CentOS – High CPU Usage at a particular time in the night

centoscpu-usagesar

I have a CentOS-5 server that has very little load. A typical output of "sar" command shows like this:

02:20:01 PM       CPU     %user     %nice   %system   %iowait    %steal     %idle
02:30:01 PM       all      0.63      0.00      1.23      0.31      0.00     97.84
02:40:01 PM       all      0.92      0.32      1.34      0.45      0.00     96.97
02:50:01 PM       all      0.76      0.00      0.93      0.77      0.00     97.54
03:00:01 PM       all      0.41      0.00      0.72      0.15      0.00     98.72
03:10:01 PM       all      0.78      0.32      1.49      1.83      0.00     95.58
03:20:01 PM       all      0.27      0.00      0.50      0.62      0.00     98.61

However, I am observing that every night at 4:10AM, the CPU usage is very high. This happens almost every night except few days in a month. The "sar" command shows something like this:

03:00:01 AM       all      0.10      0.00      0.10      0.11      0.00     99.68
03:10:01 AM       all      0.08      0.32      0.18      0.21      0.00     99.21
03:20:01 AM       all      0.03      0.00      0.03      0.19      0.00     99.76
03:30:01 AM       all      0.01      0.00      0.02      0.06      0.00     99.91
03:40:02 AM       all      0.75      0.32      3.21     15.43      0.00     80.28
03:50:01 AM       all      0.95      0.00      3.43      9.25      0.00     86.36
04:00:01 AM       all      0.69      0.00      3.79      4.86      0.00     90.66
04:10:01 AM       all     22.38      0.54      4.47     30.92      0.00     41.69
04:20:01 AM       all      2.99      0.02      4.58      4.95      0.00     87.46
04:30:01 AM       all      0.34      0.00      0.61     13.22      0.00     85.83
04:40:01 AM       all      0.05      0.32      0.17      0.52      0.00     98.95
04:50:01 AM       all      0.22      0.00      0.36      0.11      0.00     99.32
05:00:01 AM       all      0.23      0.00      0.36      0.12      0.00     99.28

How can I determine what is causing this peak in CPU usage and iowait etc. I examined /var/log/messages but could not determine. There is no other cron job or other things set to run at that time. Since this is showing under %user, I can only make out that it is some user process. How can I exactly determine the cause?

Best Answer

This is when the cron.daily scripts run... By default, it runs daily just after 4:00am.

From /etc/crontabs

SHELL=/bin/bash
PATH=/sbin:/bin:/usr/sbin:/usr/bin
MAILTO=root
HOME=/

# run-parts
01 * * * * root run-parts /etc/cron.hourly
02 4 * * * root run-parts /etc/cron.daily <-- THIS ONE!!
22 4 * * 0 root run-parts /etc/cron.weekly
42 4 1 * * root run-parts /etc/cron.monthly

And in /etc/cron.daily.

The culprit is probably your mlocate.cron, which runs updatedb and can be quite intensive on some systems:

#!/bin/sh
nodevs=$(< /proc/filesystems awk '$1 == "nodev" { print $2 }')
renice +19 -p $$ >/dev/null 2>&1
/usr/bin/updatedb -f "$nodevs"
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