Row exception in Hive while using join - hadoop

Question

I got the following exception while executing join on Hive Query and reducer hang after 68% completion.
java.lang.RuntimeException: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing row (tag=1) {"key":{"joinkey0":"12"},"value":{"_col2":"rs317647905"},"alias":1}
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:270)
at org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:506)
at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:447)
at org.apache.hadoop.mapred.Child$4.run(Child.java:268)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.mapred.Child.main(Child.java:262)
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing row (tag=1) {"key":{"joinkey0":"12"},"value":{"_col2":"rs317647905"},"alias":1}
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:258)
... 7 more
Caused by: org.apache.hadoop.
Below are my query and table structure:
create table table_llv_N_C as select table_line_n_passed.chromosome_number,table_line_n_passed.position,table_line_c_passed.id from table_line_n_passed join table_line_c_passed on (table_line_n_passed.chromosome_number=table_line_c_passed.chromosome_number)
hive> desc table_line_n_passed;
OK
chromosome_number string
position int
id string
ref string
alt string
quality double
filter string
info string
format string
line6 string
Time taken: 0.854 seconds
Why am I getting this error, and how can I solve it?
full stack trace given below.
2015-03-09 10:19:09,347 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1797000000 rows
2015-03-09 10:19:09,919 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1798000000 rows
2015-03-09 10:19:09,919 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1798000000 rows
2015-03-09 10:19:10,495 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1799000000 rows
2015-03-09 10:19:10,495 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1799000000 rows
2015-03-09 10:19:11,069 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1800000000 rows
2015-03-09 10:19:11,069 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1800000000 rows
2015-03-09 10:19:11,644 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1801000000 rows
2015-03-09 10:19:11,644 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1801000000 rows
2015-03-09 10:19:12,229 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1802000000 rows
2015-03-09 10:19:12,229 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1802000000 rows
2015-03-09 10:19:13,310 INFO org.apache.hadoop.hive.ql.exec.JoinOperator: 6 forwarding 1803000000 rows
2015-03-09 10:19:13,310 INFO org.apache.hadoop.hive.ql.exec.SelectOperator: 7 forwarding 1803000000 rows
2015-03-09 10:19:13,666 WARN org.apache.hadoop.hdfs.DFSClient: DataStreamer Exception
org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.ipc.Client.call(Client.java:1238)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:202)
at $Proxy10.addBlock(Unknown Source)
at sun.reflect.GeneratedMethodAccessor13.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:164)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:83)
at $Proxy10.addBlock(Unknown Source)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.addBlock(ClientNamenodeProtocolTranslatorPB.java:291)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:1228)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:1081)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:502)
2015-03-09 10:19:14,043 FATAL ExecReducer: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing row (tag=1) {"key":{"joinkey0":"12"},"value":{"_col2":"."},"alias":1}
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:258)
at org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:506)
at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:447)
at org.apache.hadoop.mapred.Child$4.run(Child.java:268)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.mapred.Child.main(Child.java:262)
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.hive.ql.exec.JoinOperator.processOp(JoinOperator.java:134)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:249)
... 7 more
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.hive.ql.exec.FileSinkOperator.processOp(FileSinkOperator.java:620)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.Operator.forward(Operator.java:803)
at org.apache.hadoop.hive.ql.exec.SelectOperator.processOp(SelectOperator.java:84)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.Operator.forward(Operator.java:803)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:742)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:745)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.checkAndGenObject(CommonJoinOperator.java:847)
at org.apache.hadoop.hive.ql.exec.JoinOperator.processOp(JoinOperator.java:109)
... 9 more
Caused by: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.ipc.Client.call(Client.java:1238)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:202)
at $Proxy10.addBlock(Unknown Source)
at sun.reflect.GeneratedMethodAccessor13.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:164)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:83)
at $Proxy10.addBlock(Unknown Source)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.addBlock(ClientNamenodeProtocolTranslatorPB.java:291)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:1228)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:1081)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:502)
2015-03-09 10:19:14,800 INFO org.apache.hadoop.mapred.TaskLogsTruncater: Initializing logs' truncater with mapRetainSize=-1 and reduceRetainSize=-1
2015-03-09 10:19:14,806 WARN org.apache.hadoop.mapred.Child: Error running child
java.lang.RuntimeException: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing row (tag=1) {"key":{"joinkey0":"12"},"value":{"_col2":"."},"alias":1}
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:270)
at org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:506)
at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:447)
at org.apache.hadoop.mapred.Child$4.run(Child.java:268)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.mapred.Child.main(Child.java:262)
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing row (tag=1) {"key":{"joinkey0":"12"},"value":{"_col2":"."},"alias":1}
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:258)
... 7 more
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.hive.ql.exec.JoinOperator.processOp(JoinOperator.java:134)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.ExecReducer.reduce(ExecReducer.java:249)
... 7 more
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: org.apache.hadoop.ipc.RemoteException(java.io.IOException): File /tmp/hive-root/hive_2015-03-09_10-03-59_970_3646456754594156815-1/_task_tmp.-ext-10001/_tmp.000000_0 could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
at org.apache.hadoop.hdfs.server.blockmanagement.BlockManager.chooseTarget(BlockManager.java:1361)
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:2362)
at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.addBlock(NameNodeRpcServer.java:501)
at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.addBlock(ClientNamenodeProtocolServerSideTranslatorPB.java:299)
at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44954)
at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1760)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1756)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1438)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1754)
at org.apache.hadoop.hive.ql.exec.FileSinkOperator.processOp(FileSinkOperator.java:620)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.Operator.forward(Operator.java:803)
at org.apache.hadoop.hive.ql.exec.SelectOperator.processOp(SelectOperator.java:84)
at org.apache.hadoop.hive.ql.exec.Operator.process(Operator.java:474)
at org.apache.hadoop.hive.ql.exec.Operator.forward(Operator.java:803)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:742)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:745)
at org.apache.hadoop.hive.ql.exec.CommonJoinOperator.checkAndGenObject(CommonJoinOperator.java:847)

Answer 1

The root cause may be lack of disk space in the HDFS cluster, based on the fact that the query seems to fail only after running for a while and combined with this message from the stack trace:
... could only be replicated to 0 nodes instead of minReplication (=1). There are 2 datanode(s) running and no node(s) are excluded in this operation.
That message seems to crop up when there is a network communication issue (lost communication with data nodes, for example) or if HDFS is unable to service a write operation because no data nodes with free blocks could be located. Since your query does successfully start, to me that tends to rule out the network issue; instead, it appears that your Hive query is running out of disk space trying to generate that table. You may want to check the current usage on your cluster, which can be done through something like Ambari (if you've got that installed), or through the command line with one of the following:
hdfs dfs -df -h
If you're running an older version, it might be something like:
hadoop fs -df -h