Generally it refers to applying power to the electric motor momentarily. For example, it is often done to see which direction the motor and hence the pump is rotating. When you install a 3 phase electric motor, it can rotate in either direction depending on how power is connected and unfortunately, there's no way of telling which way it will spin when it's turned on. So once power is connected, the motor is often jogged (also called "bumped") to see which way it turns. If it turns in the wrong direction then swapping any of the 2 wires will reverse the rotation. The motor may also be jogged to check belt alignment or for other reasons.
I have read somewhere about "jogging/jog" of pumps .Is it something to do with starting of a pump?
"Jog" is a term meaning to momentarily move a motor. The jog terminal is a connection that, when provided with a signal, causes momentary movement of the motor. Movement is ceased when the signal is removed.
It's a common industry term for mechatronics but usually refers only to axes (or motors) which have cyclic movement (like a pump, transport belt, rotary cutter, etc.) and not to linear motions (like a robotic arm or linear actuator).