I think I have exactly this problem. How do I confirm this? "strace" does not show me any obvious problems. Where would I look to see if the JVM "flush" was giving me problems?
Well, the easiest way to confirm is to turn off GC logging and see if your huge "GC pauses" go away. Alternatively, you could turn up the verbosity a bit - there's an extra flag for details about reference processing. In my case I was able to track down the exact line in the JVM from the log lines attributing the huge pauses to whatever trivial component occurred right after the first flush call.
If you record system metrics (eg. to ganglia) then you can also attempt to correlate large pauses to a large and rapidly declining number of dirty bytes in the fs cache.
If you record system metrics (eg. to ganglia) then you can also attempt to correlate large pauses to a large and rapidly declining number of dirty bytes in the fs cache.