The importance of adequate simulation of dispersed systems in microchannels with traps is due to the need to solve applied problems arising in the design of microfluidic devices. Depending on the purposes of the devices, the  geometry configuration of hydrodynamic traps and their spatial arrangement is chosen. The present work is dedicated to the study of the dynamics of dispersed particles in the viscous fluid flow in a microchannel with hydrodynamic traps. The computational approach is based on the Boundary Element Method, accelerated using the Fast Multipole Method on heterogeneous computing architectures. Simulation results and details of the method are discussed. In  addition, the influence of the distance between trap rows and their spatial arrangement on the flow pattern in the microchannel has been investigated.