32,296  INFO  [management.subsystems.ChildApplicationContextFactory] Startup of 'OOoJodconverter' subsystem, ID: [OOoJodconverter, default] complete
12:04:32,621  WARN  [node.index.FullIndexRecoveryComponent] The indexes are not synchronized with the database.
12:04:32,959  INFO  [repo.admin.ConfigurationChecker] The Alfresco root data directory ('dir.root') is: /opt/alfresco-3.4.5/alf_data
12:04:33,027  ERROR [web.context.ContextLoader] Context initialization failed
org.alfresco.error.AlfrescoRuntimeException: 03160000 The store 'avm://sitestore' has a duplicate root node entry.
   at org.alfresco.repo.admin.ConfigurationChecker.check(ConfigurationChecker.java:288)
   at org.alfresco.repo.admin.ConfigurationChecker.access$000(ConfigurationChecker.java:68)
   at org.alfresco.repo.admin.ConfigurationChecker$1.execute(ConfigurationChecker.java:180)
   at org.alfresco.repo.transaction.RetryingTransactionHelper.doInTransaction(RetryingTransactionHelper.java:381)
   at org.alfresco.repo.transaction.RetryingTransactionHelper.doInTransaction(RetryingTransactionHelper.java:272)
   at org.alfresco.repo.admin.ConfigurationChecker.onBootstrap(ConfigurationChecker.java:184)
   at org.springframework.extensions.surf.util.AbstractLifecycleBean.onApplicationEvent(AbstractLifecycleBean.java:56)
   at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:97)
   at org.alfresco.repo.management.SafeApplicationEventMulticaster.multicastEvent(SafeApplicationEventMulticaster.java:78)
   at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:294)
   at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:858)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:419)
   at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:261)
   at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:192)
   at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
   at org.alfresco.web.app.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:63)
   at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4135)
   at org.apache.catalina.core.StandardContext.start(StandardContext.java:4630)
   at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
   at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
   at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
   at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
   at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
   at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
   at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
   at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
   at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
   at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
   at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
   at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
   at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:445)
   at org.apache.catalina.core.StandardService.start(StandardService.java:519)
   at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
   at org.apache.catalina.startup.Catalina.start(Catalina.java:581)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
   at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Apr 16, 2015 12:04:33 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Apr 16, 2015 12:04:33 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [] startup failed due to previous errors
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.
Apr 16, 2015 12:04:33 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.

[mrogers]

you have a mismatch between your indexes and the database.      Or your index and the content store.   If you start with an empty database you also need to clear the content store.    I you care about the content store then you need to restore the db from backup.

[christopher]

Thanks for the Reply Rogers,

But mysql was completely corrupt and I was unable to connect to it due to which I couldnt take a back up of my db. what will happen if i clear content store ? Will I be able to restart alfresco without any issues?

What does this content store contains ?

[christopher]

Can someone reply,
I emptied contents of contenstore , contentstore.deleted & luceneindexes. problem still persists…