You could try looking here:

http://billauer.co.il/blog/2012/04/fpga-pcie-usb-board-ip-core/

For Xilinx-specific boards, look here (click the "resources' tab and scroll down to the 'Boards' section):

http://www.xilinx.com/technology/protocols/pciexpress.htm

I'd recommend using the Xilinx boards, as you will typically find more resources/datasheets/forum posts to get you started. Startng from the '6' series, Xilinx FPGAs have an integrated PCIe endpoint and many boards feature a dedicated PCIe connector on the edge -- see e.g.:

http://www.xilinx.com/products/boards-and-kits/EK-S6-SP605-G.htm

The full version of Xilinx tools has a dedicated PCIe IP core, which should make the design process easier.

Check out Pico Computing: http://picocomputing.com/

They make PCIe FPGA modules and provide the communication systems for you. This should let you emulate HPC communication across multiple FPGAs seamlessly.