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There seems to be consensus here that the BeagleBone Black has 1ms+ latency while toggling gpio pins due to the fact that gpio is handled outside of the cpu. Are the uart/i2c/spi lines equaly slow, or are they significantly faster?

I've seen references to people talking to the gpio more directly. Could this decrease uart/i2c/spi latencies as well?

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What level of performance do you need? – Ian Aug 5 '14 at 1:49
300 to 500μs would be ideal for my application. From what I can find the BBB supports up to 3mbaud uart, so an added 1ms can be a lot at those levels. However, I doubt it would be too noticeable in the i2c world... – daweim0 Aug 5 '14 at 5:56

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