Thread Dump Analysis Tool / Method

One set of thread dumps alone will not be too helpful to get to the root cause.

The trick is to take 4 or 5 sets of thread dumps at an interval of 5 seconds between each. so at the end you will have a single log file which has around 20 - 25 seconds worth of action on the app server.

What you want to check is when a stuck thread or long running transaction happens, all the thread dumps will show a certain thread id is at the same line in your java stack trace. In simpler terms, the transaction (say in an EJB or database) is spanning across multiple thread dumps and hence needs more investigation.

Now when you run these through Samurai (I havent used TDA myself), it will highlight these in Red colour so you can quickly click on it and get to the lines showing issues.

See an example of this here. Look at the Samurai output image in that link. The Green cells are fine. Red and Grey cells need looking at.

A Samurai example from my own web app below shows a stuck sequence for Thread'19' across a span of 5 - 10 seconds

>     Thread dump 2/3 "[ACTIVE] ExecuteThread: '19' for queue:
> 'weblogic.kernel.Default
> (self-tuning)'" daemon prio=7
> tid=07b06000 nid=108 lwp_id=222813
> waiting for monitor entry
> [2aa40000..2aa40b30]     
> java.lang.Thread.State: BLOCKED (on
> object monitor)      at
> com.bea.p13n.util.lease.JDBCLeaseManager.renewLease(JDBCLeaseManager.java:393)
> - waiting to lock <735e9f88> (a com.bea.p13n.util.lease.JDBCLeaseManager)
> at
> com.bea.p13n.util.lease.Lease$LeaseTimer.timerExpired(Lease.java:229)

...

> Thread dump 3/3 "[ACTIVE]
> ExecuteThread: '19' for queue:
> 'weblogic.kernel.Default
> (self-tuning)'"   daemon prio=7
> tid=07b06000 nid=108 lwp_id=222813
> waiting for monitor entry
> [2aa40000..2aa40b30]     
> java.lang.Thread.State: BLOCKED (on
> object monitor)      at
> com.bea.p13n.util.lease.JDBCLeaseManager.renewLease(JDBCLeaseManager.java:393)
> - waiting to lock <735e9f88> (a com.bea.p13n.util.lease.JDBCLeaseManager)
> at
> com.bea.p13n.util.lease.Lease$LeaseTimer.timerExpired(Lease.java:229)

update

I recently used the Java Thread Dump Analyzer mentioned in this answer and it's been very useful for Tomcat as opposed to Samurai

I know this is an old question but I just wrote a tool to help make long thread dumps more readable.

Java Thread Dump Analysis Tool

This tool groups threads together which have the same stack trace and allows you to only show threads which are in particular states (e.g. RUNNABLE or BLOCKED).

This makes it a bit quicker to find the interesting threads amongst the tens or hundreds of JBoss threads which spend most of their time waiting for work at the same place in the code and therefore all have the same stack trace.