what could possible take 100% cpu but not show up in (sudo) top

When I start intellij, which loads an "haxe" project at startup, it sometimes happens that intellij hangs loading. I than start htop (also tried top) with "sudo". iotop is also not showing anything interesting.

I can see that one of my cpus is used "100%" (which is normally not the case) but htop does not show any process which uses the cpu.

The information, that one cpu uses 100% comes from htop.

What else could take 100% of the cpu time and how can I find it?

Edit

I gathered some more information, the output of vmstat 10 10 (while the problem occurs) is this:

procs -----------memory---------- ---swap-- -----io---- -system-- ------cpu----- r b swpd free buff cache si so bi bo in cs us sy id wa st 8 0 0 12013656 285632 2150392 0 0 63 47 71 244 5 1 93 1 0
11 0 0 12009724 285664 2150384 0 0 0 14 737 1238 6 4 90 0 0
11 0 0 11994592 285680 2150364 0 0 0 6 720 990 6 3 91 0 0
11 0 0 11994516 285704 2150364 0 0 0 12 689 610 6 3 91 0 0
11 0 0 12000456 285736 2150360 0 0 0 12 709 702 6 3 91 0 0
11 0 0 12000696 285760 2150364 0 0 0 22 696 630 6 3 91 0 0
11 0 0 12008016 285784 2150364 0 0 0 13 728 784 6 3 91 0 0
11 0 0 12008356 285816 2150356 0 0 0 232 678 924 6 3 90 0 0
11 0 0 12007908 285840 2150400 0 0 0 15 628 548 6 3 91 0 0
11 0 0 11998248 285872 2150392 0 0 0 35 978 1432 11 4 84 0 0

Also I ran:

ps -e -o state,pid,cmd | grep ^D

but the output is empty.

And

ps -e -o state,pid,cmd | grep \^R

returns:

R 1705 /usr/bin/gnome-shell
R 7113 zsh
R 7466 ps -e -o state,pid,cmd

(and does not change even after lots of repeats)

2 Answers

The Ubuntu Kernel Team has a wiki explaining how to identify power sucking applications. This may have some useful ideas or tips to debug this issue of yours.

See:

top is a useful tool to see the top CPU consumers, however it cannot easily spot short lived processes or threads that get created and die very quickly. For these kind of CPU sucking processes, I developed forkstat to try and track these down. It is available in recent releases of Ubuntu, or you can download it from ppa:colin-king/white (see )

I had this issue recently. I discovered this was caused by an SD Adapter for microSD. When I insert a 32GB SDHC U1 Samsung microSD with two partitions (one 8GB vfat and one 24GB ext2) Lubuntu fails to detect and mount the device. In top/lxtask I do not see any processes using cpu however my cpu usage is a steady 100%. The cpu goes down to 0% when the card is removed.