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FPGA clocks are distributed by dedicated routing resources. You can't interpose additional gating logic without affecting it's timing performance. Some FPGAs have dedicated clock control blocks to switch or gate clocks, in so far the original statement isn't completely true.
I meant "how many clock domains might be controlled".What do you mean, "How big"?
In ASIC clock trees are built after all logic is implemented (placed and routed) with gates, etc. In FPGA clock trees are implemented without taking in account how the LUTs will be routed and connected one with another. Gated clocks usually introduce delays (aka skew, latency) on the clock. There is no way to balance the clock trees then. So, a synchronous design becomes an asynchronous one (clocks are not balanced/synchronized one with another) that may introduce timing problems and as a result logical errors.And what do you mean "the problem is due to the fact that clock trees are already built"? Which problem?
Usually Negative Latch with AND Gate are used to gate the clock. Is there a way to mange their timing in order to prevent glitches? Since gating is done on the negative edge of the clock, there is 1/2 of clock period a a margin. Why glitches?depending on how you use the gate, you can generate glitches