John Franklin

I see this on a local VM server.  The host VM server is an 8C/16T Xeon Debian Buster system running KVM, the guest Minecraft VM is also Debian Buster (4CPU/2GB RAM) using the VirtIO drivers for both NIC and disk. 

Inside the guest VM, the java process sustains somewhere in the 13% - 20% CPU, with occasional spikes higher.  Essentially no disk wait, nor do I see much system time.

On the host VM server, the qemu-system-x86_64 process consumes around one full core – 100% CPU, plus or minus.  Which explains @Chandler's Linode alerts.

In both of these cases, 100% CPU = 1 core/thread.  200% CPU = 2 cores/threads.

To simply look at top and other monitoring tools, you'd be at a loss as to why it looks so much higher on the host than inside the guest.  Disk activity is a few kilobytes every few seconds, network activity is also low, mostly the ssh traffic to monitor the guest.  Based on one of the duplicates (MC-154629), it looks like the server is ... well, it's not technically spin-locking, but may as well be.

Red Hat apparently found a solution for it: https://access.redhat.com/solutions/22965  Wish I knew what it was.

The sleep/knockd trick @michiel suggested sadly doesn't work.  Upon waking up, the server thinks a tick took the entire time the server was asleep and assumes the Minecraft server process just crashed.

Two users logged in, one is about 1600,65,500 (the world is taking forever to load over a LAN connection); the other has coords less than 1000,xx,1000. Tick skipping has been going on all night, sometimes hitting the 60s threshold and shutting down the server.

My favorite is the last line, skipping 3.3 seconds about three seconds after it skipped 20 seconds.

Server 1.9, 2G of memory

[02:42:26] [Server thread/INFO]: There are 2/20 players online:
[02:42:26] [Server thread/INFO]: [player names redacted]
[02:42:34] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4008ms behind, skipping 80 tick(s)
[02:42:50] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3076ms behind, skipping 61 tick(s)
[02:43:08] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3887ms behind, skipping 77 tick(s)
[02:43:24] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3853ms behind, skipping 77 tick(s)
[02:43:41] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4159ms behind, skipping 83 tick(s)
[02:44:00] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5100ms behind, skipping 102 tick(s)
[02:44:16] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4823ms behind, skipping 96 tick(s)
[02:44:31] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3766ms behind, skipping 75 tick(s)
[02:44:49] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5604ms behind, skipping 112 tick(s)
[02:45:14] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 10619ms behind, skipping 212 tick(s)
[02:45:26] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 6139ms behind, skipping 122 tick(s)
[02:45:49] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 12556ms behind, skipping 251 tick(s)
[02:46:00] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5916ms behind, skipping 118 tick(s)
[02:46:40] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 19317ms behind, skipping 386 tick(s)
[02:46:43] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3382ms behind, skipping 67 tick(s)

The player is still visible standing where he last mounted the horse. He won't ever traverse, but will still look around and gesture (placing blocks, attacking.) If the player dismounts the horse, they appear to zip to where he dismounted.