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Pick the right method depending on your environment and OS that master/agents run.
Jenkins has a built-in SSH client implementation that it can use to talk to remote sshd and start an agent.
If you start to use Jenkins a lot with just a master you will most likely find that you will run out of resources (memory, CPU, etc.).
At this point you can either upgrade your master or you can setup agents to pick up the load.
Typically, your script uses a remote program execution mechanism like SSH, or other similar means (on Windows, this could be done by the same protocols through cygwin or tools like psexec), but Jenkins doesn't really assume any specific method of connectivity.
This is the most convenient set up on Windows, but does not allow you to run programs that require display interaction (such as GUI tests).
Upon clicking it, Java Web Start will kick in, and it launches an agent on the computer where the browser was running.
This mode is convenient when the master cannot initiate a connection to agents, such as when it runs outside a firewall while the rest of the agents are in the firewall.
A "master" operating by itself is the basic installation of Jenkins and in this configuration the master handles all tasks for your build system.
In most cases installing an agent doesn't change the behavior of the master.