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From "Keith Turner (JIRA)" <j...@apache.org>
Subject [jira] [Created] (ACCUMULO-3575) Accumulo GC ran out of memory
Date Tue, 10 Feb 2015 21:05:11 GMT
Keith Turner created ACCUMULO-3575:
--------------------------------------

             Summary: Accumulo GC ran out of memory
                 Key: ACCUMULO-3575
                 URL: https://issues.apache.org/jira/browse/ACCUMULO-3575
             Project: Accumulo
          Issue Type: Bug
    Affects Versions: 1.6.0
            Reporter: Keith Turner
            Priority: Minor


During CI run (w/ agitation) on 20 node EC2 cluster the Accumulo GC died with the following
errors.

Following was in gc out file

{noformat}
#
# java.lang.OutOfMemoryError: Java heap space
# -XX:OnOutOfMemoryError="kill -9 %p"
#   Executing /bin/sh -c "kill -9 20970"...
{noformat}

Following was in last lines of .log file

{noformat}
2015-02-10 20:19:03,255 [gc.SimpleGarbageCollector] INFO : Collect cycle took 13.07 seconds
2015-02-10 20:19:03,258 [gc.SimpleGarbageCollector] INFO : Beginning garbage collection of
write-ahead logs
2015-02-10 20:19:03,265 [zookeeper.ZooUtil] DEBUG: Trying to read instance id from hdfs://ip-10-1-2-11:9000/accumulo/instance_id
{noformat}

Restarted GC and same thing happened.   Looked in walog dir and saw there were 333k walog.
 This is the problem, the GC tries to read the list of files into memory.

{noformat}
$ hadoop fs -ls -R /accumulo/wal | wc
15/02/10 20:31:35 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your
platform... using builtin-java classes where applicable
 333053 2664424 43629314
{noformat}

I suspect the reason there were so many walogs is because there were many many failure like
the following (which resulted in 0 length walogs, only 199 of the 333K have non-zero length).
 The following error is from a tserver, which is probably a result of killing datanodes.

{noformat}
2015-02-10 03:45:00,447 [log.TabletServerLogger] ERROR: Unexpected error writing to log, retrying
attempt 122
java.lang.RuntimeException: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File
/accumulo/wal/ip-10-1-2-21+9997/9906de55-bc93-47f4-887c-4b9540fc3528 could only be replicated
to 0 nodes instead of minReplication (=1).  There 
are 16 datanode(s) running and no node(s) are excluded in this operation.
        at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget4NewBlock(BlockManager.java:1549)
        at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:3200)
        at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:641)
        at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:482)
        at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
        at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:619)
        at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:962)
        at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2039)
        at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2035)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:415)
        at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1628)
        at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2033)

        at org.apache.accumulo.tserver.log.TabletServerLogger.createLoggers(TabletServerLogger.java:190)
        at org.apache.accumulo.tserver.log.TabletServerLogger.access$300(TabletServerLogger.java:53)
        at org.apache.accumulo.tserver.log.TabletServerLogger$1.withWriteLock(TabletServerLogger.java:148)
        at org.apache.accumulo.tserver.log.TabletServerLogger.testLockAndRun(TabletServerLogger.java:115)
        at org.apache.accumulo.tserver.log.TabletServerLogger.initializeLoggers(TabletServerLogger.java:137)
        at org.apache.accumulo.tserver.log.TabletServerLogger.write(TabletServerLogger.java:245)
        at org.apache.accumulo.tserver.log.TabletServerLogger.write(TabletServerLogger.java:230)
        at org.apache.accumulo.tserver.log.TabletServerLogger.log(TabletServerLogger.java:345)
        at org.apache.accumulo.tserver.TabletServer$ThriftClientHandler.update(TabletServer.java:1817)
        at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.accumulo.trace.instrument.thrift.RpcServerInvocationHandler.invoke(RpcServerInvocationHandler.java:46)
        at org.apache.accumulo.server.util.RpcWrapper$1.invoke(RpcWrapper.java:47)
        at com.sun.proxy.$Proxy22.update(Unknown Source)
        at org.apache.accumulo.core.tabletserver.thrift.TabletClientService$Processor$update.getResult(TabletClientService.java:2394)
        at org.apache.accumulo.core.tabletserver.thrift.TabletClientService$Processor$update.getResult(TabletClientService.java:2378)
        at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
        at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
        at org.apache.accumulo.server.util.TServerUtils$TimedProcessor.process(TServerUtils.java:168)
        at org.apache.thrift.server.AbstractNonblockingServer$FrameBuffer.invoke(AbstractNonblockingServer.java:516)
        at org.apache.accumulo.server.util.CustomNonBlockingServer$1.run(CustomNonBlockingServer.java:77)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at org.apache.accumulo.trace.instrument.TraceRunnable.run(TraceRunnable.java:47)
        at org.apache.accumulo.core.util.LoggingRunnable.run(LoggingRunnable.java:34)
        at java.lang.Thread.run(Thread.java:744)
Caused by: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /accumulo/wal/ip-10-1-2-21+9997/9906de55-bc93-47f4-887c-4b9540fc3528
could only be replicated to 0 nodes instead of minReplication (=1).  There are 16 datanode(s
) running and no node(s) are excluded in this operation.
        at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget4NewBlock(BlockManager.java:1549)
        at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:3200)
        at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:641)
        at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:482)
        at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java)
        at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:619)
        at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:962)
        at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2039)
        at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2035)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:415)
        at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1628)
        at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2033)

        at org.apache.hadoop.ipc.Client.call(Client.java:1468)
        at org.apache.hadoop.ipc.Client.call(Client.java:1399)
        at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:232)
        at com.sun.proxy.$Proxy20.addBlock(Unknown Source)
        at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.addBlock(ClientNamenodeProtocolTranslatorPB.java:399)
        at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:187)
        at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
        at com.sun.proxy.$Proxy21.addBlock(Unknown Source)
        at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:1532)
        at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:1349)
        at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:588)
{noformat}


Upped gc max mem from 256k to 2G and it ran ok.



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