When you run 1.9.5 (with Ardour 2.8.8 and Hydrogen 0.9.5-beta2 at least) you don't have to set Ardour as Master.
As regards jack master transport, latest ardour2 is working fine with jackd
0.118.0 but it still has this little problem with jackdmp 1.9.5:
http://tracker.ardour.org/bug_view_advanced_page.php?bug_id=2856
Without it, if I click anywhere on the timeline in Ardour, Hydrogen jumps to that spot.
It also works the other way around if I click somewhere in Hydrogen.
Yes, but then, who is the tempo master? I have an ardour song with several tempo changes I made from a tempo map with klick2ardour. I have hydrogen which follows the tempo changes perfectly but only as long as I set ardour transport as jack master. I have just tested it again with jack2. I am back to jack1.
Regards, Pablo
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