Sure, let me give it a try. I'm going to take 0.11 and patch it with https://issues.apache.org/jira/browse/CRUNCH-553 https://issues.apache.org/jira/browse/CRUNCH-517
as we also rely on 517. On Tue, Aug 18, 2015 at 4:09 PM, Josh Wills <[email protected]> wrote: > (In particular, I'm wondering if something in CRUNCH-481 is related to > this problem.) > > On Tue, Aug 18, 2015 at 4:07 PM, Josh Wills <[email protected]> wrote: > >> Hey Everett, >> >> Shot in the dark-- would you mind trying it w/0.11.0-hadoop2 w/the 553 >> patch? Is that easy to do? >> >> J >> >> On Tue, Aug 18, 2015 at 3:18 PM, Everett Anderson <[email protected]> >> wrote: >> >>> Hi, >>> >>> I verified that the pipeline succeeds on the same cc2.8xlarge hardware >>> when setting crunch.max.running.jobs to 1. I generally feel like the >>> pipeline application itself logic is sound, at this point. It could be that >>> this is just taxing these machines too hard and we need to increase the >>> number of retries? >>> >>> It reliably fails on this hardware when crunch.max.running.jobs set to >>> its default. >>> >>> Can you explain a little what the /tmp/crunch-XXXXXXX files are as well >>> as how Crunch uses side effect files? Do you know if HDFS would clean up >>> those directories from underneath Crunch? >>> >>> There are usually 4 failed applications, failing due to reduces. The >>> failures seem to be one of the following three kinds -- (1) No lease on >>> <side effect file>, (2) File not found </tmp/crunch-XXXXXXX> file, (3) >>> SocketTimeoutException. >>> >>> Examples: >>> >>> [1] No lease exception >>> >>> Error: org.apache.crunch.CrunchRuntimeException: >>> org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): >>> No lease on >>> /tmp/crunch-4694113/p662/output/_temporary/1/_temporary/attempt_1439917295505_out7_0018_r_000003_1/out7-r-00003: >>> File does not exist. Holder >>> DFSClient_attempt_1439917295505_0018_r_000003_1_824053899_1 does not have >>> any open files. at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2944) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.completeFileInternal(FSNamesystem.java:3008) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.completeFile(FSNamesystem.java:2988) >>> at >>> org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.complete(NameNodeRpcServer.java:641) >>> at >>> org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.complete(ClientNamenodeProtocolServerSideTranslatorPB.java:484) >>> at >>> org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java) >>> at >>> org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:599) >>> at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:928) at >>> org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2013) at >>> org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2009) at >>> java.security.AccessController.doPrivileged(Native Method) at >>> javax.security.auth.Subject.doAs(Subject.java:415) at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2007) at >>> org.apache.crunch.impl.mr.run.CrunchTaskContext.cleanup(CrunchTaskContext.java:74) >>> at >>> org.apache.crunch.impl.mr.run.CrunchReducer.cleanup(CrunchReducer.java:64) >>> at org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:195) at >>> org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:656) at >>> org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:394) at >>> org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:175) at >>> java.security.AccessController.doPrivileged(Native Method) at >>> javax.security.auth.Subject.doAs(Subject.java:415) at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:170) Caused by: >>> org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): >>> No lease on >>> /tmp/crunch-4694113/p662/output/_temporary/1/_temporary/attempt_1439917295505_out7_0018_r_000003_1/out7-r-00003: >>> File does not exist. Holder >>> DFSClient_attempt_1439917295505_0018_r_000003_1_824053899_1 does not have >>> any open files. at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.checkLease(FSNamesystem.java:2944) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.completeFileInternal(FSNamesystem.java:3008) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.completeFile(FSNamesystem.java:2988) >>> at >>> org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.complete(NameNodeRpcServer.java:641) >>> at >>> org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.complete(ClientNamenodeProtocolServerSideTranslatorPB.java:484) >>> at >>> org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java) >>> at >>> org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:599) >>> at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:928) at >>> org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2013) at >>> org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2009) at >>> java.security.AccessController.doPrivileged(Native Method) at >>> javax.security.auth.Subject.doAs(Subject.java:415) at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2007) at >>> org.apache.hadoop.ipc.Client.call(Client.java:1410) at >>> org.apache.hadoop.ipc.Client.call(Client.java:1363) at >>> org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:215) >>> at com.sun.proxy.$Proxy13.complete(Unknown Source) at >>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at >>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) >>> 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:190) >>> at >>> org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:103) >>> at com.sun.proxy.$Proxy13.complete(Unknown Source) at >>> org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.complete(ClientNamenodeProtocolTranslatorPB.java:404) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream.completeFile(DFSOutputStream.java:2130) >>> at org.apache.hadoop.hdfs.DFSOutputStream.close(DFSOutputStream.java:2114) >>> at >>> org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72) >>> at >>> org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:105) >>> at org.apache.hadoop.io.SequenceFile$Writer.close(SequenceFile.java:1289) >>> at >>> org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat$1.close(SequenceFileOutputFormat.java:87) >>> at >>> org.apache.crunch.io.CrunchOutputs$OutputState.close(CrunchOutputs.java:300) >>> at org.apache.crunch.io.CrunchOutputs.close(CrunchOutputs.java:180) at >>> org.apache.crunch.impl.mr.run.CrunchTaskContext.cleanup(CrunchTaskContext.java:72) >>> ... 9 more >>> >>> >>> [2] File does not exist >>> >>> 2015-08-18 17:36:10,195 INFO [AsyncDispatcher event handler] >>> org.apache.hadoop.mapreduce.v2.app.job.impl.TaskAttemptImpl: Diagnostics >>> report from attempt_1439917295505_0034_r_000004_1: Error: >>> org.apache.crunch.CrunchRuntimeException: Could not read runtime node >>> information >>> at >>> org.apache.crunch.impl.mr.run.CrunchTaskContext.<init>(CrunchTaskContext.java:48) >>> at >>> org.apache.crunch.impl.mr.run.CrunchReducer.setup(CrunchReducer.java:40) >>> at org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:172) >>> at >>> org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:656) >>> at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:394) >>> at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:175) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at javax.security.auth.Subject.doAs(Subject.java:415) >>> at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:170) >>> Caused by: java.io.FileNotFoundException: File does not exist: >>> /tmp/crunch-4694113/p470/REDUCE >>> at >>> org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:65) >>> at >>> org.apache.hadoop.hdfs.server.namenode.INodeFile.valueOf(INodeFile.java:55) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsUpdateTimes(FSNamesystem.java:1726) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocationsInt(FSNamesystem.java:1669) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1649) >>> at >>> org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getBlockLocations(FSNamesystem.java:1621) >>> at >>> org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.getBlockLocations(NameNodeRpcServer.java:497) >>> at >>> org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.getBlockLocations(ClientNamenodeProtocolServerSideTranslatorPB.java:322) >>> at >>> org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java) >>> at >>> org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:599) >>> at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:928) >>> at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2013) >>> at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:2009) >>> at java.security.AccessController.doPrivileged(Native Method) >>> at javax.security.auth.Subject.doAs(Subject.java:415) >>> at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.ipc.Server$Handler.run(Server.java:2007) >>> >>> 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:73) >>> at >>> org.apache.hadoop.hdfs.DFSClient.callGetBlockLocations(DFSClient.java:1147) >>> at >>> org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1135) >>> at >>> org.apache.hadoop.hdfs.DFSClient.getLocatedBlocks(DFSClient.java:1125) >>> at >>> org.apache.hadoop.hdfs.DFSInputStream.fetchLocatedBlocksAndGetLastBlockLength(DFSInputStream.java:273) >>> at >>> org.apache.hadoop.hdfs.DFSInputStream.openInfo(DFSInputStream.java:240) >>> at org.apache.hadoop.hdfs.DFSInputStream.<init>(DFSInputStream.java:233) >>> at org.apache.hadoop.hdfs.DFSClient.open(DFSClient.java:1298) >>> at >>> org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:300) >>> at >>> org.apache.hadoop.hdfs.DistributedFileSystem$3.doCall(DistributedFileSystem.java:296) >>> at >>> org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81) >>> at >>> org.apache.hadoop.hdfs.DistributedFileSystem.open(DistributedFileSystem.java:296) >>> at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:768) >>> at org.apache.crunch.util.DistCache.read(DistCache.java:72) >>> at >>> org.apache.crunch.impl.mr.run.CrunchTaskContext.<init>(CrunchTaskContext.java:46) >>> ... 9 more >>> >>> [3] SocketTimeoutException >>> >>> Error: org.apache.crunch.CrunchRuntimeException: >>> java.net.SocketTimeoutException: 70000 millis timeout while waiting for >>> channel to be ready for read. ch : >>> java.nio.channels.SocketChannel[connected local=/10.55.1.229:35720 >>> remote=/10.55.1.230:9200] at >>> org.apache.crunch.impl.mr.run.CrunchTaskContext.cleanup(CrunchTaskContext.java:74) >>> at >>> org.apache.crunch.impl.mr.run.CrunchReducer.cleanup(CrunchReducer.java:64) >>> at org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:195) at >>> org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:656) at >>> org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:394) at >>> org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:175) at >>> java.security.AccessController.doPrivileged(Native Method) at >>> javax.security.auth.Subject.doAs(Subject.java:415) at >>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1548) >>> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:170) Caused by: >>> java.net.SocketTimeoutException: 70000 millis timeout while waiting for >>> channel to be ready for read. ch : >>> java.nio.channels.SocketChannel[connected local=/10.55.1.229:35720 >>> remote=/10.55.1.230:9200] at >>> org.apache.hadoop.net.SocketIOWithTimeout.doIO(SocketIOWithTimeout.java:164) >>> at >>> org.apache.hadoop.net.SocketInputStream.read(SocketInputStream.java:161) at >>> org.apache.hadoop.net.SocketInputStream.read(SocketInputStream.java:131) at >>> org.apache.hadoop.net.SocketInputStream.read(SocketInputStream.java:118) at >>> java.io.FilterInputStream.read(FilterInputStream.java:83) at >>> java.io.FilterInputStream.read(FilterInputStream.java:83) at >>> org.apache.hadoop.hdfs.protocolPB.PBHelper.vintPrefixed(PBHelper.java:1985) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.transfer(DFSOutputStream.java:1075) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.addDatanode2ExistingPipeline(DFSOutputStream.java:1042) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.setupPipelineForAppendOrRecovery(DFSOutputStream.java:1186) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.processDatanodeError(DFSOutputStream.java:935) >>> at >>> org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:491) >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Fri, Aug 14, 2015 at 3:54 PM, Everett Anderson <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Fri, Aug 14, 2015 at 3:26 PM, Josh Wills <[email protected]> >>>> wrote: >>>> >>>>> Hey Everett, >>>>> >>>>> Initial thought-- there are lots of reasons for lease expired >>>>> exceptions, and their usually more symptomatic of other problems in the >>>>> pipeline. Are you sure none of the jobs in the Crunch pipeline on the >>>>> non-SSD instances are failing for some other reason? I'd be surprised if >>>>> no >>>>> other errors showed up in the app master, although there are reports of >>>>> some weirdness around LeaseExpireds when writing to S3-- but you're not >>>>> doing that here, right? >>>>> >>>> >>>> We're reading from and writing to HDFS, here. (We've copied in input >>>> from S3 to HDFS in another step.) >>>> >>>> There are a few exceptions in the logs. Most seem related to missing >>>> temp files. >>>> >>>> Let me see if I can reproduce it with crunch.max.running.jobs set to 1 >>>> to try to narrow down the originating failure. >>>> >>>> >>>> >>>> >>>>> >>>>> J >>>>> >>>>> On Fri, Aug 14, 2015 at 2:10 PM, Everett Anderson <[email protected]> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I recently started trying to run our Crunch pipeline on more data and >>>>>> have been trying out different AWS instance types in anticipation of our >>>>>> storage and compute needs. >>>>>> >>>>>> I was using EMR 3.8 (so Hadoop 2.4.0) with Crunch 0.12 (patched with >>>>>> the CRUNCH-553 <https://issues.apache.org/jira/browse/CRUNCH-553> >>>>>> fix). >>>>>> >>>>>> Our pipeline finishes fine in these cluster configurations: >>>>>> >>>>>> - 50 c3.4xlarge Core, 0 Task >>>>>> - 10 c3.8xlarge Core, 0 Task >>>>>> - 25 c3.8xlarge Core, 0 Task >>>>>> >>>>>> However, it always fails on the same data when using 10 cc2.8xlarge >>>>>> Core instances. >>>>>> >>>>>> The biggest obvious hardware difference is that the cc2.8xlarges use >>>>>> hard disks instead of SSDs. >>>>>> >>>>>> While it's a little hard to track down the exact originating failure, >>>>>> I think it's from errors like: >>>>>> >>>>>> 2015-08-13 21:34:38,379 ERROR [IPC Server handler 24 on 45711] >>>>>> org.apache.hadoop.mapred.TaskAttemptListenerImpl: Task: >>>>>> attempt_1439499407003_0028_r_000153_1 - exited : >>>>>> org.apache.crunch.CrunchRuntimeException: >>>>>> org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.LeaseExpiredException): >>>>>> No lease on >>>>>> /tmp/crunch-970849245/p662/output/_temporary/1/_temporary/attempt_1439499407003_out7_0028_r_000153_1/out7-r-00153: >>>>>> File does not exist. Holder >>>>>> DFSClient_attempt_1439499407003_0028_r_000153_1_609888542_1 does not have >>>>>> any open files. >>>>>> >>>>>> Those paths look like these side effect files >>>>>> <https://hadoop.apache.org/docs/r2.4.1/api/org/apache/hadoop/mapred/FileOutputFormat.html#getWorkOutputPath(org.apache.hadoop.mapred.JobConf)> >>>>>> . >>>>>> >>>>>> Would Crunch have generated applications that depend on side effect >>>>>> paths as input across MapReduce applications and something in HDFS is >>>>>> cleaning up those paths, unaware of the higher level dependencies? AWS >>>>>> configures Hadoop differently for each instance type, and might have more >>>>>> aggressive cleanup settings on HDs, though this is very uninformed >>>>>> hypothesis. >>>>>> >>>>>> A sample full log is attached. >>>>>> >>>>>> Thanks for any guidance! >>>>>> >>>>>> - Everett >>>>>> >>>>>> >>>>>> *DISCLAIMER:* The contents of this email, including any attachments, >>>>>> may contain information that is confidential, proprietary in nature, >>>>>> protected health information (PHI), or otherwise protected by law from >>>>>> disclosure, and is solely for the use of the intended recipient(s). If >>>>>> you >>>>>> are not the intended recipient, you are hereby notified that any use, >>>>>> disclosure or copying of this email, including any attachments, is >>>>>> unauthorized and strictly prohibited. If you have received this email in >>>>>> error, please notify the sender of this email. Please delete this and all >>>>>> copies of this email from your system. Any opinions either expressed or >>>>>> implied in this email and all attachments, are those of its author only, >>>>>> and do not necessarily reflect those of Nuna Health, Inc. >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Director of Data Science >>>>> Cloudera <http://www.cloudera.com> >>>>> Twitter: @josh_wills <http://twitter.com/josh_wills> >>>>> >>>> >>>> >>> >>> *DISCLAIMER:* The contents of this email, including any attachments, >>> may contain information that is confidential, proprietary in nature, >>> protected health information (PHI), or otherwise protected by law from >>> disclosure, and is solely for the use of the intended recipient(s). If you >>> are not the intended recipient, you are hereby notified that any use, >>> disclosure or copying of this email, including any attachments, is >>> unauthorized and strictly prohibited. If you have received this email in >>> error, please notify the sender of this email. Please delete this and all >>> copies of this email from your system. Any opinions either expressed or >>> implied in this email and all attachments, are those of its author only, >>> and do not necessarily reflect those of Nuna Health, Inc. >>> >> >> >> >> -- >> Director of Data Science >> Cloudera <http://www.cloudera.com> >> Twitter: @josh_wills <http://twitter.com/josh_wills> >> > > > > -- > Director of Data Science > Cloudera <http://www.cloudera.com> > Twitter: @josh_wills <http://twitter.com/josh_wills> > -- *DISCLAIMER:* The contents of this email, including any attachments, may contain information that is confidential, proprietary in nature, protected health information (PHI), or otherwise protected by law from disclosure, and is solely for the use of the intended recipient(s). If you are not the intended recipient, you are hereby notified that any use, disclosure or copying of this email, including any attachments, is unauthorized and strictly prohibited. If you have received this email in error, please notify the sender of this email. Please delete this and all copies of this email from your system. Any opinions either expressed or implied in this email and all attachments, are those of its author only, and do not necessarily reflect those of Nuna Health, Inc.
