A memory system includes a substrate, control circuitry on the substrate, a three dimensional memory array (above the substrate) that includes a plurality of memory cells with reversible resistance-switching elements, and a circuit for detecting the setting and resetting of the reversible resistance-switching elements. In one aspect a circuit that has one or more clock inputs is run for a predetermined number of clock cycles. The circuit generates an amount of charge over the predetermined number of clock cycles. At most the amount of charge is provided to non-volatile storage element to program the non-volatile storage element. It is determined whether the non-volatile storage element is programmed to a desired state as a result of providing at most the amount of charge to the non-volatile storage element. Techniques disclosed herein can be applied to program memory cells other than memory cells with reversible resistance-switching elements.