Making your CPU in FPGA is a bit laike making real car out of LEGO cubes.
Xilinx, ALtera etc certainly know their stuff, but FPGAs are still trying to be very univeresal, which also means far from optimum for any specialised application.
High density, high speed FPGA chips cost a fortune and they are still usually much slower than equivalent design in "real" silicon.
Besides that, they tend to be power hog, since they have toa have extensive, high power, low skew clock grids through entire chip.
There are useful applications for CPU on FPGA, though. Many times smallish CPU is implemented so that running some complex protocol is simpler ( for the designer) etc.
Brane214.. thanks for the explanation. I really like your saying "Making your CPU in FPGA is a bit laike making real car out of LEGO cubes".
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