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I am using jp@gc - PerfMon Metrics Collector Lister for this and as you know it requires 'ServerAgent' running on the connecting server.
Step by step instruction would be very helpful.
And also, if anyone knows of any better alternatives to monitor the servers using jmeter then please share with me, it would be a great help.
Did you try the documentation or used a search engine like Google?
I found a couple of resources:
I think from the documentation is pretty clear how to install, run and use it.
As an alternative you can look at my favorite web loadtester FunkLoad which also has server side monitoring, this blog post explains about how to use it in more detail including the monitoring.
