thanks Michael but the presence of the drupal filter does seem to take Fedora
down. If Fedora messaging is enabled it also runs out of memory. Without
messaging fedora tries to restart when it detects the filter and then crashes:
**************************
** FEDORA STARTUP ERROR **
**************************
Fedora startup failed
org.fcrepo.server.errors.ServerInitializationException:
java.lang.RuntimeException: org.fcrepo.server.Server.<init>(Server.java:673)
org.fcrepo.server.BasicServer.<init>(BasicServer.java:41)
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
java.lang.reflect.Constructor.newInstance(Constructor.java:513)
org.fcrepo.server.Server.getInstance(Server.java:1001)
org.fcrepo.server.ServerController.init(ServerController.java:402)
javax.servlet.GenericServlet.init(GenericServlet.java:212)
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
org.apache.catalina.core.StandardContext.reload(StandardContext.java:3461)
org.apache.catalina.loader.WebappLoader.backgroundProcess(WebappLoader.java:426)
org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1361)
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653)
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642)
java.lang.Thread.run(Thread.java:662)
at org.fcrepo.server.Server.getInstance(Server.java:1044)
at org.fcrepo.server.ServerController.init(ServerController.java:402)
at javax.servlet.GenericServlet.init(GenericServlet.java:212)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
at
org.apache.catalina.core.StandardContext.reload(StandardContext.java:3461)
at
org.apache.catalina.loader.WebappLoader.backgroundProcess(WebappLoader.java:426)
at
org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1361)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
at
org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642)
at java.lang.Thread.run(Thread.java:662)
23-Jan-2012 12:14:27 org.apache.catalina.loader.WebappClassLoader modified
INFO: Additional JARs have been added : 'fcrepo-drupalauthfilter-3.4.2.jar'
23-Jan-2012 12:14:27 org.apache.catalina.core.StandardContext reload
INFO: Reloading Context with name [/fedora] has started
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/fedora] appears to have started a thread named
[MySQL Statement Cancellation Timer] but has failed to stop it. This is very
likely to create a memory leak.
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/fedora] appears to have started a thread named
[JotmBatch] but has failed to stop it. This is very likely to create a memory
leak.
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/fedora] appears to have started a thread named
[JotmClock] but has failed to stop it. This is very likely to create a memory
leak.
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads
SEVERE: The web application [/fedora] appears to have started a thread named
[Write-lock Reaper] but has failed to stop it. This is very likely to create a
memory leak.
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearThreadLocalMap
SEVERE: The web application [/fedora] created a ThreadLocal with key of type
[ch.qos.logback.core.UnsynchronizedAppenderBase$1] (value
[ch.qos.logback.core.UnsynchronizedAppenderBase$1@1d6733c]) and a value of type
[java.lang.Boolean] (value [false]) but failed to remove it when the web
application was stopped. This is very likely to create a memory leak.
23-Jan-2012 12:14:29 org.apache.catalina.loader.WebappClassLoader
clearThreadLocalMap
SEVERE: The web application [/fedora] created a ThreadLocal with key of type
[org.apache.axis.utils.XMLUtils.ThreadLocalDocumentBuilder] (value
[org.apache.axis.utils.XMLUtils$ThreadLocalDocumentBuilder@27a180]) and a value
of type [org.apache.xerces.jaxp.DocumentBuilderImpl] (value
[org.apache.xerces.jaxp.DocumentBuilderImpl@1dc0fec]) but failed to remove it
when the web application was stopped. This is very likely to create a memory
leak.
--
mov eax,1
mov ebx,0
int 80h
On 23 Jan 2012, at 12:02, Michael Della Bitta wrote:
> Hello, Alistair,
>
> A number of those memory leak errors will happen as a matter of
> course... I see them in our install. They may be a red herring... Have
> you tried adding " -XX:+HeapDumpOnOutOfMemoryError" to your JVM args?
> That will dump a file when the process runs out of RAM that shows what
> was tying things up.
>
> Michael Della Bitta
>
> Senior Applications Developer
> Information Technology Group
> The New York Public Library
> 40 West 20th Street, 5th Floor
> New York, NY 10011-4211
> (212) 621-0609
>
>
>
> On Mon, Jan 23, 2012 at 6:51 AM, Alistair Young
> <alistair.yo...@uhi.ac.uk> wrote:
>> I switched to Fedora 3.4.2 and removed gsearch and narrowed it down to:
>>
>> fcrepo-drupalauthfilter-3.4.2.jar
>>
>> Has anyone come across this before?
>>
>> 23-Jan-2012 11:49:06 org.apache.catalina.loader.WebappClassLoader modified
>> INFO: Additional JARs have been added :
>> 'fcrepo-drupalauthfilter-3.4.2.jar'
>> 23-Jan-2012 11:49:06 org.apache.catalina.core.StandardContext reload
>> INFO: Reloading Context with name [/fedora] has started
>> 23-Jan-2012 11:49:09 org.apache.catalina.loader.WebappClassLoader
>> clearReferencesThreads
>> SEVERE: The web application [/fedora] appears to have started a thread named
>> [MySQL Statement Cancellation Timer] but has failed to stop it. This is very
>> likely to create a memory leak.
>> 23-Jan-2012 11:49:09 org.apache.catalina.loader.WebappClassLoader
>> clearThreadLocalMap
>> SEVERE: The web application [/fedora] created a ThreadLocal with key of type
>> [ch.qos.logback.core.UnsynchronizedAppenderBase$1] (value
>> [ch.qos.logback.core.UnsynchronizedAppenderBase$1@f180d9]) and a value of
>> type [java.lang.Boolean] (value [false]) but failed to remove it when the
>> web application was stopped. This is very likely to create a memory leak.
>> 23-Jan-2012 11:49:09 org.apache.catalina.loader.WebappClassLoader
>> clearThreadLocalMap
>> SEVERE: The web application [/fedora] created a ThreadLocal with key of type
>> [org.apache.axis.utils.XMLUtils.ThreadLocalDocumentBuilder] (value
>> [org.apache.axis.utils.XMLUtils$ThreadLocalDocumentBuilder@1426497]) and a
>> value of type [org.apache.xerces.jaxp.DocumentBuilderImpl] (value
>> [org.apache.xerces.jaxp.DocumentBuilderImpl@1da11d8]) but failed to remove
>> it when the web application was stopped. This is very likely to create a
>> memory leak.
>>
>>
>> thanks,
>>
>> Alistair
>>
>> --
>> mov eax,1
>> mov ebx,0
>> int 80h
>>
>>
>>
>>
>> On 23 Jan 2012, at 10:45, Alistair Young wrote:
>>
>>> Would anyone know why this is the case? The log fills with this error on
>>> every startup and within 30s tomcat runs out of memory. I'm running fedora
>>> 3.5 with a drupal filter for allowing drupal admins to get at it. Also
>>> running gsearch 2.4.
>>>
>>> SEVERE: The web application [/fedora] created a ThreadLocal with key of
>>> type [org.slf4j.impl.CopyOnInheritThreadLocal] (value
>>> [org.slf4j.impl.CopyOnInheritThreadLocal@1e8b327]) and a value of type
>>> [java.util.HashMap] (value [{activemq.broker=localhost}]) but failed to
>>> remove it when the web application was stopped. This is very likely to
>>> create a memory leak.
>>>
>>> thanks,
>>>
>>> Alistair
>>>
>>>
>>> --
>>> mov eax,1
>>> mov ebx,0
>>> int 80h
>>>
>>>
>>>
>>>
>>>
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