Methods and apparatus are disclosed for programming reconfigurable logic devices such as FPGAs in a multi-tenant server environment. In one example, a computing host includes one or more processors configured to execute a supervisor process and two or more user processes and a single FPGA integrated circuit configured into a plurality of partitions. The partitions include a host logic partition that is accessible only to the supervisor process executing on the computing host, and two or more accelerator partitions. Each of the accelerator partitions is configured to include a virtual debug unit with a logic analyzer that collects logic signals generated by logic within the respective accelerator partition and sends debug data indicating values of the logic signals to one of the user processes. In some examples, the host logic partitions and/or the accelerator partitions can be independently reprogrammed of each other within their respective portions of the single FPGA.