Details
-
Bug
-
Status: Closed
-
Critical
-
Resolution: Cannot Reproduce
-
0.19.0
-
None
-
None
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4 Node cluster with poor hardware: (DN+RS / DN+RS / RS / MA+NN)
1 Gb memory each
Ubuntu linux
Java 6
Description
One of my region server falls in a long GC time that get it unresponsive during about 10 minutes.
As I can see in the log, it seems that its DFSClient component was sending a file to hdfs, the sending times out when it recovers from GC:
1. Region server log after recovering from GC
2009-02-21 01:22:26,454 WARN org.apache.hadoop.hdfs.DFSClient: DFSOutputStream ResponseProcessor exception
for block blk_7545556036225037274_1820952java.io.IOException: Bad response 1 for block
blk_7545556036225037274_1820952 from datanode 192.168.1.10:50010
at org.apache.hadoop.hdfs.DFSClient$DFSOutputStream$ResponseProcessor.run(DFSClient.java:2342)
2. corresponding error in receiving datanode
2009-02-21 01:23:56,608 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: Exception in receiveBlock for block
blk_7545556036225037274_1820952 java.io.EOFException: while trying to read 65557 bytes
[...]
2009-02-21 01:23:59,076 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: PacketResponder 0 for block
blk_7545556036225037274_1820952 Interrupted.
2009-02-21 01:24:01,484 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: PacketResponder 0 for block
blk_7545556036225037274_1820952 terminating
2009-02-21 01:24:01,485 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: writeBlock
blk_7545556036225037274_1820952 received exception java.io.EOFException: while trying to read 65557 bytes
Since region server misses its lease to report to the master, it has to close all its regions before recover, and reopens them when the master asks for.
From this time, it tries to recover this block, as seen in the regionserver log:
3. Region server log in an endless loop to recover
009-02-21 01:22:29,327 WARN org.apache.hadoop.hdfs.DFSClient: Error Recovery for block
blk_7545556036225037274_1820952 bad datanode[1] 192.168.1.10:50010
2009-02-21 01:22:29,327 WARN org.apache.hadoop.hdfs.DFSClient: Error Recovery for block
blk_7545556036225037274_1820952 in pipeline 192.168.1.13:50010,
192.168.1.10:50010: bad datanode 192.168.1.10:50010
2009-02-21 01:22:29,689 WARN org.apache.hadoop.hdfs.DFSClient: Error Recovery for block
blk_7545556036225037274_1820952 failed because recovery from primary datanode 192.168.1.13:50010 failed 2 times. Will retry...
To this recover request, all datanodes fail with this Exception
4.
2009-02-21 01:24:18,650 INFO org.apache.hadoop.ipc.Server: IPC Server handler 1 on 50020, call
recoverBlock(blk_7545556036225037274_1820952, false, [Lorg.apache.hadoop.hdfs.protocol.DatanodeInfo;@311c4f) from
192.168.1.13:56968: error: org.apache.hadoop.ipc.RemoteException: java.io.IOException:
blk_7545556036225037274_1820952 is already commited, storedBlock == null.
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.nextGenerationStampForBlock(FSNamesystem.java:4536)
at org.apache.hadoop.hdfs.server.namenode.NameNode.nextGenerationStamp(NameNode.java:402)
at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:452)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:892)
org.apache.hadoop.ipc.RemoteException: java.io.IOException: blk_7545556036225037274_1820952 is already commited,
storedBlock == null.
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.nextGenerationStampForBlock(FSNamesystem.java:4536)
at org.apache.hadoop.hdfs.server.namenode.NameNode.nextGenerationStamp(NameNode.java:402)
at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:452)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:892)
at org.apache.hadoop.ipc.Client.call(Client.java:696)
at org.apache.hadoop.ipc.RPC$Invoker.invoke(RPC.java:216)
at $Proxy4.nextGenerationStamp(Unknown Source)
at org.apache.hadoop.hdfs.server.datanode.DataNode.syncBlock(DataNode.java:1466)
at org.apache.hadoop.hdfs.server.datanode.DataNode.recoverBlock(DataNode.java:1440)
at org.apache.hadoop.hdfs.server.datanode.DataNode.recoverBlock(DataNode.java:1506)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:452)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:892)
The problem is that, in this case, the RegionServer and therefore the master fails to stop when I launch the stop-hbase script.
A kill (-TERM) on the region server launches the SIGTERM handler thread, but the loop which try to reach the block does not stop.
here is a thread dump of the region server at this time:
5. Thread dump of the region server
Full thread dump Java HotSpot(TM) Server VM (10.0-b23 mixed mode):
"Thread-16" prio=10 tid=0x081c3c00 nid=0x6e81 in Object.wait() [0x8f74f000..0x8f74fec0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Thread.join(Thread.java:1143)
- locked <0x93d0d060> (a java.lang.Thread)
at java.lang.Thread.join(Thread.java:1196)
at org.apache.hadoop.hbase.util.Threads.shutdown(Threads.java:78)
at org.apache.hadoop.hbase.util.Threads.shutdown(Threads.java:66)
at org.apache.hadoop.hbase.regionserver.HRegionServer$ShutdownThread.run(HRegionServer.java:814)
"SIGTERM handler" daemon prio=10 tid=0x08dbcc00 nid=0x6e80 in Object.wait() [0x8edaf000..0x8edaff40]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Thread.join(Thread.java:1143)
- locked <0x93d0f3c0> (a org.apache.hadoop.hbase.regionserver.HRegionServer$ShutdownThread)
at java.lang.Thread.join(Thread.java:1196)
at java.lang.ApplicationShutdownHooks.run(ApplicationShutdownHooks.java:79)
at java.lang.Shutdown.runHooks(Shutdown.java:89)
at java.lang.Shutdown.sequence(Shutdown.java:133)
at java.lang.Shutdown.exit(Shutdown.java:178)
- locked <0xb0d3ed60> (a java.lang.Class for java.lang.Shutdown)
at java.lang.Terminator$1.handle(Terminator.java:35)
at sun.misc.Signal$1.run(Signal.java:195)
at java.lang.Thread.run(Thread.java:619)
"Attach Listener" daemon prio=10 tid=0x081e8800 nid=0x6e50 waiting on condition [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"IPC Client (47) connection to /192.168.1.13:50020 from an unknown user" daemon prio=10 tid=0x8e97a400 nid=0x39d1 in Object.wait() [0x8ec81000..0x8ec81fc0]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.apache.hadoop.ipc.Client$Connection.waitForWork(Client.java:395)
- locked <0xa44a36a0> (a org.apache.hadoop.ipc.Client$Connection)
at org.apache.hadoop.ipc.Client$Connection.run(Client.java:437)
"IPC Client (47) connection to /192.168.1.10:50020 from an unknown user" daemon prio=10 tid=0x8e5f1c00 nid=0x523f in Object.wait() [0x8ecd3000..0x8ecd3140]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.apache.hadoop.ipc.Client$Connection.waitForWork(Client.java:395)
- locked <0xa448ca50> (a org.apache.hadoop.ipc.Client$Connection)
at org.apache.hadoop.ipc.Client$Connection.run(Client.java:437)
"BlockFSInputStreamReferenceQueueChecker" daemon prio=10 tid=0x085a9400 nid=0x8c8 waiting on condition [0x8ee6c000..0x8ee6cdc0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93e76068> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.DelayQueue.take(DelayQueue.java:160)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:582)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:575)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:946)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:906)
at java.lang.Thread.run(Thread.java:619)
"IPC Server handler 9 on 60020" daemon prio=10 tid=0x0882e000 nid=0x889 waiting on condition [0x8eebd000..0x8eebdfc0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 8 on 60020" daemon prio=10 tid=0x0882cc00 nid=0x888 waiting on condition [0x8ef0e000..0x8ef0f040]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 7 on 60020" daemon prio=10 tid=0x0882b800 nid=0x887 waiting on condition [0x8ef5f000..0x8ef5fec0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 6 on 60020" daemon prio=10 tid=0x0882a400 nid=0x886 waiting on condition [0x8efb0000..0x8efb0f40]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 5 on 60020" daemon prio=10 tid=0x08829000 nid=0x885 waiting on condition [0x8f001000..0x8f001dc0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 4 on 60020" daemon prio=10 tid=0x083bcc00 nid=0x884 waiting on condition [0x8f052000..0x8f052e40]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 3 on 60020" daemon prio=10 tid=0x083bb800 nid=0x883 waiting on condition [0x8f0a3000..0x8f0a40c0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 2 on 60020" daemon prio=10 tid=0x083ba400 nid=0x882 waiting on condition [0x8f0f4000..0x8f0f5140]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 1 on 60020" daemon prio=10 tid=0x083b9400 nid=0x881 waiting on condition [0x8f145000..0x8f145fc0]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server handler 0 on 60020" daemon prio=10 tid=0x083b8400 nid=0x880 waiting on condition [0x8f196000..0x8f197040]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e9c8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1925)
at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:358)
at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:881)
"IPC Server listener on 60020" daemon prio=10 tid=0x083bfc00 nid=0x87f runnable [0x8f1e7000..0x8f1e7ec0]
java.lang.Thread.State: RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:215)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:65)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69)
- locked <0x93d0c090> (a sun.nio.ch.Util$1)
- locked <0x93d0c120> (a java.util.Collections$UnmodifiableSet)
- locked <0x93d0c0b0> (a sun.nio.ch.EPollSelectorImpl)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84)
at org.apache.hadoop.hbase.ipc.HBaseServer$Listener.run(HBaseServer.java:299)
"IPC Server Responder" daemon prio=10 tid=0x083bec00 nid=0x87e runnable [0x8f238000..0x8f238f40]
java.lang.Thread.State: RUNNABLE
at sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
at sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:215)
at sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:65)
at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69)
- locked <0x93d0c0f0> (a sun.nio.ch.Util$1)
- locked <0x93d0c100> (a java.util.Collections$UnmodifiableSet)
- locked <0x93d0be30> (a sun.nio.ch.EPollSelectorImpl)
at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80)
at org.apache.hadoop.hbase.ipc.HBaseServer$Responder.run(HBaseServer.java:458)
"SocketListener0-1" prio=10 tid=0x088d5000 nid=0x87c in Object.wait() [0x8f2da000..0x8f2dae40]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.mortbay.util.ThreadPool$PoolThread.run(ThreadPool.java:522)
- locked <0x93e39bc8> (a org.mortbay.util.ThreadPool$PoolThread)
"SocketListener0-0" prio=10 tid=0x08ab5000 nid=0x87b in Object.wait() [0x8f32b000..0x8f32c0c0]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.mortbay.util.ThreadPool$PoolThread.run(ThreadPool.java:522)
- locked <0x93e39920> (a org.mortbay.util.ThreadPool$PoolThread)
"Acceptor ServerSocket[addr=0.0.0.0/0.0.0.0,port=0,localport=60030]" prio=10 tid=0x084f6800 nid=0x87a
runnable [0x8f37c000..0x8f37d140]
java.lang.Thread.State: RUNNABLE
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:384)
- locked <0x93e382a8> (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.mortbay.util.ThreadedServer.acceptSocket(ThreadedServer.java:432)
at org.mortbay.util.ThreadedServer$Acceptor.run(ThreadedServer.java:631)
"SessionScavenger" daemon prio=10 tid=0x088f1400 nid=0x879 waiting on condition [0x8f3cd000..0x8f3cdfc0]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.mortbay.jetty.servlet.AbstractSessionManager$SessionScavenger.run(AbstractSessionManager.java:587)
"SessionScavenger" daemon prio=10 tid=0x08ab5c00 nid=0x878 waiting on condition [0x8f41e000..0x8f41f040]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.mortbay.jetty.servlet.AbstractSessionManager$SessionScavenger.run(AbstractSessionManager.java:587)
"regionserver/0.0.0.0:60020.leaseChecker" prio=10 tid=0x086d5800 nid=0x877 waiting on condition [0x8f476000..0x8f476ec0]
java.lang.Thread.State: TIMED_WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x93d0e980> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1963)
at java.util.concurrent.DelayQueue.poll(DelayQueue.java:201)
at org.apache.hadoop.hbase.Leases.run(Leases.java:78)
"regionserver/0.0.0.0:60020.majorCompactionChecker" daemon prio=10 tid=0x086d4000 nid=0x876 waiting on
condition [0x8f4c7000..0x8f4c7f40]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.apache.hadoop.hbase.util.Sleeper.sleep(Sleeper.java:74)
at org.apache.hadoop.hbase.Chore.run(Chore.java:72)
"LeaseChecker" daemon prio=10 tid=0x0837cc00 nid=0x870 waiting on condition [0x8f6ad000..0x8f6ae040]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.apache.hadoop.hdfs.DFSClient$LeaseChecker.run(DFSClient.java:979)
at java.lang.Thread.run(Thread.java:619)
"DataStreamer for file /hbase/log_192.168.1.13_1235129194745_60020/hlog.dat.1235129195649 block blk_7545556036225037274_1820952"
daemon prio=10 tid=0x08375400 nid=0x86f in Object.wait() [0x8f6fe000..0x8f6feec0]
java.lang.Thread.State: TIMED_WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at org.apache.hadoop.hdfs.DFSClient$DFSOutputStream$DataStreamer.run(DFSClient.java:2166)
- locked <0x93d0ea10> (a java.util.LinkedList)
"DestroyJavaVM" prio=10 tid=0x0805a000 nid=0x855 waiting on condition [0x00000000..0xb7dd2090]
java.lang.Thread.State: RUNNABLE
"regionserver/0.0.0.0:60020" prio=10 tid=0x085b2400 nid=0x863 in Object.wait() [0x8f7f7000..0x8f7f7f40]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at org.apache.hadoop.hdfs.DFSClient$DFSOutputStream.flushInternal(DFSClient.java:3015)
- locked <0x93d0ea10> (a java.util.LinkedList)
- locked <0x93d0ec58> (a org.apache.hadoop.hdfs.DFSClient$DFSOutputStream)
at org.apache.hadoop.hdfs.DFSClient$DFSOutputStream.closeInternal(DFSClient.java:3104)
- locked <0x93d0ec58> (a org.apache.hadoop.hdfs.DFSClient$DFSOutputStream)
at org.apache.hadoop.hdfs.DFSClient$DFSOutputStream.close(DFSClient.java:3053)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:59)
at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:79)
at org.apache.hadoop.io.SequenceFile$Writer.close(SequenceFile.java:959)
- locked <0x93d50d20> (a org.apache.hadoop.io.SequenceFile$Writer)
at org.apache.hadoop.hbase.regionserver.HLog.close(HLog.java:421)
- locked <0x93d4ce00> (a java.lang.Integer)
at org.apache.hadoop.hbase.regionserver.HLog.closeAndDelete(HLog.java:404)
at org.apache.hadoop.hbase.regionserver.HRegionServer.run(HRegionServer.java:373)
at java.lang.Thread.run(Thread.java:619)
"Low Memory Detector" daemon prio=10 tid=0x080dd800 nid=0x85e runnable [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x080dc400 nid=0x85d waiting on condition [0x00000000..0x8fbc1588]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x080d9c00 nid=0x85c waiting on condition [0x00000000..0x8fc42608]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x080d8800 nid=0x85b runnable [0x00000000..0x8fc93e80]
java.lang.Thread.State: RUNNABLE
"Surrogate Locker Thread (CMS)" daemon prio=10 tid=0x080d7800 nid=0x85a waiting on condition [0x00000000..0x8fce522c]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x080bbc00 nid=0x859 in Object.wait() [0x8fd7b000..0x8fd7bec0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
- locked <0x93d0bdc0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0x080ba800 nid=0x858 in Object.wait() [0x8fdcc000..0x8fdccf40]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0x93d0c110> (a java.lang.ref.Reference$Lock)
"VM Thread" prio=10 tid=0x080b7800 nid=0x857 runnable
"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x0806c800 nid=0x856 runnable
"VM Periodic Task Thread" prio=10 tid=0x080df000 nid=0x85f waiting on condition
JNI global references: 922
Notice the DataStreamer thread that seems to work on the concerned block
This force me to kill (-KILL) the region server, and restart the hdfs (if I don't restart hdfs some regions are not available because the block is still not available).
Note that the Hbase master does not end as well, and I have to kill (-KILL). Here is the thread dump of the HMaster process:
6. Master thread dump:
Full thread dump Java HotSpot(TM) Server VM (10.0-b23 mixed mode):
"Attach Listener" daemon prio=10 tid=0x0805a000 nid=0x2326 waiting on condition [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"SIGTERM handler" daemon prio=10 tid=0x089f0c00 nid=0x2303 waiting for monitor entry [0x8a6a5000..0x8a6a5ec0]
java.lang.Thread.State: BLOCKED (on object monitor)
at java.lang.Shutdown.exit(Shutdown.java:178)
- waiting to lock <0xb0beed60> (a java.lang.Class for java.lang.Shutdown)
at java.lang.Terminator$1.handle(Terminator.java:35)
at sun.misc.Signal$1.run(Signal.java:195)
at java.lang.Thread.run(Thread.java:619)
"Thread-1" prio=10 tid=0x8f666000 nid=0x653c waiting on condition [0x8f1fe000..0x8f1fef40]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.apache.hadoop.ipc.Client.stop(Client.java:667)
at org.apache.hadoop.ipc.RPC$ClientCache.stopClient(RPC.java:189)
at org.apache.hadoop.ipc.RPC$ClientCache.access$400(RPC.java:138)
at org.apache.hadoop.ipc.RPC$Invoker.close(RPC.java:229)
- locked <0x938a1b18> (a org.apache.hadoop.ipc.RPC$Invoker)
at org.apache.hadoop.ipc.RPC$Invoker.access$500(RPC.java:196)
at org.apache.hadoop.ipc.RPC.stopProxy(RPC.java:353)
at org.apache.hadoop.hdfs.DFSClient.close(DFSClient.java:213)
- locked <0x93878470> (a org.apache.hadoop.hdfs.DFSClient)
at org.apache.hadoop.hdfs.DistributedFileSystem.close(DistributedFileSystem.java:243)
at org.apache.hadoop.fs.FileSystem$Cache.closeAll(FileSystem.java:1413)
- locked <0x937d3c00> (a org.apache.hadoop.fs.FileSystem$Cache)
at org.apache.hadoop.fs.FileSystem.closeAll(FileSystem.java:236)
at org.apache.hadoop.fs.FileSystem$ClientFinalizer.run(FileSystem.java:221)
- locked <0x937b8a78> (a org.apache.hadoop.fs.FileSystem$ClientFinalizer)
"DestroyJavaVM" prio=10 tid=0x8f66c800 nid=0x36e9 in Object.wait() [0xb7d7d000..0xb7d7e0e0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Thread.join(Thread.java:1143)
- locked <0x937b8a78> (a org.apache.hadoop.fs.FileSystem$ClientFinalizer)
at java.lang.Thread.join(Thread.java:1196)
at java.lang.ApplicationShutdownHooks.run(ApplicationShutdownHooks.java:79)
at java.lang.Shutdown.runHooks(Shutdown.java:89)
at java.lang.Shutdown.sequence(Shutdown.java:133)
at java.lang.Shutdown.shutdown(Shutdown.java:200)
- locked <0xb0beed60> (a java.lang.Class for java.lang.Shutdown)
"Low Memory Detector" daemon prio=10 tid=0x8fe03800 nid=0x36f4 runnable [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x8fe01c00 nid=0x36f3 waiting on condition [0x00000000..0x8f9ee488]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x8fe00800 nid=0x36f2 waiting on condition [0x00000000..0x8fa6f508]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x0813e800 nid=0x36f1 runnable [0x00000000..0x8fac0d80]
java.lang.Thread.State: RUNNABLE
"Surrogate Locker Thread (CMS)" daemon prio=10 tid=0x0813d800 nid=0x36f0 waiting on condition [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x08125000 nid=0x36ef in Object.wait() [0x8fba1000..0x8fba1dc0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
- locked <0x937bafd8> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0x08120c00 nid=0x36ee in Object.wait() [0x8fbf2000..0x8fbf2e40]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0x937baf18> (a java.lang.ref.Reference$Lock)
"VM Thread" prio=10 tid=0x0811d800 nid=0x36ed runnable
"Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x0805e000 nid=0x36ea runnable
"Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x0805f000 nid=0x36eb runnable
"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x080cd000 nid=0x36ec runnable
"VM Periodic Task Thread" prio=10 tid=0x8fe05000 nid=0x36f5 waiting on condition
JNI global references: 1044
When I restart dfs, the log shows me that the concerned block is marked as invalidate, and it is therefore deleted:
7. Namenode log
2009-02-23 10:33:49,245 INFO org.apache.hadoop.hdfs.StateChange: BLOCK* NameSystem.processReport: block blk_7545556036225037274_1820952 on 192.168.1.10:50010 size 27895296 does not belong to any file. 2009-02-23 10:33:49,245 INFO org.apache.hadoop.hdfs.StateChange: BLOCK* NameSystem.addToInvalidates: blk_7545556036225037274 is added to invalidSet of 192.168.1.10:50010
Finally, when I restart HBase, I can see some of these messages in region server log, and I have some data loss. (this log entry may not be linked with the block traced before)
8. Region server log:
2009-02-23 10:38:55,831 WARN org.apache.hadoop.hbase.regionserver.HStore: Exception processing reconstruction log
hdfs://lab5-2:9000/hbase/test-D-0.3/510178748/oldlogfile.log opening [B@ff65bf -- continuing. Probably lack-of-HADOOP-1700
causing DATA LOSS!
java.io.EOFException
at java.io.DataInputStream.readFully(DataInputStream.java:180)
at org.apache.hadoop.hbase.io.DataOutputBuffer$Buffer.write(DataOutputBuffer.java:70)
at org.apache.hadoop.hbase.io.DataOutputBuffer.write(DataOutputBuffer.java:116)
at org.apache.hadoop.hbase.io.SequenceFile$Reader.next(SequenceFile.java:1944)
at org.apache.hadoop.hbase.io.SequenceFile$Reader.next(SequenceFile.java:1844)
at org.apache.hadoop.hbase.io.SequenceFile$Reader.next(SequenceFile.java:1890)
at org.apache.hadoop.hbase.regionserver.HStore.doReconstructionLog(HStore.java:352)
at org.apache.hadoop.hbase.regionserver.HStore.runReconstructionLog(HStore.java:297)
at org.apache.hadoop.hbase.regionserver.HStore.<init>(HStore.java:237)
at org.apache.hadoop.hbase.regionserver.HRegion.instantiateHStore(HRegion.java:1764)
at org.apache.hadoop.hbase.regionserver.HRegion.initialize(HRegion.java:276)
at org.apache.hadoop.hbase.regionserver.HRegionServer.instantiateRegion(HRegionServer.java:1367)
at org.apache.hadoop.hbase.regionserver.HRegionServer.openRegion(HRegionServer.java:1338)
at org.apache.hadoop.hbase.regionserver.HRegionServer$Worker.run(HRegionServer.java:1253)
at java.lang.Thread.run(Thread.java:619)
In my sense, since my hardware is in cause for RegionServer lease miss, I have to deal with the fact that I have to stop/restart hbase + hadoop in such a case. The problem in my sense is that a stop request should be able to perform a clean shutdown, and to avoid dataloss.
Hope this description helps.