There are a few ways.
If you build your kernel with SND_HDA_INPUT_BEEP_MODE=2, or set the
option of snd-hda-intel module beep_mode=2, you'll be able to switch
to the native beep from HD-audio codec digital beep via muting "Beep"
mixer switch.
Or, if the value above is 0, it'll be always the system-native beep.
This can be done also via writing sysfs codec hint, as documented in
HD-Audio.txt.
Alternatively, you can reload pcspkr module so that it grabs the beep
output again over snd-hda-intel, "modprobe -r pcspkr; modprobe pcspkr"
Takashi
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