A method for programming a cluster-based field programmable gate array (FPGA) device includes providing a netlist and cluster size information, translating the netlist into a hypergraph, partitioning the hypergraph into multiple partitions and optimizing the Rent characteristic, translating the partitions into clusters, placing the clusters on the FPGA device, routing interconnects using a pre-fabricated routing resource on the FPGA device, generating a programming bitstream in response to the placing and routing, and providing the programming bitstream to the FPGA device to realize the user design.
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