It happens from time to time that my system is less responsible. It is usually caused by extensive disk operations, e.g. searching disk for something, moving a lot of data. A solution would be to run these problematic tasks with ionice. But I think that desktop user should not need to take care of this. Also some of the operations are even caused by system tools and normal user has problems to affect it. I wonder if we could somehow improve the desktop setting or it it would even need some hacks into the scheduler.
I have just heard that this should be fined in the last kernels. But I also heard that it still does not work well, for example when copying from/to USB memory stick.
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