Closed loop control of first piston according to output pressure to accommodate pressure variations.

A method for controlling a pump unit for, e.g. a chromatograph separator, the unit comprising fluidically connected alternating primary and secondary piston pumps having respective pistons and displacements p1, p2. The primary pump comprises an inlet and an outlet valve with settlement periods 201, 208, and the unit operates periodically to a pump cycle. The method determines unit delivery pressure and performs a closed loop primary piston position control 401 according to delivered pressure during a first cycle time interval 206. The primary piston stroke 203, 205 raises fluid to system pressure then fills 215 the secondary pump while delivering to the system. To stabilize the output the control swaps 400, 401, 402 between pistons and imposes additional movements on the controlled piston.