A system may include a host processor, a coprocessor for accelerating tasks received from the host processor, and one or more memory dies mounted to the coprocessor. The coprocessor and the memory die may be part of an integrated circuit package. The memory die may convey configuration bit streams to one or more logic sectors in programmable circuitry of the coprocessor over through-silicon vias. Each logic sector may include one or more data registers that are loaded with configuration data from the memory die. Multiple data registers may be loaded with configuration data simultaneously. The configuration data may be loaded onto an array of configuration memory cells using the data registers. Multiple data registers may be pipelined to allow simultaneous loading of configuration data into multiple sub-arrays of the array of configuration memory cells.