Created attachment 826013 [details]
screenshot showing availability

I am hitting this issue as well and I might have repro steps: 

keep rhq server running at least 2.7 days

see screenshot2

Prepared set up which monitors availability of rhq.ear/rhq-core-domain-ejb3.jar#rhqpu. Let's see after a few days.

The rhq.ear/rhq-core-domain-ejb3.jar#rhqpu resource is still UP after ~3 days -> VERIFIED

Version :	
4.10.0-SNAPSHOT
Build Number :	
c526922

Ignore comment 4. It applies on RHQ master. I will do it again with JON3.2.1

The issue is still visible on JON3.2.1.DR2 Build Number :	
d18651a:f535707

TODO: Another retest on JON3.3.x

Still visible in
Version :	
3.3.0.ER01.1
Build Number :	
9941660:f3aa7e7

The exception from description is not visible in server.log but the resource rhq.ear/rhq-core-domain-ejb3.jar#rhqpu is still down.

Following warning is visible in agent.log:
2014-08-27 10:44:51,836 WARN  [InventoryManager.availability-1] (rhq.core.pc.inventory.AvailabilityExecutor)- Availability collection failed with exception on Resource[id=10235, uuid=980c0b17-b9af-4738-a462-596ae39f730b, type={JBossAS7}Hibernate Persistence Unit, key=deployment=rhq.ear,subdeployment=rhq-core-domain-ejb3.jar,subsystem=jpa,hibernate-persistence-unit=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, name=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, parent=jpa], availability will be reported as DOWN, reason=Availability check ran too long [60015ms], canceled for [ResourceContainer[resource=Resource[id=10235, uuid=980c0b17-b9af-4738-a462-596ae39f730b, type={JBossAS7}Hibernate Persistence Unit, key=deployment=rhq.ear,subdeployment=rhq-core-domain-ejb3.jar,subsystem=jpa,hibernate-persistence-unit=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, name=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, parent=jpa], syncState=SYNCHRONIZED, componentState=STARTED, avail=DOWN]]; Stack trace includes the timed out thread's stack trace.


Stack trace visible in UI:
org.rhq.core.pc.inventory.TimeoutException: Availability check ran too long [60015ms], canceled for [ResourceContainer[resource=Resource[id=10235, uuid=980c0b17-b9af-4738-a462-596ae39f730b, type={JBossAS7}Hibernate Persistence Unit, key=deployment=rhq.ear,subdeployment=rhq-core-domain-ejb3.jar,subsystem=jpa,hibernate-persistence-unit=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, name=rhq.ear/rhq-core-domain-ejb3.jar#rhqpu, parent=jpa], syncState=SYNCHRONIZED, componentState=STARTED, avail=DOWN]]; Stack trace includes the timed out thread's stack trace.
	at org.rhq.core.pc.inventory.AvailabilityProxy.getAvailability(AvailabilityProxy.java:187)
	at org.rhq.core.pc.inventory.AvailabilityExecutor.checkInventory(AvailabilityExecutor.java:339)
	at org.rhq.core.pc.inventory.AvailabilityExecutor.startScan(AvailabilityExecutor.java:174)
	at org.rhq.core.pc.inventory.CustomScanRootAvailabilityExecutor.startScan(CustomScanRootAvailabilityExecutor.java:71)
	at org.rhq.core.pc.inventory.AvailabilityExecutor.call(AvailabilityExecutor.java:130)
	at org.rhq.core.pc.inventory.AvailabilityExecutor.call(AvailabilityExecutor.java:60)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:178)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:292)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.Throwable
	at java.net.SocketInputStream.socketRead0(Native Method)
	at java.net.SocketInputStream.read(SocketInputStream.java:152)
	at java.net.SocketInputStream.read(SocketInputStream.java:122)
	at org.apache.http.impl.io.AbstractSessionInputBuffer.fillBuffer(AbstractSessionInputBuffer.java:166)
	at org.apache.http.impl.io.SocketInputBuffer.fillBuffer(SocketInputBuffer.java:90)
	at org.apache.http.impl.io.AbstractSessionInputBuffer.readLine(AbstractSessionInputBuffer.java:281)
	at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:92)
	at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:62)
	at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:254)
	at org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:289)
	at org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:252)
	at org.apache.http.impl.conn.ManagedClientConnectionImpl.receiveResponseHeader(ManagedClientConnectionImpl.java:191)
	at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:300)
	at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:127)
	at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:715)
	at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:520)
	at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:906)
	at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:805)
	at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:784)
	at org.rhq.modules.plugins.jbossas7.ASConnection.executeRaw(ASConnection.java:301)
	at org.rhq.modules.plugins.jbossas7.ASConnection.execute(ASConnection.java:512)
	at org.rhq.modules.plugins.jbossas7.ASConnection.execute(ASConnection.java:465)
	at org.rhq.modules.plugins.jbossas7.BaseComponent.getAvailability(BaseComponent.java:154)
	at org.rhq.core.pc.inventory.AvailabilityProxy.call(AvailabilityProxy.java:141)
	at org.rhq.core.pc.inventory.AvailabilityProxy.call(AvailabilityProxy.java:50)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	... 3 more

Filip, this is not the same stack trace. The stack trace you pasted in Comment 8 is a consequence of the problem described in Bug 1132091 - High CPU usage in hibernate thread (java.util.regex.Pattern$Start.match)

I'm setting the BZ to MODIFIED and target milestone ER02, in case you want to verify this one after Bug 1132091.

Moving to ON_QA as available for test with the following brew build:
https://brewweb.devel.redhat.com//buildinfo?buildID=381194

Verified on
Version :	
3.3.0.ER02
Build Number :	
4fbb183:7da54e2