In general, secondary refers to the second in an order. For example, with a computer, a secondary storage device is a hard drive. All programs run from the primary storage (memory), and the data is stored in the secondary storage.
Secondary jumper setting
A secondary jumper setting is found on a hard drive or CD drive, and adjusted using jumpers, as shown below. The secondary setting allows for two devices to be attached to a single IDE/ATAPI connection.
With early hard drives, this setting was referred to as a "slave" setting. However, because "slave" is offensive, it's better to refer to this drive as "primary" or "device0."