How to diagnose Ubuntu CPU spikes / IO wait?

There are two additional tools that you may want to check out:

• IOTop
  
• LatencyTop

If you don't get what you want from those two tools, then you may need to use developer-tools like OProfile or Sysprof.

All the tools listed are available from ubuntu repositories

Regarding your observation with usb, from what I've heard, some usb-controllers behave a bit flaky with certain hardware which can cause Interrupt-storms, this could cause what you are describing. Try searching for usb interrupt storm and you will get quite a few hits.

I used htop for years and I finally found how to get Cpu Utilization by numbers and percentages, I am surprised I have missed this.

htop iowait image

Press F2

Arrow to "Available meters"

Highlight CPU average

F5 or F6 to add to column

Arrow to the item "CPU [Bar]"

Press F4 till you get "CPU [Text]"

You can also get IORates

F2->Columns->Available

Add IO_RATE, IO_READ_RATE, IO_WRITE_RATE

The best way to see this is to use a command-line application like top or htop .

top

htop

You would need to be watching it for a while though until you see what causes the spike (if it is indeed a spike in CPU usage and not in i/o wait, which may not be caught in all cases).