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Issues installing OpenClinica-3.1.2 on Linux Debian [created a ThreadLocal ...]

Hi at all,
I’m facing some issues installing OpenClinica-3.1.2 on Linux Debian.

When I try to startup Tomcat, the following logs appear:

INFO: Deploying web application directory examples
Sep 12, 2012 9:36:38 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Sep 12, 2012 9:36:38 AM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Sep 12, 2012 9:36:38 AM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/266 config=null
Sep 12, 2012 9:36:38 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 10204 ms
SLF4J: The requested version 1.5.11 by your slf4j binding is not compatible with [1.5.5, 1.5.6]
SLF4J: See http://www.slf4j.org/codes.html#version_mismatch for further details.
AbandonedObjectPool is used ([email protected])
LogAbandoned: true
RemoveAbandoned: true
RemoveAbandonedTimeout: 300
Sep 12, 2012 9:37:12 AM liquibase.database.template.JdbcTemplate comment
INFO: Lock Database
Sep 12, 2012 9:37:12 AM liquibase.lock.LockHandler acquireLock
INFO: Successfully acquired change log lock
Sep 12, 2012 9:37:13 AM liquibase.database.AbstractDatabase getRanChangeSetList
INFO: Reading from databasechangelog
Sep 12, 2012 9:37:13 AM liquibase.database.template.JdbcTemplate comment
INFO: Changeset migration/2.5/changeLogCreateTables.xml::1235684743487-0::pgawade (generated)::(MD5Sum: 6077be15943c12e7ae9a2a647dd2ff2)
Sep 12, 2012 9:37:13 AM liquibase.database.template.JdbcTemplate comment
INFO: Release Database Lock
Sep 12, 2012 9:37:13 AM liquibase.lock.LockHandler releaseLock
INFO: Successfully released change log lock
Sep 12, 2012 9:37:13 AM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Sep 12, 2012 9:37:13 AM org.apache.catalina.core.StandardContext start
SEVERE: Context [/OpenClinica] startup failed due to previous errors
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/OpenClinica] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [Timer-1] but has failed to stop it. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.core.UnsynchronizedAppenderBase$1] (value [[email protected]]) and a value of type [java.lang.Boolean] (value [false]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.

I don’t understand why this ThreadLocal error appears.

Thanks in advance for your support.

Ennio

Comments

  • zwetszwets Posts: 59
    Hi Ennio,
    The errors you are referring to are red herrings. They are not relevant to your issue, just Tomcat reporting about resources not released by a stopped application. The hint is in the first two error messages occurring in your log:
    > SEVERE: Error listenerStart
    > SEVERE: Context [/OpenClinica] startup failed due to previous errors
    Meaning it could not start the application due to errors that occurred earlier. You will have to look into the other log files for the cause of the error.
    Best regards,
    Marco
    On 12 Sep 2012, at 18:53, Ennio Masi - Hippocrates Sintech S.r.l. wrote:
    > Hi at all,
    > I’m facing some issues installing OpenClinica-3.1.2 on Linux Debian.
    >
    > When I try to startup Tomcat, the following logs appear:
    >
    > INFO: Deploying web application directory examples
    > Sep 12, 2012 9:36:38 AM org.apache.coyote.http11.Http11Protocol start
    > INFO: Starting Coyote HTTP/1.1 on http-8080
    > Sep 12, 2012 9:36:38 AM org.apache.jk.common.ChannelSocket init
    > INFO: JK: ajp13 listening on /0.0.0.0:8009
    > Sep 12, 2012 9:36:38 AM org.apache.jk.server.JkMain start
    > INFO: Jk running ID=0 time=0/266 config=null
    > Sep 12, 2012 9:36:38 AM org.apache.catalina.startup.Catalina start
    > INFO: Server startup in 10204 ms
    > SLF4J: The requested version 1.5.11 by your slf4j binding is not compatible with [1.5.5, 1.5.6]
    > SLF4J: See http://www.slf4j.org/codes.html#version_mismatch for further details.
    > AbandonedObjectPool is used ([email protected])
    > LogAbandoned: true
    > RemoveAbandoned: true
    > RemoveAbandonedTimeout: 300
    > Sep 12, 2012 9:37:12 AM liquibase.database.template.JdbcTemplate comment
    > INFO: Lock Database
    > Sep 12, 2012 9:37:12 AM liquibase.lock.LockHandler acquireLock
    > INFO: Successfully acquired change log lock
    > Sep 12, 2012 9:37:13 AM liquibase.database.AbstractDatabase getRanChangeSetList
    > INFO: Reading from databasechangelog
    > Sep 12, 2012 9:37:13 AM liquibase.database.template.JdbcTemplate comment
    > INFO: Changeset migration/2.5/changeLogCreateTables.xml::1235684743487-0::pgawade (generated)::(MD5Sum: 6077be15943c12e7ae9a2a647dd2ff2)
    > Sep 12, 2012 9:37:13 AM liquibase.database.template.JdbcTemplate comment
    > INFO: Release Database Lock
    > Sep 12, 2012 9:37:13 AM liquibase.lock.LockHandler releaseLock
    > INFO: Successfully released change log lock
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.core.StandardContext start
    > SEVERE: Error listenerStart
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.core.StandardContext start
    > SEVERE: Context [/OpenClinica] startup failed due to previous errors
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
    > SEVERE: The web application [/OpenClinica] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    > SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    > SEVERE: The web application [/OpenClinica] appears to have started a thread named [Timer-1] but has failed to stop it. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    > SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    > SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.core.UnsynchronizedAppenderBase$1] (value [[email protected]]) and a value of type [java.lang.Boolean] (value [false]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    > SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    > SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    > Sep 12, 2012 9:37:13 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    > SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=debian.hippocrates.ge, WEBAPP=/home/ennio/oc/install/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    >
    > I don’t understand why this ThreadLocal error appears.
    >
    > Thanks in advance for your support.
    >
    > Ennio
    >
This discussion has been closed.