Pokemon Red has slowdowns for some configurations #1730
It can be easily observed during main screen, where slideshow of Pokemons happens, nearly every change of Pokemon sprite slows done emulation from 60 to circa about 55 fps which is accompanied by sound lag. Changing audio buffer doesn't help. The same issue happens most often while wild Pokemon appears/my Pokemon comes from Pokeball.
Every time that lag is preceeded by GB memory savedata sync log.
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That might be your hard disk. Is it mechanical? (not SSD) Is it in a laptop?
Sometimes, specially in laptops, the OS or HDD firmware try to reduce power consumption and noise by "parking" the hard drive head, disabling it, and that may cause a brief lag and noise when the system tries to read or write something.
If you were using Windows I would tell you to install quietHDD, which modify APM/AAM values to prevent that behavior. I think there are commands in Linux to do the same.
I have also observed strange laggy behavior with Pokemon FireRed that sounds similar to this. Turning on video sync seems to help, but as I play for a while the problem gets worse and the game suffers from stuttering or even freezing for up to a second. Restarting clears it up, for a short while.
So I've been able to reproduce this on Windows, but my fix for the Windows version (still uncommitted; was looking to close this bug but now I see it's not just Windows...) doesn't affect the Linux version. I'm not sure what I can do to fix it on Linux, but I'll continue to look into it.