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top on one of hex cores with hyper threading shows the following

Cpu0  :  2.3%us, 58.8%sy,  0.0%ni, 38.2%id,  0.7%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu1  :  4.7%us, 62.1%sy,  0.0%ni, 31.2%id,  0.7%wa,  0.3%hi,  1.0%si,  0.0%st
..
Cpu23 :  4.0%us, 55.0%sy,  0.0%ni, 40.3%id,  0.7%wa,  0.0%hi,  0.0%si,  0.0%st

I checked with sar -I XALL 1 and the corresponding interrupts in /proc/interrupt . Most of the interrupts seem to point to network interface. ifconfig didn't show any errors or retx on the interface. How can we check for these kind of high system usages?

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I'd try using htop instead of top. You can navigate the processes that are running on box much more easily and you can drill down to processes that are consuming resource much easier than you can in top.

Here's a good tutorial to get you started with htop.

         ss of htop

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