To program a first programmable gate array, for example a first FPGA, in a distributed computer system, a configuration of a first configuration logic on the first programmable gate array is provided. The first configuration logic is configured to receive a first user bitstream from a configuration software for configuring a first user logic on the first programmable gate array and to store the first user bitstream on a non-volatile memory of the first programmable gate array for the purpose of subsequently configuring a first user logic on the first programmable gate array according to the specifications from the first user bitstream. In an expansion stage of the invention, a configuration of a programming logic on the first programmable gate array is also provided for programming a second programmable gate array, which is connected to the first programmable gate array to form a daisy chain.