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Sometimes, after a few hours, my system works slowly. I have checked status of these resources:

  • Hard disk using iotop
  • Ram usage using free
  • CPU usage using top

None of them are busy. top also shows that there is no process using too much memory or cpu.

Slowness is in switching between windows, typing, etc...

Is there anything else I should check?

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if possible post top output , and also check in logs for any error. – Rahul Patil Jan 8 '13 at 18:09
If GUI-related things slow down, it may be a video driver / hardware fault: try Unity 2D if possible. – 9000 Jan 8 '13 at 18:41

You might want to check to see if your disk drive is having problems. I've had cases over the years when drives get a little warm they do a lot of retries before getting the data and thus the system really acts slow.

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Or accumulating bad blocks if the drive doesn't automagically compensate. – dmckee Jan 8 '13 at 23:57

Analyzing top output may give much more information than simple CPU load. For example: load average shows average number of blocked processes waiting for resources. It could be CPU or IO. Three number represent period of time of 1 minute, 5 minute or 15 minutes, respectively. %wa column represents percentage of processor time waiting for IO.

I guess it could be useful to collect some information for analysis:

# nohup sar -A -o /tmp/sar.out.bin 10 1440 &
# nohup vmstat -t 10 1440 > /tmp/vmstat.log  &
# nohup top -bc -d 10 -n 1440 > /tmp/top.log &
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