[Critical] Spamming Errors - Too Many Open Files

I recently switched to a new server, and now I'm getting errors I've never gotten before. The server will run fine for a couple of hours, and then it starts to spam errors like this:

Code:

16:30:59 [WARNING] Task of 'NoLagg' generated an exception
java.lang.NullPointerException
        at net.minecraft.server.RegionFile.a(SourceFile:374)
        at net.minecraft.server.RegionFileCache.a(SourceFile:73)
        at net.minecraft.server.ServerNBTManager.e(SourceFile:54)
        at net.minecraft.server.WorldServer.saveLevel(WorldServer.java:252)
        at com.bergerkiller.bukkit.nolagg.AutoSaveChanger$1.run(AutoSaveChanger.java:43)
        at com.bergerkiller.bukkit.nolagg.logging.TimedWrapper.run(TimedWrapper.java:17)
        at org.bukkit.craftbukkit.scheduler.CraftScheduler.mainThreadHeartbeat(CraftScheduler.java:137)
        at net.minecraft.server.MinecraftServer.w(MinecraftServer.java:503)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:435)
        at net.minecraft.server.ThreadServerApplication.run(SourceFile:465)

Code:

16:32:15 [SEVERE] java.lang.NullPointerException
16:32:15 [SEVERE]      at net.minecraft.server.RegionFile.a(SourceFile:289)
16:32:15 [SEVERE]      at net.minecraft.server.ChunkBuffer.close(SourceFile:259)
16:32:15 [SEVERE]      at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:166)
16:32:15 [SEVERE]      at java.io.FilterOutputStream.close(FilterOutputStream.java:160)
16:32:15 [SEVERE]      at net.minecraft.server.ChunkRegionLoader.a(ChunkRegionLoader.java:129)
16:32:15 [SEVERE]      at net.minecraft.server.ChunkRegionLoader.c(ChunkRegionLoader.java:116)
16:32:15 [SEVERE]      at net.minecraft.server.FileIOThread.b(SourceFile:29)
16:32:15 [SEVERE]      at net.minecraft.server.FileIOThread.run(SourceFile:22)
16:32:15 [SEVERE]      at java.lang.Thread.run(Thread.java:636)

At first, I had no clue why this was happening. However, after I experienced some other errors, it seems to because I have too many open files. I googled a fix for this, and I ended up raising the max number of file descriptors allowed, but I still have this issue.
Running cat /proc/sys/fs/file-nr shows that only about 1216/362590 of them are being used, which means there shouldn't be a problem. Here is a list of the plugins I run:

Code:

Plugins: Minequery, ScheduledAnnouncer, WorldEdit, BlockHat, AutoHelp, CommandBook, Buycraft, Spout, Help, Vault, LogBlockQuestioner, PermissionsEx, Multiverse-Core, Jail, WorldGuard, AntiGrief, MineBackup, iConomy, Creativity, TimeFold, Permissions, BKCommonLib, KonseptGate, mcbans, Modifyworld, PluginInfo, NoCheat, Votifier, MyWarp, FalseBookCore, CleanroomGenerator, Residence, WorldBorder, ChatManager, CommandIConomy, FalseBookBlock, LogBlock, dynmap, NoLagg, FalseBookIC, FalseBookExtra, VanishNoPacket

If anybody thinks they know another reason for this, or they have a solution, please post it.

 

Code:

2012-02-23 02:46:41 [SEVERE] java.lang.IndexOutOfBoundsException: Index: 1408, Size: 1408
2012-02-23 02:46:41 [SEVERE] at java.util.ArrayList.RangeCheck(Unknown Source)
2012-02-23 02:46:41 [SEVERE] at java.util.ArrayList.set(Unknown Source)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.RegionFile.a(SourceFile:285)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.ChunkBuffer.close(SourceFile:259)
2012-02-23 02:46:41 [SEVERE] at java.util.zip.DeflaterOutputStream.close(Unknown Source)
2012-02-23 02:46:41 [SEVERE] at java.io.FilterOutputStream.close(Unknown Source)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.ChunkRegionLoader.a(ChunkRegionLoader.java:129)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.ChunkRegionLoader.c(ChunkRegionLoader.java:116)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.FileIOThread.b(SourceFile:29)
2012-02-23 02:46:41 [SEVERE] at net.minecraft.server.FileIOThread.run(SourceFile:22)
2012-02-23 02:46:41 [SEVERE] at java.lang.Thread.run(Unknown Source)
2012-02-23 02:47:13 [INFO] There are 2 out of maximum 35 players online.

Need help...

 

I have this same problem from time to time. I'm also on Linux and though I fail to see the relevance, "cat /proc/sys/fs/file-nr" shows 9600/308401 (when java is completely shut down). The drive I'm running on has a bad sector (can't afford a new one just yet - I make lots of backups...)
Have you checked your drive recently? smartctl -t long /dev/sda (followed by 'smartctl -l selftest /dev/sda' after the test is complete - note the time specified when you run the test).

Here are the plugins I have in common with you (ashlmi):
Vault, Multiverse-Core, Jail, WorldGuard, iConomy, MyWarp, WorldBorder, dynmap

I personally would suspect dynmap, since it uses thousands of map 'tiles' to function. Is yours up to date? Mine probably isn't.

 

Same Problem with MC 1.2.5 R3.0.

This morning all players were kicked and we restartet the server.
However, the log file was 1 GB (!) big, because it spammed this message "Too many open files" a million times until the server crashed.

Many players lost their whole inventory too.

 

Same problem

 

NoLagg throws a NPE because you have too many files? I think not.

It's a bug in NoLagg, or an error in NoLagg config most likely.