My external disk made a clicking noise. How to do

It's simple. Heat comes from the drive motors spinning - so more heat implies more time spinning. (And since these drives spin at constant rates - it's more the duty cycle that the motors are on, then how the motors are being controlled that affects heat generation.)

I will assume you have selected "Put hard disk(s) to sleep when possible." in energy saver since that needs to be checked for Mac OS X to tell the drives they are no longer needed. When they are idled the heat generation is less.

If you asked to idle the drives by selecting the choice above, then you need to find what process is polling the drives which keeps them in a non-idle status. The fs_usage command would be a great place to start to monitor what writes/reads are happening.

Once you know what processes are responsible, you have a chance to change things.

Alternatively, you can use Disk Utility to unmount the drives. They should sleep well but at the cost of not being mounted.

A couple of questions that might shed some light on your subject:

1. By chance, did you clone your HDD onto the SSD?
2. If so, is your original OS X install still on the HDD?
3. Are any of your active data files located on the HDD?
4. Is the HDD activity constant or intermittent?

If (1&2) or 3 are true, the system on the SSD might be making calls to files on the HDD. This could be happening, especially if you didn't rename the HDD since your transplant. If 4 is constant, the activity cold be due to the USB 3 chipset attached via USB 2.

Here's a simple way to check:

1. SSD to HDD calls:
   • Launch a program on the dock
   • Does the external HDD activity light start flashing as the program launches or shortly thereafter?
2. Use your Mac "normally" for a while.
   • Close all obviously open data files.
   • Eject your external HDD by dragging the icon to the trash.
   • Does the OS show an error that it cannot eject the drive because files are open?
3. HDD dependency
   • Shut down your MacBook.
   • Disconnect your HHD.
   • Reboot your Mac.
   • Run programs you don't expect to need anything from the HDD and watch for errors or "missing" data that could be attributable to an older data file.

If any of the above conditions happen, your Mac has open files on the external drive.

Compared with "old" operating systems, recent editions of OS X are rather advanced operating systems, especially when compared with our "archaic" notions of how computers work. Power constraints, most noticeable in notebooks and tablets, are the new target for today's advancements. Newer hardware is often "asleep" when we are actively using the computer--not just powering down the processor or video subsystem when it can. Today's systems shut down motherboard-level systems, like the network connection, whenever it can... sometimes even while we're surfing the net!

Today's Macs have what Apple calls "power nap". This is a sleep state where the computer "wakes up" portions of the system to download updates, make back ups, and other necessary system maintenance. Even if your MacBook doesn't fully support power nap, your MacBook is probably making periodic updates to various system files.