Hi All,
I'm getting the following error (sorry, it is the full error stack) when I run the IndexTool MR job to populate an index I created with ASYNC. I have been able to use IndexTool successfully previously.

2016-08-17 13:30:48,024 INFO  [main] mapreduce.Job: Task Id : attempt_1471372816200_0005_m_000051_0, Status : FAILED
Error: java.lang.RuntimeException: org.apache.phoenix.exception.PhoenixIOException: 60209ms passed since the last invocation, timeout is currently set to 60000
at org.apache.phoenix.mapreduce.PhoenixRecordReader.nextKeyValue(PhoenixRecordReader.java:159)
at org.apache.hadoop.mapred.MapTask$NewTrackingRecordReader.nextKeyValue(MapTask.java:565)
at org.apache.hadoop.mapreduce.task.MapContextImpl.nextKeyValue(MapContextImpl.java:80)
at org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.nextKeyValue(WrappedMapper.java:91)
at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:145)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:796)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:342)
at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164)
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:1657)
at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
Caused by: org.apache.phoenix.exception.PhoenixIOException: 60209ms passed since the last invocation, timeout is currently set to 60000
at org.apache.phoenix.util.ServerUtil.parseServerException(ServerUtil.java:111)
at org.apache.phoenix.iterate.ScanningResultIterator.next(ScanningResultIterator.java:65)
at org.apache.phoenix.iterate.TableResultIterator.next(TableResultIterator.java:110)
at org.apache.phoenix.iterate.LookAheadResultIterator$1.advance(LookAheadResultIterator.java:47)
at org.apache.phoenix.iterate.LookAheadResultIterator.next(LookAheadResultIterator.java:67)
at org.apache.phoenix.iterate.RoundRobinResultIterator$RoundRobinIterator.next(RoundRobinResultIterator.java:309)
at org.apache.phoenix.iterate.RoundRobinResultIterator.next(RoundRobinResultIterator.java:97)
at org.apache.phoenix.jdbc.PhoenixResultSet.next(PhoenixResultSet.java:778)
at org.apache.phoenix.mapreduce.PhoenixRecordReader.nextKeyValue(PhoenixRecordReader.java:152)
... 11 more
Caused by: org.apache.hadoop.hbase.client.ScannerTimeoutException: 60209ms passed since the last invocation, timeout is currently set to 60000
at org.apache.hadoop.hbase.client.ClientScanner.loadCache(ClientScanner.java:438)
at org.apache.hadoop.hbase.client.ClientScanner.next(ClientScanner.java:370)
at org.apache.phoenix.iterate.ScanningResultIterator.next(ScanningResultIterator.java:55)
... 18 more
Caused by: org.apache.hadoop.hbase.UnknownScannerException: org.apache.hadoop.hbase.UnknownScannerException: Name: 149, already closed?
at org.apache.hadoop.hbase.regionserver.RSRpcServices.scan(RSRpcServices.java:2374)
at org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(ClientProtos.java:33648)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java:2180)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner.java:112)
at org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(RpcExecutor.java:133)
at org.apache.hadoop.hbase.ipc.RpcExecutor$1.run(RpcExecutor.java:108)
at java.lang.Thread.run(Thread.java:745)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.apache.hadoop.ipc.RemoteException.instantiateException(RemoteException.java:106)
at org.apache.hadoop.ipc.RemoteException.unwrapRemoteException(RemoteException.java:95)
at org.apache.hadoop.hbase.protobuf.ProtobufUtil.getRemoteException(ProtobufUtil.java:329)
at org.apache.hadoop.hbase.client.ScannerCallable.call(ScannerCallable.java:262)
at org.apache.hadoop.hbase.client.ScannerCallable.call(ScannerCallable.java:64)
at org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithoutRetries(RpcRetryingCaller.java:200)
at org.apache.hadoop.hbase.client.ScannerCallableWithReplicas$RetryingRPC.call(ScannerCallableWithReplicas.java:360)
at org.apache.hadoop.hbase.client.ScannerCallableWithReplicas$RetryingRPC.call(ScannerCallableWithReplicas.java:334)
at org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithRetries(RpcRetryingCaller.java:126)
at org.apache.hadoop.hbase.client.ResultBoundedCompletionService$QueueingFuture.run(ResultBoundedCompletionService.java:65)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.hadoop.hbase.ipc.RemoteWithExtrasException(org.apache.hadoop.hbase.UnknownScannerException): org.apache.hadoop.hbase.UnknownScannerException: Name: 149, already closed?
at org.apache.hadoop.hbase.regionserver.RSRpcServices.scan(RSRpcServices.java:2374)
at org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(ClientProtos.java:33648)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java:2180)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner.java:112)
at org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(RpcExecutor.java:133)
at org.apache.hadoop.hbase.ipc.RpcExecutor$1.run(RpcExecutor.java:108)
at java.lang.Thread.run(Thread.java:745)
at org.apache.hadoop.hbase.ipc.RpcClientImpl.call(RpcClientImpl.java:1268)
at org.apache.hadoop.hbase.ipc.AbstractRpcClient.callBlockingMethod(AbstractRpcClient.java:226)
at org.apache.hadoop.hbase.ipc.AbstractRpcClient$BlockingRpcChannelImplementation.callBlockingMethod(AbstractRpcClient.java:331)
at org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$BlockingStub.scan(ClientProtos.java:34094)
at org.apache.hadoop.hbase.client.ScannerCallable.call(ScannerCallable.java:219)
... 9 more


It seems like I need to set either/both of 'phoenix.query.timeoutMs'/'hbase.rpc.timeout'. But not sure how to configure those settings for the MR job's internal HBase client...

Thanks for the help,
-nathan