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We have a server with unusual high load and cpu util, but we can't figure out why. When we run top all the procs seem to be very low cpu.

http://cl.ly/2d1g0K3q261r0R0K3e35

Is there a better way to look for what is causing this?

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I should note I am on Ubuntu 10.04 – Ben May 22 '11 at 4:55
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7 Answers

up vote 1 down vote accepted

I think this bug is your case. From what I see from the output, you have enough memory (note the cached 14 GB or so), no I/O issues, but you have xen-related processes running. This make me think it is a bug.

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It turned out to be a bug in Ubuntu 10.04 and the hardware that AWS was using – Ben Jun 3 '11 at 7:14
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up vote 5 down vote

Load is a measure of the workload a system has had on a 1, 5 and 15 minute basis.

The most common misconception is that Load Average is purely connected to the CPU usage of a system.
Load does however incorporate additional measurements such as CPU waiting for I/O which I think is your issue.

Based on the image I'm guessing you ran out of memory and started swapping data to disk.

A simple free -m will tell you how much RAM and swap is used.
The interesting column is the free column besides -/+ buffers/cache.
If it's close to zero you've run out of RAM and should act accordingly.

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+1 for swap. You could use iotop or vmstat to try and see if it is I/O. – Axel Knauf May 22 '11 at 9:32
-/+ buffers/cache: 2933 14586 – Ben May 22 '11 at 15:06
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up vote 2 down vote

Noticed that the load average is quite high (68, wow). Is it possible that there are a lot of processes which takes up a little bit of CPU, thus add up consuming all CPU time? Maybe, those processes just start and finish very quickly thus top cannot capture the existence of them, you may try to see if atop can see that or not.

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up vote 2 down vote

Are you inside a virtual server? The high load may come from processes in other virtual servers, which you can't see from inside yours.

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yes ... I am on EC2 – Ben May 22 '11 at 16:25
I believe that top reports CPU load for that virtual server only, regardless of who else uses the machine. If the physical machine is slow that will have an impact on your virtual machine, but you will not be able to tell just with top in your virtual machine. – asoundmove May 22 '11 at 20:06
@Ben, which instance-type are you on? – Mark May 23 '11 at 5:46
@asoundmove I guess it depends on the implementation, I observed (on Linux-VServer) top and uptime reporting high CPU usage while all the processes would stay below 1%. Turned out a faulty blog in a different vserver had its comments spammed, bloating the database with a few million rows causing MySQL to wreak havoc on the systems performance. – vmp32k May 24 '11 at 13:55
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up vote 1 down vote

Try using:

top -o cpu

The -o flag will force top to order the processes by CPU usage in descending order.

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when i ran top -o cpu I got "top: unknown argument 'o'" – Ben May 22 '11 at 4:54
Ok, try running top and hitting o while it is running. It should ask you for a primary key. Type cpu and hit enter. – Bandit May 22 '11 at 6:10
even when sorted by cpu there is nothing at the top of the list above 1% and there are only a handful (2-3) at any given time. The rest are 0% – Ben May 22 '11 at 6:40
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up vote 1 down vote

It could be locked files on nfs or any other thing that locks a file that another process needs access to

could also be missed configured service with too many threads active

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up vote 1 down vote

Try 

iotop

IO was it for me most of the time.

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