Thank you. I have looked it up and tried the following:

ThreadMXBean threadBean = ManagementFactory.getThreadMXBean();
long beginCPUTime = threadBean.getCurrentThreadCpuTime();  //in units of
nanosecond

for-loop  //my heavy duty computation

long endCPUTime = threadBean.getCurrentThreadCpuTime(); //nanosecond
System.out.println("CPU Time used (millis): " +
(endCPUTime-beginCPUTime)/1000000);

The print out value is very close to the one I obtained from the
difference of System.currentMillis() after and before the loop. So it
looks like giving me the "apparent" time user has spent for this block
code, not CPU time.

I really like:

time java MyComputation

It gives the user time and system time spent for the whole program from
beginning to the end.

I came a "silly" idea for measuring the system time of the for-loop by
using "time" command:

for(int i=1; i<=20; i++)
{
    for-loop //my heavy duty computation
}

Then

time java MyComputation

The extra system time is due to 19 runs of for-loop. Divided it by 19
gives me the system time for a single for-loop.

I am going to use this to report to my boss.

 This reminded me of the fact that the JDK already contains a profiler.

 Search for »-Xprof« within the page

http://download.java.net/jdk7/docs/technotes/tools/windows/java.html