It looks like this has something to do with APIC but I am not sure. I have similar CPUs with a different MB and BIOS that work fine on the same type of kernel. A lot of time the issue is because of the C-step setting in the BIOS. The same thing happened on the 2.6 kernel with Centos 6 but this is a homebrew 4.4 kernel soI am not sure why it is happening when even Centos 7 (3.2) kernel works OK. Solution - It comes down to the BIOS set........

Here's a proven example of what a bad hard drive can do, it was technically functioning OKin a RAID array but the system became extremely low and the load become high and IOWAIT was even higher and I always thought it was a bad application. The truth is that this failing 1TBHitachi has slowly gotten worse and caused huge slowdowns, (eg. 100% load on Thunderbird waiting for e-mails to load etc..). After swapping it out, tabs change instantly, emails are not lagged, and........