Colloidal particles with active boundary layers - regions surrounding the particles where non-equilibrium processes produce large velocity gradients - are common in many physical, chemical and biological contexts. The velocity or stress at the edge of the boundary layer determines the exterior fluid flow and, hence, the many-body interparticle hydrodynamic interaction. Here, we present a method to compute the many-body hydrodynamic interaction between N spherical active particles induced by their exterior microhydrodynamic flow. First, we use a boundary integral representation of the Stokes equation to eliminate bulk fluid degrees of freedom. Then, we expand the boundary velocities and tractions of the integral representation in an infinite-dimensional basis of tensorial spherical harmonics and, on enforcing boundary conditions in a weak sense on the surface of each particle, obtain a system of linear algebraic equations for the unknown expansion coefficients. The truncation of the infinite series, fixed by the degree of accuracy required, yields a finite linear system that can be solved accurately and efficiently by iterative methods. The solution linearly relates the unknown rigid body motion to the known values of the expansion coefficients, motivating the introduction of propulsion matrices. These matrices completely characterize hydrodynamic interactions in active suspensions just as mobility matrices completely characterize hydrodynamic interactions in passive suspensions. The reduction in the dimensionality of the problem, from a three-dimensional partial differential equation to a two-dimensional integral equation, allows for dynamic simulations of hundreds of thousands of active particles on multi-core computational architectures. In our simulation of 104 active colloidal particle in a harmonic trap, we find that the necessary and sufficient ingredients to obtain steady-state convective currents, the so-called 'self-assembled pump', are (a) one-body self-propulsion and (b) two-body rotation from the vorticity of the Stokeslet induced in the trap. © 2015 IOP Publishing Ltd and SISSA Medialab srl.