Server thread throwing 'Can't keep up! Did the system time change, or is the server overloaded?' warnings

Is this still a concern in the current Minecraft version 14w11b or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases. - bot

It is a lot better on version 1.7.5 but we still get some of the messages when only 2 players is online.

Is this still a concern in the current Minecraft version 14w30c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Still getting the messages.
Did a test with 14w32d now, and the can't keep up message shows up even without players logged in.

I get these errors, lots of them, when I'm discovering new parts of the world. It can even become so much that it never ends. I reached land and began walking around, it kept lagging and the server kept reporting that error. I solved it by logging out and logging back in on the server. I think fast traveling is causing it.
I suggest making chunk generation threaded and separate from the normal ticking of the game. The machine itself is not under heavy load. The latency is fine (one Linksys SE2800, gigabit switch) between the gigabit interfaces of the client and server.
The boat is also out of sync and I crash into land that I'm not even close to. The boat breaks by the coast but I, the player, end up where I, the client, think I was. The boat also keeps glitching, like microstuttering when I travel. It sometimes lags when I slow down and stop and then resume travel instantly or just dropping speed near to standing still or when I travel att full speed for longer periods.
Once it start complaining about "Can't keep up!", leaving the boat and going on foot doesn't solve it. It will keep warning as long as you travel.
This seems to be two issues combined. Boat gets out of sync and traveling far and fast causes chunk generation to clog up the server. The chunk generation should be run in separate threads, one thread for each chunk being generated.

I have a 8 core Avaton C2750 and the CPU is very cool (as if it was idle) but the server threads clog up with chunk generation.

I'm currently running 14w34b. I had the same problems in 14w32a.
Running it on FreeBSD 10.0-RELEASE (64-bit), OpenJDK 8 64-bit JRE and 8 GC threads as well as 4 GB of RAM allocated.
This seems to be easily reproducable. The devs should explore the world by traveling by boat really fast and see where the server spends its valuable time.
More threading should be a part of the solution, making the server scale better with multi CPU and multi CPU core enviroments, allowing large servers with lots of players.

I've updated to 14w34c.
I entered the nether and began traveling on foot to a fortress. Inside the fortress, I put up a new portal and went through it to the over world where I continued on foot and kept running until I found a jungle. The server had major problems with keeping up. I kept getting the warnings until I had patrolled a limited area. When ever I start running in a unexplored direction it lags really bad and the server keeps telling me that it can't keep up.

I'm still getting the error, even moving around and attacking enemies can result in the feeling that the server can't keep up but the error doesn't show up on the server. However, traveling on foot at high average speed for quite some time will result in the same error. So any kind of traveling will make it happen. I do not think that Minecraft server can put a Intel Avaton C2750 to its knees, which is my first thought. The C2750 should be more than enough to run Minecraft server, since there's no graphics involved. I has 8 cores so there's no problem in getting enough time to run the threads. I'm running 1.8-pre2 in FreeBSD 10.0 and OpenJDK 8 64-bit JRE.
I'm running the server with the following command arguements:

java -d64 -server -Xmx8G -Xms4G \ -Xincgc \ -XX:+CMSIncrementalMode \ -XX:+UseConcMarkSweepGC \ -XX:+DisableExplicitGC \ -XX:+UseParNewGC \ -XX:ParallelGCThreads=6 \ -XX:+AggressiveOpts \ -XX:CompileThreshold=1500 \ -XX:TargetSurvivorRatio=90 \ -XX:MaxTenuringThreshold=15 \ -XX:+UseGCOverheadLimit \ -XX:+UseBiasedLocking \ -XX:UseSSE=42 \ -XX:+UseStringCache \ -XX:+OptimizeStringConcat \ -XX:+UseFastAccessorMethods \ -XX:+AggressiveOpts \ -jar minecraft_server.1.8-pre2.jar nogui

(I've tried to run it without most arguments, I've found these hints for arguments around the web on on this bug reporting forum, in a comment regarding optimal arguments and RAM usage, there's a slight improvement but it still shows up)

Okay, so I've checked CPU use and the server uses several percent when nobody is on the server.
When I log in and stand still inside my desert cave, CPU use goes between 15% to 21%. I heard a spider just now and I have a few animals outside, 6 chickens, 2 sheep and 2 pigs.
The server should be paused when nobody is online and CPU use is just too high for one player.

Here is some benchmarks for the CPU I have: http://www.servethehome.com/Server-detail/intel-atom-c2750-8-core-avoton-rangeley-benchmarks-fast-power/
How in the hell does it use up to 21% for one player? I run Minecraft as normal user in the system and there are lots of Java threads but only one is using the CPU, the others use less than 0.5% of time compared to the major Java thread.

I'm also running a different OS and JRE than the original reporter, however, we see similar problems. I would understand that my CPU can't handle as much as an equally new Xeon but this doesn't feel right.

Tried ut 1.8 pre2 now, still getting the can't keep up message with only 1 player logged in. It's around 2-4 seconds behind.
The cpuload is around 20% on a dual xeon cpu setup with 4 cores each.
Memory usage is 2.5GB of 12GB total.
The message isn't showing up when there's no player logged in anymore.

When I'm moving away from the main place where people live and got their farms everything seems ok. But when I enter that area the messages appear. On 1.7.10 this works fine with 1 player.
Getting a bit worried when 1.8 is coming out and the other 10 players start playing this again.

I am suspecting that this bug is part of a chain that looks like this: MC-17630 > MC-46812 > MC-63590. This is not true according to @unknown.

I confirm this bug but for me, there is no lag while this error message come on the console.
But i haven't try with more of two players on my server.

I confirm this bug with 1.8.1.pre2
No lag for me, but don't try with more of two players online on my server.

Still getting the warnings with 1.8.1 and only 1 player on the server.

I also get this same error. I removed minecraft entirely, reinstalled 1.7.1 and it ran fine with none of these messages. Upgraded it to 1.8.1 and the issues came back. I've read numerous threads stating the same online and many of those people are running i7 with 8+ gigs of ram. This does not appear to be a hardware issue. Why this is marked as "resolved" and why no one seems to even want to admit there is a problem is more frustrating than the actual issue itself.

I confirm this bug for 1.8.1 version.
With one player and more online, this warning come all 2 minutes.
Without player online, this warning come all 10 minutes minimum, and 40 minutes maximum.

still making 1.8.1 games unplayable in single player worlds

This is still effecting a 1.8.1 server.

It's the same on 1.8.3

Confirmed, ongoing issue.

JUST after boot...

22.10 17:36:28 [Server] Query Listener #1/INFO Query running on 162.244.164.11:56141
22.10 17:36:32 [Server] Server thread/WARN Can't keep up! Did the system time change, or is the server overloaded? Running 2353ms behind, skipping 47 tick(s)

I already removed any command blocks that might be hogging ticks. We don't have very much redstone, no command blocks as mentioned, nobody logged in yet, but we've only four players at most. MCProHosting, Stone plan (1 Gb). This is an ongoing issue with 1.9 snapshots, this latest was 15w43b.

same issue here on 1.16.1