We present a fast method for producing mock galaxy catalogues that can be used to compute the covariance of large-scale clustering measurements and test analysis techniques. Our method populates a second-order Lagrangian perturbation theory (2LPT) matter field, where we calibrate masses of dark matter haloes by detailed comparisons with N-body simulations. We demonstrate that the clustering of haloes is recovered at ∼10 per cent accuracy. We populate haloes with mock galaxies using a halo occupation distribution (HOD) prescription, which has been calibrated to reproduce the clustering measurements on scales between 30 and 80  h −1 Mpc. We compare the sample covariance matrix from our mocks with analytic estimates, and discuss differences. We have used this method to make catalogues corresponding to Data Release 9 of the Baryon Oscillation Spectroscopic Survey (BOSS), producing 600 mock catalogues of the 'CMASS' galaxy sample. These mocks have enabled detailed tests of methods and errors, and have formed an integral part of companion analyses of these galaxy data.