RedHat server updates its time every minute

For this answer, I'll assume that there may be several elements working hard to set your time straight. Since I don't really want to wild-guess about which one is working against you, I'll try and give you an answer which should help you find it yourself instead.

On a UNIX system, the clock can typically be set using the stime system call. As things evolved, it also became possible to set the clocks more accurately using the clock_settime call instead. You might also come accross settimeofday. When running date --set on a CentOS machine, strace revealed that it used clock_settime.

Knowing this, a solution would be to trace these system calls. Good thing is, Linux has a mechanism for that: debugfs. On my system, calling mount, I can see that this is available at /sys/kernel/debug :

$ mount
none on /sys/kernel/debug type debugfs (rw)
...

However, on some systems (including RedHat and probably CentOS), it isn't mounted at boot time. You'll therefore need to run...

# mount -t debugfs nodev /sys/kernel/debug

Also note that if you were in that directory before mounting, you might have to go out and back in before files start to appear in it.

Now we're ready to go. Let's enable the trace for our systems calls. I'm tracing all of them because I don't really want to check which one is really being used. Tracing for system calls can be set in /sys/kernel/debug/tracing/events/syscalls. In this directory, you should find...

• sys_enter_stime
• sys_enter_clock_settime
• sys_enter_settimeofday

... depending on what's available on your system.

These correspond to the events of entering our system calls, which is what we want to trace (you'll also find sys_exit_* directories). Within each directory, you'll find a file named enable, the contents of which should appear to be 0. To trace these calls, set that to 1 instead:

# echo 1 > /sys/kernel/debug/tracing/events/syscalls/sys_enter_stime/enable
# echo 1 > /sys/kernel/debug/tracing/events/syscalls/sys_enter_clock_settime/enable
# echo 1 > /sys/kernel/debug/tracing/events/syscalls/sys_enter_settimeofday/enable

Now that we've set up our trap, just wait until something sets your time to its correct value. Once it has happened, run for the trace logs at...

# cat /sys/kernel/debug/tracing/trace 

Now, unless something wrong occured, you should see one of the following lines:

stime-xxxxx [xxx] .... x.x: sys_stime(...)
clock_settime-xxxxx [xxx] .... x.x: sys_clock_settime(...)
settimeofday-xxxxx [xxx] .... x.x: sys_settimeofday(...)

The number right after stime- (or another call's name) is the PID of the process which made the system call. Now go get it:

# ps -fp xxxxx
UID        PID  PPID  C STIME TTY          TIME CMD
root     XXXXX XXXXX  0 hh:mm ?        hh:mm:ss time_warrior

You should now have everything you need to make sure your system stops getting the time right. The simplest thing would probably be to kill the process, and make sure it isn't spawned at boot time ; of course, you'll have to make sure it doesn't serve a more important purpose before doing so : you don't want to completely crash your system...

Also remember to disable the trace when you're done by writing 0 to the files we edited earlier. A shortcut could be:

# echo 0 > /sys/kernel/debug/tracing/events/syscalls/enable

(this file acts as a master switch for all others ; it allows you to switch all system calls tracing off)

Note: as Mark Plotnick said in a comment systemtap could be a slightly easier way to achieve similar results. I'll let him write a stap answer if he feels like it, since I'm not fluent with stap scripts at all.

There are two things you should do. Make sure ntpd is started as early as possible in the boot sequence, and put an ntp-wait somewhere in the boot sequence before any of your applications start.

Depending on your version of Linux, how you achieve that will vary. You should, however, make your application startup dependant on the ntp-wait finishing.

ntp-wait simply waits for the ntpd daemon to report it is synced.

The right way to do this on Debian 8 would be to configure systemd, and to add a new service for the ntp-wait, which your applications would then be dependant upon.

The easy way to do it, is put an ntp-wait in the startup scripts for your apps.