debiandebian-wheezyshutdown
I logged in to my Debian 7 server, did an upgrade using apt and wanted to shutdown+reboot using shutdown -r now as i did a lot of times before. This time, the shutdown command can't be found anymore. I've already read somewhere that i can try it with the whole path /sbin/shutdown, but the programm isn't there, too. I also can't find the reboot command anywhere.
What went wrong? What can i do to restore the shutdown command?
This is caused by a livelock when ntpd calls adjtimex(2) to tell the kernel to insert a leap second. See lkml posting http://lkml.indiana.edu/hypermail/linux/kernel/1203.1/04598.html
Red Hat should also be updating their KB article as well. https://access.redhat.com/knowledge/articles/15145
UPDATE: Red Hat has a second KB article just for this issue here: https://access.redhat.com/knowledge/solutions/154713 - the previous article is for an earlier, unrelated problem
The work-around is to just turn off ntpd. If ntpd already issued the adjtimex(2) call, you may need to disable ntpd and reboot to be 100% safe.
This affects RHEL 6 and other distros running newer kernels (newer than approx 2.6.26), but not RHEL 5.
The reason this is occurring before the leap second is actually scheduled to occur is that ntpd lets the kernel handle the leap second at midnight, but needs to alert the kernel to insert the leap second before midnight. ntpd therefore calls adjtimex(2) sometime during the day of the leap second, at which point this bug is triggered.
If you have adjtimex(8) installed, you can use this script to determine if flag 16 is set. Flag 16 is "inserting leap second":
adjtimex -p | perl -p -e 'undef $_, next unless m/status: (\d+)/; (16 & $1) && print "leap second flag is set:\n"'
UPDATE:
Red Hat has updated their KB article to note: "RHEL 6 customers may be affected by a known issue that causes NMI Watchdog to detect a hang when receiving the NTP leapsecond announcement. This issue is being addressed in a timely manner. If your systems received the leapsecond announcement and did not experience this issue, then they are no longer affected."
UPDATE: The above language was removed from the Red Hat article; and a second KB solution was added detailing the adjtimex(2) crash issue: https://access.redhat.com/knowledge/solutions/154713
However, the code change in the LKML post by IBM Engineer John Stultz notes there may also be a deadlock when the leap second is actually applied, so you may want to disable the leap second by rebooting or using adjtimex(8) after disabling ntpd.
FINAL UPDATE:
Well, I'm no kernel dev, but I reviewed John Stultz's patch again here: https://git.kernel.org/?p=linux/kernel/git/torvalds/linux-2.6.git;a=commit;h=6b43ae8a619d17c4935c3320d2ef9e92bdeed05d
If I'm reading it right this time, I was wrong about there being another deadlock when the leap second is applied. That seems to be Red Hat's opinion as well, based on their KB entry. However, if you have disabled ntpd, keep it disabled for another 10 minutes, so that you don't hit the deadlock when ntpd calls adjtimex(2).
We'll find out if there are any more bugs soon :)
POST-LEAP SECOND UPDATE:
I spent the last few hours reading through the ntpd and pre-patch (buggy) kernel code, and while I may be very wrong here, I'll attempt to explain what I think was going on:
First, ntpd calls adjtimex(2) all the time. It does this as part of its "clock loop filter", defined in local_clock in ntp_loopfilter.c. You can see that code here: http://www.opensource.apple.com/source/ntp/ntp-70/ntpd/ntp_loopfilter.c (from ntp version 4.2.6).
The clock loop filter runs quite often -- it runs every time ntpd polls its upstream servers, which by default is every 17 minutes or more. The relevant bit of the clock loop filter is:
if (sys_leap == LEAP_ADDSECOND)
ntv.status |= STA_INS;
And then:
ntp_adjtime(&ntv)
In other words, on days when there's a leap second, ntpd sets the "STA_INS" flag and calls adjtimex(2) (via its portability-wrapper).
That system call makes its way to the kernel. Here's the relevant kernel code: https://github.com/mirrors/linux/blob/a078c6d0e6288fad6d83fb6d5edd91ddb7b6ab33/kernel/time/ntp.c
The kernel codepath is roughly this:
There are a couple interesting things here.
First, line 691 cancels the existing timer every time adjtimex(2) is called. Then, 554 re-creates that timer. This means each time ntpd ran its clock loop filter, the buggy code was invoked.
Therefore I believe Red Hat was wrong when they said that once ntpd had set the leap-second flag, the system would not crash. I believe each system running ntpd had the potential to livelock every 17 minutes (or more) for the 24-hour period before the leap-second. I believe this may also explain why so many systems crashed; a one-time chance of crashing would be much less likely to hit as compared to 3 chances an hour.
UPDATE: In Red Hat's KB solution at https://access.redhat.com/knowledge/solutions/154713 , Red Hat engineers did come to the same conclusion (that running ntpd would continuously hit the buggy code). And indeed they did so several hours before I did. This solution wasn't linked to the main article at https://access.redhat.com/knowledge/articles/15145 , so I didn't notice it until now.
Second, this explains why loaded systems were more likely to crash. Loaded systems will be handling more interrupts, causing the "do_tick" kernel function to be called more often, giving more of a chance for this code to run and grab the ntp_lock while the timer was being created.
Third, is there a chance of the system crashing when the leap-second actually occurs? I don't know for sure, but possibly yes, because the timer that fires and actually executes the leap-second adjustment (ntp_leap_second, on line 388) also grabs the ntp_lock spinlock, and has a call to hrtimer_add_expires_ns. I don't know if that call might also be able to cause a livelock, but it doesn't seem impossible.
Finally, what causes the leap-second flag to be disabled after the leap-second has run? The answer there is ntpd stops setting the leap-second flag at some point after midnight when it calls adjtimex(2). Since the flag isn't set, the check on line 554 will not be true, and no timer will be created, and line 598 will reset the time_state global variable to TIME_OK. This explains why if you checked the flag with adjtimex(8) just after the leap second, you would still see the leap-second flag set.
In short, the best advice for today seems to be the first I gave after all: disable ntpd, and disable the leap-second flag.
And some final thoughts:
06/02 Update from John Stultz:
https://lkml.org/lkml/2012/7/1/203
The post contained a step-by-step walk-through of why the leap second caused the futex timers to expire prematurely and continuously, spiking the CPU load.
The arguments you gave to rm told it to remove everything in the current directory except from hidden files (*) as well as the /tmp directory with all contents (/tmp/).
To know what the consequences of that command may have been, we need to know two things. Which user did you run the command as, and what was the current directory.
If you executed the command from your home directory, and you were not logged in as root, the damage would be limited to losing contents of your home directory. In that case you could create a new user or copy over the standard contents for a new home directory from /etc/skel.
If you ran the command as root, you would not only have removed all contents of /tmp but the /tmp directory as well. That could cause many applications to fail. You can create a new /tmp directory by running mkdir -m 1777 /tmp as root. What other damage you would have done by running that rm command as root depends on what your current directory was.
Best Answer
You probably "upgraded" to
systemd, removingshutdownand friends. If so, you now need to dosystemctl poweroffto shutdown the system. Why does systemd not provide an alias to shutdown? Why not indeed...EDIT:
/sbin/shutdownshould be available if you install thesystemd-sysvpackage. It would be nice ifsystemdwould recommend or even just suggestsystemd-sysv.