Mark Needham

Thoughts on Software Development

Archive for the ‘hadoop’ tag

Mahout/Hadoop: org.apache.hadoop.ipc.RemoteException: Server IPC version 9 cannot communicate with client version 4

without comments

I’ve been working my way through Dragan Milcevski’s mini tutorial on using Mahout to do content based filtering on documents and reached the final step where I needed to read in the generated item-similarity files.

I got the example compiling by using the following Maven dependency:

<dependency>
      <groupId>org.apache.mahout</groupId>
      <artifactId>mahout-core</artifactId>
      <version>0.9</version>
</dependency>

Unfortunately when I ran the code I ran into a version incompatibility problem:

Exception in thread "main" org.apache.hadoop.ipc.RemoteException: Server IPC version 9 cannot communicate with client version 4
	at org.apache.hadoop.ipc.Client.call(Client.java:1113)
	at org.apache.hadoop.ipc.RPC$Invoker.invoke(RPC.java:229)
	at com.sun.proxy.$Proxy1.getProtocolVersion(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:85)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:62)
	at com.sun.proxy.$Proxy1.getProtocolVersion(Unknown Source)
	at org.apache.hadoop.ipc.RPC.checkVersion(RPC.java:422)
	at org.apache.hadoop.hdfs.DFSClient.createNamenode(DFSClient.java:183)
	at org.apache.hadoop.hdfs.DFSClient.<init>(DFSClient.java:281)
	at org.apache.hadoop.hdfs.DFSClient.<init>(DFSClient.java:245)
	at org.apache.hadoop.hdfs.DistributedFileSystem.initialize(DistributedFileSystem.java:100)
	at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:1446)
	at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:67)
	at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:1464)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:263)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:124)
	at com.markhneedham.mahout.Similarity.getDocIndex(Similarity.java:86)
	at com.markhneedham.mahout.Similarity.main(Similarity.java:25)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:144)

Version 0.9.0 of mahout-core was published in early 2014 so I expect it was built against an earlier version of Hadoop than I’m using (2.7.2).

I tried updating the Hadoop dependencies that were being called in the stack trace to no avail.

<dependency>
    <groupId>org.apache.hadoop</groupId>
    <artifactId>hadoop-client</artifactId>
    <version>2.7.2</version>
</dependency>
 
<dependency>
    <groupId>org.apache.hadoop</groupId>
    <artifactId>hadoop-hdfs</artifactId>
    <version>2.7.2</version>
</dependency>

When stepping through the stack trace I noticed that my program was still using an old version of hadoop-core, so with one last throw of the dice I decided to try explicitly excluding that:

<dependency>
    <groupId>org.apache.mahout</groupId>
    <artifactId>mahout-core</artifactId>
    <version>0.9</version>
 
    <exclusions>
        <exclusion>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-core</artifactId>
        </exclusion>
    </exclusions>
</dependency>

And amazingly it worked. Now, finally, I can see how similar my documents are!

Written by Mark Needham

July 22nd, 2016 at 1:55 pm

Posted in Hadoop

Tagged with ,

Hadoop: DataNode not starting

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In my continued playing with Mahout I eventually decided to give up using my local file system and use a local Hadoop instead since that seems to have much less friction when following any examples.

Unfortunately all my attempts to upload any files from my local file system to HDFS were being met with the following exception:

java.io.IOException: File /user/markneedham/book2.txt could only be replicated to 0 nodes, instead of 1
at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.getAdditionalBlock(FSNamesystem.java:1448)
at org.apache.hadoop.hdfs.server.namenode.NameNode.addBlock(NameNode.java:690)
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.WritableRpcEngine$Server.call(WritableRpcEngine.java:342)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1350)
at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1346)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:742)
at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1344)
 
at org.apache.hadoop.ipc.Client.call(Client.java:905)
at org.apache.hadoop.ipc.WritableRpcEngine$Invoker.invoke(WritableRpcEngine.java:198)
at $Proxy0.addBlock(Unknown Source)
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.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:82)
at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:59)
at $Proxy0.addBlock(Unknown Source)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.locateFollowingBlock(DFSOutputStream.java:928)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.nextBlockOutputStream(DFSOutputStream.java:811)
at org.apache.hadoop.hdfs.DFSOutputStream$DataStreamer.run(DFSOutputStream.java:427)

I eventually realised, from looking at the output of jps, that the DataNode wasn’t actually starting up which explains the error message I was seeing.

A quick look at the log files showed what was going wrong:


/usr/local/Cellar/hadoop/2.7.1/libexec/logs/hadoop-markneedham-datanode-marks-mbp-4.zte.com.cn.log

2016-07-21 18:58:00,496 WARN org.apache.hadoop.hdfs.server.common.Storage: java.io.IOException: Incompatible clusterIDs in /usr/local/Cellar/hadoop/hdfs/tmp/dfs/data: namenode clusterID = CID-c2e0b896-34a6-4dde-b6cd-99f36d613e6a; datanode clusterID = CID-403dde8b-bdc8-41d9-8a30-fe2dc951575c
2016-07-21 18:58:00,496 FATAL org.apache.hadoop.hdfs.server.datanode.DataNode: Initialization failed for Block pool <registering> (Datanode Uuid unassigned) service to /0.0.0.0:8020. Exiting.
java.io.IOException: All specified directories are failed to load.
        at org.apache.hadoop.hdfs.server.datanode.DataStorage.recoverTransitionRead(DataStorage.java:477)
        at org.apache.hadoop.hdfs.server.datanode.DataNode.initStorage(DataNode.java:1361)
        at org.apache.hadoop.hdfs.server.datanode.DataNode.initBlockPool(DataNode.java:1326)
        at org.apache.hadoop.hdfs.server.datanode.BPOfferService.verifyAndSetNamespaceInfo(BPOfferService.java:316)
        at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.connectToNNAndHandshake(BPServiceActor.java:223)
        at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.run(BPServiceActor.java:801)
        at java.lang.Thread.run(Thread.java:745)
2016-07-21 18:58:00,497 WARN org.apache.hadoop.hdfs.server.datanode.DataNode: Ending block pool service for: Block pool <registering> (Datanode Uuid unassigned) service to /0.0.0.0:8020
2016-07-21 18:58:00,602 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: Removed Block pool <registering> (Datanode Uuid unassigned)
2016-07-21 18:58:02,607 WARN org.apache.hadoop.hdfs.server.datanode.DataNode: Exiting Datanode
2016-07-21 18:58:02,608 INFO org.apache.hadoop.util.ExitUtil: Exiting with status 0
2016-07-21 18:58:02,610 INFO org.apache.hadoop.hdfs.server.datanode.DataNode: SHUTDOWN_MSG:

I’m not sure how my clusterIDs got out of sync, although I expect it’s because I reformatted HDFS without realising at some stage. There are other ways of solving this problem but the quickest for me was to just nuke the DataNode’s data directory which the log file told me sits here:

sudo rm -r /usr/local/Cellar/hadoop/hdfs/tmp/dfs/data/current

I then re-ran the hstart script that I stole from this tutorial and everything, including the DataNode this time, started up correctly:

$ jps
26736 NodeManager
26392 DataNode
26297 NameNode
26635 ResourceManager
26510 SecondaryNameNode

And now I can upload local files to HDFS again. #win!

Written by Mark Needham

July 22nd, 2016 at 1:31 pm

Posted in Hadoop

Tagged with

Hadoop: HDFS – ava.lang.NoSuchMethodError: org.apache.hadoop.fs.FSOutputSummer.(Ljava/util/zip/Checksum;II)V

without comments

I wanted to write a little program to check that one machine could communicate a HDFS server running on the other and adapted some code from the Hadoop wiki as follows:

package org.playground;
 
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
 
import java.io.IOException;
 
public class HadoopDFSFileReadWrite {
 
    static void printAndExit(String str) {
        System.err.println( str );
        System.exit(1);
    }
 
    public static void main (String[] argv) throws IOException {
        Configuration conf = new Configuration();
        conf.addResource(new Path("/Users/markneedham/Downloads/core-site.xml"));
 
        FileSystem fs = FileSystem.get(conf);
 
        Path inFile = new Path("hdfs://192.168.0.11/user/markneedham/explore.R");
        Path outFile = new Path("hdfs://192.168.0.11/user/markneedham/output-" + System.currentTimeMillis());
 
        // Check if input/output are valid
        if (!fs.exists(inFile))
            printAndExit("Input file not found");
        if (!fs.isFile(inFile))
            printAndExit("Input should be a file");
        if (fs.exists(outFile))
            printAndExit("Output already exists");
 
        // Read from and write to new file
        byte buffer[] = new byte[256];
        try ( FSDataInputStream in = fs.open( inFile ); FSDataOutputStream out = fs.create( outFile ) )
        {
            int bytesRead = 0;
            while ( (bytesRead = in.read( buffer )) > 0 )
            {
                out.write( buffer, 0, bytesRead );
            }
        }
        catch ( IOException e )
        {
            System.out.println( "Error while copying file" );
        }
    }
}

I initially thought I only had the following in my POM file:

<dependency>
    <groupId>org.apache.hadoop</groupId>
    <artifactId>hadoop-common</artifactId>
    <version>2.7.0</version>
</dependency>

But when I ran the script I got the following exception:

Exception in thread "main" java.lang.NoSuchMethodError: org.apache.hadoop.fs.FSOutputSummer.<init>(Ljava/util/zip/Checksum;II)V
	at org.apache.hadoop.hdfs.DFSOutputStream.<init>(DFSOutputStream.java:1553)
	at org.apache.hadoop.hdfs.DFSOutputStream.<init>(DFSOutputStream.java:1582)
	at org.apache.hadoop.hdfs.DFSOutputStream.newStreamForCreate(DFSOutputStream.java:1614)
	at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1465)
	at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1390)
	at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:394)
	at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:390)
	at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
	at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:390)
	at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:334)
	at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:909)
	at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:890)
	at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:787)
	at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:776)
	at org.playground.HadoopDFSFileReadWrite.main(HadoopDFSFileReadWrite.java:37)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:140)

From following the stack trace I realised I’d made a mistake and had accidentally pulled in a dependency on hadoop-hdfs 2.4.1. If we don’t have the hadoop-hdfs dependency we’d actually see this error instead:

Exception in thread "main" java.io.IOException: No FileSystem for scheme: hdfs
	at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2644)
	at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2651)
	at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:92)
	at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2687)
	at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2669)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:371)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:170)
	at org.playground.HadoopDFSFileReadWrite.main(HadoopDFSFileReadWrite.java:22)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:140)

Now let’s add the correct version of the dependency and make sure it all works as expected:

<dependency>
    <groupId>org.apache.hadoop</groupId>
    <artifactId>hadoop-hdfs</artifactId>
    <version>2.7.0</version>
    <exclusions>
        <exclusion>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
        </exclusion>
        <exclusion>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
        </exclusion>
    </exclusions>
</dependency>

When we run that a new file is created in HDFS on the other machine with the current timestamp:

$ date +%s000
1446336801000
 
$ hdfs dfs -ls
...
-rw-r--r--   3 markneedham supergroup       9249 2015-11-01 00:13 output-1446337098257
...

Written by Mark Needham

October 31st, 2015 at 11:58 pm

Posted in Software Development

Tagged with ,