I have been using jack_iodelay in the past to get the round-trip latency of my sound-card. I remember its results to correlate very well with the lag I could observe comparing, say, a square wave track with the square wave I would record by looping back the track through the sound-card and another track, using a DAW.
However, I have been playing with jack_iodelay today and there's something I don't quite get. If I launch jack_iodelay and loop its output directly to its input, without passing through the soundcard, the latency should be 0 since the output is just being copied back to the input. Instead, I read the JACK Frames/Period value:
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/usr/bin/jackd -P70 -t5000 -dalsa -r96000 -p4096 -n3 -D -Chw:USB,0 -Phw:USB,0
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4096.000 frames 42.667 ms total roundtrip latency
extra loopback latency: 4096 frames
use 2048 for the backend arguments -I and -O