A system has a linear accelerator, ion pump and a compensating magnet. The ion pump includes an ion pump magnet position, an ion pump magnet shape, an ion pump magnet orientation, and an ion pump magnet magnetic field profile. The compensating magnet has a position, a shape, an orientation, and a magnetic field profile, where at least one of the position, shape, orientation, and magnetic field profile of the compensating magnet reduce at least one component of a magnetic field in the linear accelerator resulting from the ion pump magnet.