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I execute some background scripts, and need to know when they end. For this I play system beeps. The thing is I just moved in an open space, and I don't want to annoy my co-workers with beeps every ten minutes...

I've searched the web looking for a solution and still did not find any satisfying answer.

Is there a way to play system beeps in my headphones instead of the motherboard speaker ?

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I don't believe that redirecting the "beep" output to anything other than the system speaker is possible.

(I get an error when trying to change the device to e.g beep --device /dev/snd/controlC0)

But perhaps this kernel module might help you:

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I'll try it, thanks – Cyctemic Nov 27 '12 at 15:43
Just out of curiosity: Did it work? – genomicsio Dec 18 '12 at 14:19
For now, I replaced system beeps by a beep wav file, played by mpg123. This is enough for me. As a Linux newbie, the words "kernel module" frighten me a little. I'll try it at home some day, but I don't want to mess with my work computer ^^ – Cyctemic Dec 26 '12 at 14:39

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