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I have a Scarlett 18i20 audio interface running well on a Samsung laptop with Linux Mint 19.3 Tricia and with the 5.0.21-rt16 real time kernel with fully preemptive configuration.
The same set up on a desktop machine results in regular audio glitches between 3 and 4 seconds apart. I am testing with a sine wave in puredata and the problem occurs with alsa and with jack. The problem occurs with other audio apps too.
I came across a similar problem on this link:
The solution was related to the "system RTC clock having about a 4% drift" and was solved using the adjtimexconfig utility. When I run this utility, after stopping the NTP server, it reports:
Adjusting system time by -11.4326 sec/day to agree with CMOS clock...done.
"adjtimex -p" reveals the following:
mode: 0
offset: 14679795
frequency: 4435324
maxerror: 289636
esterror: 22136
status: 8193
time_constant: 7
precision: 1
tolerance: 32768000
tick: 9998
raw time: 1582195310s 628559316us = 1582195310.628559316
The adjustment however makes no improvement in the glitches.
For the hardware set up of the desktop, please see: