I've been testing a copy of my 1.12.2 world in the prerelease and while its been laggy and run out of memory a couple of times, now I have a situation where
I login and cannot interact with anything
The client is booted with 'Timed Out'
The server crashes shortly afterward.
I've repeated this several times and had the same results. I've increased the memory available to 4G and had the same result.
[16:10:51] [Server thread/INFO]: Preparing spawn area: 96%
[16:10:51] [Server thread/INFO]: Preparing spawn area: 100%
[16:10:51] [Server thread/INFO]: Time elapsed: 1416 ms
[16:10:51] [Server thread/INFO]: Done (2.346s)! For help, type "help"
[16:11:18] [User Authenticator #1/INFO]: UUID of player aeduna is e96c9253-be4d-44cb-8981-60eda991a208
[16:11:19] [Server thread/INFO]: aeduna[/192.168.1.200:36008] logged in with entity id 176 at (1024.77793444543, 97.9931355636394, -2062.776598736978)
[16:11:19] [Server thread/INFO]: aeduna joined the game
[16:12:19] [Server Watchdog/FATAL]: A single server tick took 60.00 seconds (should be max 0.05)
[16:12:19] [Server Watchdog/FATAL]: Considering it to be crashed, server will forcibly shutdown.
[16:12:20] [Server Watchdog/ERROR]: This crash report has been saved to: /home/minecraft/preniu/./crash-reports/crash-2018-06-06_16.12.20-server.txt
[16:12:20] [Server Shutdown Thread/INFO]: Stopping server
[16:12:20] [Server Shutdown Thread/INFO]: Saving players
Memory: 3049217984 bytes (2907 MB) / 4194304000 bytes (4000 MB) up to 4194304000 bytes (4000 MB)
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Please attach the server.log , This watchdog reboot is only the result of another cause.

its, uh, not more informative....
[media]
I could probably pull out the particular region and attach that if it'd help...

This isn't really a resolution, but I took backups of the offending regions and restored them.
Started with 2G and it crashed again
Started with 4G and managed to login, move about, then quit.
Restarted with 2G and I've managed to login.

.... but 30s later i couldn't interact with things properly, and its using 390% of CPU and then crashed again
[18:51:52] [WorldGen-Scheduler-1/ERROR]: Something went wrong upgrading!
java.lang.OutOfMemoryError: GC overhead limit exceeded
so yah.

Huh, too much GC ? Please see if the adding of -XX:+DisableExplicitGC
like proposed in MC-103656 changes something.

And please attach that logfile with "Something went wrong upgrading!", maybe we can find something there.

Crash report and log file
[media]
DisableExplicitGC - nope, sorry
Immediately jumps up to 390% cpu as soon as I login and crashes ~ 60s later. (let me know if I should attach logs from that run too)

Thanks for testing, but I think a new log isn't necessary.

Not gunna lie, wish there was a seperate utility for converting worlds to 1.13 so that it was clearer where issues were, in the conversion or the generation of new chunks.

Please check if that's still an issue for you in 1.13.1.