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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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.

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).
 
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?

I am running Debian 6.0.7

Java:
java version "1.6.0_18"
OpenJDK Runtime Environment (IcedTea6 1.8.13) (6b18-1.8.13-0+squeeze2)
OpenJDK Server VM (build 14.0-b16, mixed mode)
 
Okay OpenJDK is meant to be buggy as hell and not very good for minecraft... so try this (copied from the wiki since I don't use Debian myself):

Ensure that the non-free repository is being scanned by apt. You do this by adding non-free to your /etc/apt/sources.list file

deb http://ftp.uk.debian.org/debian/ squeeze main contrib non-free

Update your sources list (as root):

apt-get update

Then to install Java, simply type this in terminal and press enter (as root):

apt-get install sun-java6-jre

...

Then try printing the version again, you want it to be the proper Oracle java

Did that, it installed something, got a blue ToC screen. But I still get:
java version "1.6.0_18"
OpenJDK Runtime Environment (IcedTea6 1.8.13) (6b18-1.8.13-0+squeeze2)
OpenJDK Server VM (build 14.0-b16, mixed mode)

Also, I am very hesitant with this server as I do not have physical access to it.
 
I uninstalled and reinstalled java, I now get:
java version "1.6.0_26"
Java(TM) SE Runtime Environment (build 1.6.0_26-b03)
Java HotSpot(TM) Server VM (build 20.1-b02, mixed mode)

Although, the server is same as before.
 
Not that I think it is likely to be your problem but you may want to update to Java 7.

You may want to experiment with downloading and trying Bukkit instead of vanilla Minecraft. Sometimes there are bugs with the original server that are fixed in Bukkit (once again I doubt this is likely to be your issue but you may as well try everything at this point).

Any idea on how to install Java 7?
 
I have tried this on a more powerful dual 2.4Ghz dual core Xeon in the same server room. I get the same issue, only part of the map loads. This server has the same OS and version of Java.
 
Hmm... I take it you're using matching versions of the server .jar and java (i.e. 32bit for both or 64bit for both)? Did you try Bukkit? Even if you don't want to use any mods you can just run Bukkit without them and it should appear pretty much like the normal server

Yes they are both running 32bit Debian 6.0.7, Java 6 and the latest version of Minecraft. Furthermore I installed the 32bit version of Debian 6.0.7, Java 6 and Minecraft on a VM and it worked fine.

So it is not Java or the OS, it is something that both the main servers have in common but not the VM. Which would be HDD speed, memory speed and the network.
 
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