In a multi-tenant environment, separate virtual machines can be used for configuring and operating different subsets of programmable integrated circuits, such as a Field Programmable Gate Array (FPGA). The programmable integrated circuits can communicate directly with each other within a subset, but cannot communicate between subsets. Generally, all of the subsets of programmable ICs are within a same host server computer within the multi-tenant environment, and are sandboxed or otherwise isolated from each other so that multiple customers can share the resources of the host server computer without knowledge or interference with other customers.