Transferring the partial bitstream from the host to the FPGA is easily accomplished using the Xilinx DMA reference driver, available here: AR#65444.
The reference driver is available for both Windows and Linux and contains example applications that make it easy to transfer data from the host to the FPGA.
Follow the instructions within the answer record to install the driver. In this application note, Linux is used to accomplish the transfer, but Windows can be used as well.
Once the driver is installed, use the dma_to_device program to transfer the partial bitstream from the host to the ICAP. An example command is shown below:
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./dma_to_device –d /dev/xdma/card0/h2c1 –s 475956 –c 1 –f ./inst_shift_shift_left_partial.bin
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-d - Character device for channel one. This location may vary so check that this path is correct for the specific Linux environment.
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-s - Size of the partial bin file in bytes.
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-c - Number of times to send the bin file. In this case, one time is all that is needed.
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-f - Actual partial bin file to be sent.
Different bin files can be sent using this same command, but be sure to update the size and the file location before executing the command.