I have tested a lot of those open source profiler. My preference goes definitely to the integrated Netbeans profiler. It was simply the easiest and unified solution adapted to all the different settings I ever met, including profiling java applications that (i) were not developed under netbeans (ii) were only in the form of standalone jar (iii) were running on a remote Linux machine for which no X server were running (i.e. no UI), and other cases.

Here I describe how in 3 simple steps you can profile any java application using the wonderful Netbeans profiler.

Step 1: Download and install the latest Netbeans version on your machine(s)

On the netbeans download page choose the version adapted for your environment (Windows,Linux,Solaris,Mac…) and download/install it. All the bundles contain the profiler so I choose the lightest one: the JavaSE. If you want to profile a program running on a remote machine(s), you’ll have to download/install it on each machine.

Step 2: Modify the command line that runs the java application that you want to profile/monitor

You just have to add an argument to the Java VM.
On windows, the argument to add is of the form:

 -agentpath:"C:Program FilesNetBeans 6.7.1profiler3libdeployedjdk16windowsprofilerinterface.dll"="C:Program FilesNetBeans 6.7.1profiler3lib,5140"

Replace the portion “C:Program FilesNetBeans 6.7.1profiler3” by the correct path (located where you installed Netbeans). Keep 5140, it is the port on which the application will listen for a remote profiler session (that you can also perform locally, as in this tutorial).
On Linux, it is exactly the same, just look for the right path containing the profiler3 folder.
So the java command line of the application to profile should look something like:

java -agentpath:"C:Program FilesNetBeans 6.7.1profiler3libdeployedjdk16windowsprofilerinterface.dll"="C:Program FilesNetBeans 6.7.1profiler3lib,5140" MyApp param1 param2

When launching this command, you should see on your console a message saying:
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meaning that the application is listening and waiting for a profiler session on port 5140.

Note the flexibility behind this approach: it allows you to add this simple argument to the exsiting command of (i) any java applications running inside eclipse (in that case just open the “Run configuration” windows, in the “Arguments” tab just add the -agentpath option in the “VM arguments” section) or other IDE than Netbeans, (ii) any remote java applications (iii) any standalone jar file, or whatever existing java command that runs any kind of java application you can imagine…

Step 3: Run the Netbeans profiler GUI

Just open Netbeans, profile -> attach profiler. Choose which kind of profiling/monitoring you need, you can also configure it.

Press Attach. Note that the first time you attach a profiler it may fail since you have to calibrate the profiler (in that case, a simple textbox will tell you how, it takes seconds).

That’s it!! You can now see in real time which part of your application is the heaviest, estimate what its memory footprint, analyze the threads and much more.

If you want even more, note that it also exists specific profilers for collections (HashMap, HashSet, ArrayList, …) like collection spy (not free).