Minecraft server not working

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I installed java and Minecraft on my Linux server, I changed the port to one that is open, but it does not seems to work. Most the time when I join I am falling and just see the sky then I get an end of read error. Once a small bit of the world did load, but as soon as I walked off the edge I just fell again then got the same error. Sometimes I start falling but then the world seems to load and I am stuck in stone.

The server meets the minimum requirements, dual P3s at 1.3Ghz with 2.25GB of memory, I am trying to make use of the archaic machine (most of servers won't run because of SSE).
 
I am allocating 1GB of memory, https://dl.dropboxusercontent.com/u/19573402/log.txt.

I have tried making a new world, it does seem to be better now, although the loading of the world and the server is still slow. I have no idea what HDD is in the server, but maybe a RamDisk would help?

Done a bit more testing, the game sort of worked for a bit, but now each time I join only a small bit of the map is there and nothing saves.
 
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Remove plugins you've got installed as one of them might be causing the problem, re-add them on at a time.

looks like it's struggling to get resources, RAM, CPU or even HDD aren't enough. Out of interest what plugins do you have, log doesn't show you rendering the world etc so really can't see why it's struggling with that spec.

Definitely got the correct java version on the server?

FT will be able to give you better advice probably, been a couple of months since I helped on a server :)
 
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To be honest with you the only thing I can see in that log that is worrying is that your server seems to be generating spawn areas over and over again. This suggests to me that your map isn't saving properly or the region files are getting corrupted in some way.

To test this maybe you could try downloading a pre-gen'd map and putting it on your server. After you've done that try using it for a bit, running around and changing things in a way that you can test again later (e.g. try spelling out a word in blocks and ensure that after a server restart the changes still exist). If changes revert or you still get map errors it's likely that you've got some kind of issue with your disk/file system.
 
Are you running the server as a special user, and if so does said user have ownership of all the necessary directories where it will be trying to create the world files?
 
I am not running any plugins, I have tried running it as super user and it worked for a while but not anymore. I seem to be running java 1.6.0_18, I am trying to update java, but I am a bit new to Linux server management.
 
I am not running any plugins, I have tried running it as super user and it worked for a while but not anymore. I seem to be running java 1.6.0_18, I am trying to update java, but I am a bit new to Linux server management.

Try chown -R 'username you're running the server as /path/to/server/files

e.g for user 'mcserver' with files in /home/servers/mcserver it would be:

chown -R mcserver /home/servers/mcserver

You will likely need to run this command as a root user. You shouldn't ever run Minecraft as root however.

edit: If you ran it as root for a bit and it created files then it is extremely likely that it is failing to overwrite those files when you run it as a normal user.
 
Try chown -R 'username you're running the server as /path/to/server/files

e.g for user 'mcserver' with files in /home/servers/mcserver it would be:

chown -R mcserver /home/servers/mcserver

You will likely need to run this command as a root user. You shouldn't ever run Minecraft as root however.

edit: If you ran it as root for a bit and it created files then it is extremely likely that it is failing to overwrite those files when you run it as a normal user.

Done that, I removed the old Minecraft directory and created a new one, did chown on the whole server folder by mistake, downloaded Mincraft again. And same problem, the first time I join a world it works fine. However if I disconnect and rejoin it doesn't (only a small part of the map is there or I am falling).
 
Maybe just double check that:

A. All folders and files are owned by the user you think they should be, do " ls -l " in each directory and make sure it lists the user you're expecting as the owner of each file and directory (the directories are more important than the files really)

B. Is that same user *definitely* who the server is running as when you run it? Do you log into the server as that user and run the server directly, or do you start it off using " su " as the user... If you're not sure you can start it running and then from another terminal try doing " ps -ef | grep minecraft " and change "minecraft" to any string which appears in the name of the server executable - you should be able to see it running as the user you're expecting.

If you have a startup script or similar can you post it here for us to look at? Or are you currently just testing and running things at the command line (still be useful to see what you're running either way).

Final thing that springs to mind - have you installed the "proper" java platform... I believe the one which appears as standard in the normal repos is actually rubbish and there is an alternative which is thought of as better - will try to look up the details if I can find them
 
This is what I get with ls -l.

-rw-r--r--. 1 myuser myuser 106 Jul 8 18:20 banned-ips.txt
-rw-r--r--. 1 myuser myuser 106 Jul 8 18:20 banned-players.txt
-rw-r--r--. 1 myuser myuser 6134331 Jul 5 15:29 minecraft_server.1.6.2.jar
-rw-r--r--. 1 myuser myuser 0 Jul 8 18:20 ops.txt
-rw-r--r--. 1 myuser myuser 16306 Jul 8 18:50 server.log
-rw-r--r--. 1 myuser myuser 545 Jul 8 18:20 server.properties
-rw-r--r--. 1 myuser myuser 0 Jul 8 18:07 white-list.txt
drwxr-xr-x. 7 myuser myuser 4096 Jul 8 18:50 world

Also I am not running any scripts I just downloaded Minecraft and ran "java -Xmx1024M -Xms1024M -jar minecraft_server.1.6.2.jar nogui". I have tried installing a newer\different version of java, but it didn't work, presumably since I already had java installed.
 
What's the output of

java -version

edit: also when you run the command you quoted there are you logged in as "myuser"? Also what Distro - Ubuntu?
 
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