Server Lagging then Crashing

I started up my server it runs for a few minutes displays this message:

[Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 5700ms behind, skipping 114 tick(s)
[16:05:53] [Server Watchdog/FATAL]: A single server tick took 48.72 seconds (should be max 0.05)
[16:05:53] [Server Watchdog/FATAL]: Considering it to be crashed, server will forcibly shutdown.
[16:05:53] [Server Watchdog/ERROR]: This crash report has been saved to: /home/minecraft/./crash-reports/crash-2014-07-25_16.05.53-server.txt

It then crashes, here is the crash report. - http://pastebin.com/kncJvzFr

Can't keep up! Did the system time change, or is the server overloaded? Running 5700ms behind, skipping 114 tick(s)
: A single server tick took 48.72 seconds (should be max 0.05)
: Considering it to be crashed, server will forcibly shutdown.
: This crash report has been saved to: /home/minecraft/./crash-reports/crash-2014-07-25_16.05.53-server.txt
then crashes, here is the crash report.
---- Minecraft Crash Report ----
// Why did you do that?
Time: 7/25/14 4:25 PM
Description: Watching Server
java.lang.Error
at java.lang.StrictMath.atan2(Native Method)
at java.lang.Math.atan2(Math.java:517)
at yi.a(SourceFile:51)
at xi.bE(SourceFile:472)
at xh.l(SourceFile:1431)
at xi.l(SourceFile:327)
at aex.l(SourceFile:39)
at afg.l(SourceFile:151)
at xh.j(SourceFile:1299)
at xi.j(SourceFile:206)
at aex.j(SourceFile:44)
at aqa.a(SourceFile:1410)
at ql.a(SourceFile:592)
at aqa.g(SourceFile:1388)
at aqa.i(SourceFile:1281)
at ql.i(SourceFile:470)
at net.minecraft.server.MinecraftServer.y(SourceFile:605)
at ph.y(SourceFile:303)
at net.minecraft.server.MinecraftServer.x(SourceFile:529)
at net.minecraft.server.MinecraftServer.run(SourceFile:445)
at java.lang.Thread.run(Thread.java:745)
A detailed walkthrough of the error, its code path and all known details is as follows:
---------------------------------------------------------------------------------------
– Head –
Stacktrace:
at java.lang.StrictMath.atan2(Native Method)
at java.lang.Math.atan2(Math.java:517)
at yi.a(SourceFile:51)
at xi.bE(SourceFile:472)
at xh.l(SourceFile:1431)
at xi.l(SourceFile:327)
at aex.l(SourceFile:39)
at afg.l(SourceFile:151)
at xh.j(SourceFile:1299)
at xi.j(SourceFile:206)
at aex.j(SourceFile:44)
at aqa.a(SourceFile:1410)
at ql.a(SourceFile:592)
at aqa.g(SourceFile:1388)
at aqa.i(SourceFile:1281)
at ql.i(SourceFile:470)
at net.minecraft.server.MinecraftServer.y(SourceFile:605)
at ph.y(SourceFile:303)
at net.minecraft.server.MinecraftServer.x(SourceFile:529)
– Thread Dump –
Details:
Threads: "File IO Thread" Id=33 TIMED_WAITING
at java.lang.Thread.sleep(Native Method)
at bqk.c(SourceFile:44)
at bqk.run(SourceFile:30)
at java.lang.Thread.run(Thread.java:745)
"Netty Server IO #3" Id=22 RUNNABLE
at sun.misc.Cleaner.create(Cleaner.java:133)
at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:139)
at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:311)
at io.netty.buffer.UnpooledUnsafeDirectByteBuf.allocateDirect(UnpooledUnsafeDirectByteBuf.java:108)
at io.netty.buffer.UnpooledUnsafeDirectByteBuf.<init>(UnpooledUnsafeDirectByteBuf.java:69)
at io.netty.buffer.UnpooledByteBufAllocator.newDirectBuffer(UnpooledByteBufAllocator.java:50)
at io.netty.buffer.AbstractByteBufAllocator.directBuffer(AbstractByteBufAllocator.java:155)
at io.netty.buffer.AbstractByteBufAllocator.directBuffer(AbstractByteBufAllocator.java:146)
...
"Netty Server IO #2" Id=21 RUNNABLE (in native)
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:79)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
locked io.netty.channel.nio.SelectedSelectionKeySet@5b46caf9
locked java.util.Collections$UnmodifiableSet@55812fe1
locked sun.nio.ch.EPollSelectorImpl@51bea189
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
...
"Netty Server IO #1" Id=20 RUNNABLE (in native)
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:79)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
locked io.netty.channel.nio.SelectedSelectionKeySet@14bc25da
locked java.util.Collections$UnmodifiableSet@794034b6
locked sun.nio.ch.EPollSelectorImpl@25e2f258
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
...
"Java2D Disposer" Id=27 WAITING on java.lang.ref.ReferenceQueue$Lock@1f4bd84
at java.lang.Object.wait(Native Method)
waiting on java.lang.ref.ReferenceQueue$Lock@1f4bd84
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:142)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:158)
at sun.java2d.Disposer.run(Disposer.java:148)
at java.lang.Thread.run(Thread.java:745)
"Server Watchdog" Id=26 RUNNABLE
at sun.management.ThreadImpl.dumpThreads0(Native Method)
at sun.management.ThreadImpl.dumpAllThreads(ThreadImpl.java:446)
at pm.run(SourceFile:36)
at java.lang.Thread.run(Thread.java:745)
"Query Listener #1" Id=25 RUNNABLE
at java.net.PlainDatagramSocketImpl.receive0(Native Method)
locked java.net.PlainDatagramSocketImpl@7493da95
at java.net.AbstractPlainDatagramSocketImpl.receive(AbstractPlainDatagramSocketImpl.java:143)
locked java.net.PlainDatagramSocketImpl@7493da95
at java.net.DatagramSocket.receive(DatagramSocket.java:781)
locked java.net.DatagramPacket@c8ea535
locked java.net.DatagramSocket@37859123
at sx.run(SourceFile:261)
at java.lang.Thread.run(Thread.java:745)
"Netty Server IO #0" Id=19 RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:79)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
locked io.netty.channel.nio.SelectedSelectionKeySet@3e4ce6ce
locked java.util.Collections$UnmodifiableSet@1af0741e
locked sun.nio.ch.EPollSelectorImpl@70dd42a7
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
at io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:618)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:306)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
...
"Server console handler" Id=15 RUNNABLE (in native)
at java.io.FileInputStream.readBytes(Native Method)
at java.io.FileInputStream.read(FileInputStream.java:234)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
locked java.io.BufferedInputStream@903e684
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
locked java.io.InputStreamReader@50a00bfc
at java.io.InputStreamReader.read(InputStreamReader.java:184)
...
"DestroyJavaVM" Id=16 RUNNABLE
"Server thread" Id=13 RUNNABLE
at java.lang.StrictMath.atan2(Native Method)
at java.lang.Math.atan2(Math.java:517)
at yi.a(SourceFile:51)
at xi.bE(SourceFile:472)
at xh.l(SourceFile:1431)
at xi.l(SourceFile:327)
at aex.l(SourceFile:39)
at afg.l(SourceFile:151)
...
"Server Infinisleeper" Id=12 TIMED_WAITING
at java.lang.Thread.sleep(Native Method)
at pi.run(SourceFile:64)
"Snooper Timer" Id=11 TIMED_WAITING on java.util.TaskQueue@4969c572
at java.lang.Object.wait(Native Method)
waiting on java.util.TaskQueue@4969c572
at java.util.TimerThread.mainLoop(Timer.java:552)
at java.util.TimerThread.run(Timer.java:505)
"Attach Listener" Id=5 RUNNABLE
"Finalizer" Id=3 WAITING on java.lang.ref.ReferenceQueue$Lock@533b7e82
at java.lang.Object.wait(Native Method)
waiting on java.lang.ref.ReferenceQueue$Lock@533b7e82
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:142)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:158)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)
"Reference Handler" Id=2 RUNNABLE
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:502)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)
Stacktrace:
at pm.run(SourceFile:52)
at java.lang.Thread.run(Thread.java:745)
– System Details –
Details:
Minecraft Version: 14w30c
Operating System: Linux (amd64) version 2.6.32-042stab076.5
Java Version: 1.8.0_05, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 360023480 bytes (343 MB) / 891781120 bytes (850 MB) up to 2605973504 bytes (2485 MB)
JVM Flags: 36 total; -XX:ThreadPriorityPolicy=42 -XX:CompileThreshold=1500 -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:ParallelGCThreads=1 -XX:TargetSurvivorRatio=90 -XX:MaxTenuringThreshold=15 -XX:+UnlockExperimentalVMOptions -XX:+UseAdaptiveGCBoundary -XX:MaxMetaspaceSize=512M -XX:+UseGCOverheadLimit -XX:+UseBiasedLocking -Xnoclassgc -Xverify:none -XX:UseSSE=3 -XX:+UseThreadPriorities -XX:+UseLargePages -XX:NewRatio=3 -XX:SurvivorRatio=3 -XX:MaxTenuringThreshold=8 -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:MaxGCPauseMillis=10 -XX:GCPauseIntervalMillis=50 -XX:MaxGCMinorPauseMillis=7 -XX:+ExplicitGCInvokesConcurrent -XX:+UseCMSInitiatingOccupancyOnly -XX:CMSInitiatingOccupancyFraction=60 -XX:+BindGCTaskThreadsToCPUs -XX:+UseStringCache -XX:+OptimizeStringConcat -XX:+UseFastAccessorMethods -Xrs -XX:+UseCompressedOops -XX:+AggressiveOpts -Xmx2616M
IntCache: cache: 0, tcache: 0, allocated: 12, tallocated: 98
Profiler Position: N/A (disabled)
Player Count: 1 / 15; [qo]
Is Modded: Unknown (can't tell)
Type: Dedicated Server (map_server.txt)