Ryan, Thanks for the quick feedback. I will check the other nodes on the cluster to see if they have been properly updated.
However, I am now really confused as to use of the guava*.jar file that you talk about. This is the first time I've heard about this. I presume we are talking about a jar file packaging the guava libraries from Google? I cannot find this guava*.jar in either the /home/hadoop/hadoop directory or in the /home/hbase/hbase directories, where the Hadoop and Hbase installs place the other *.jar files. I'm afraid that I don't even know where we should have downloaded it. Does it come with Hbase, or with Hadoop? Where should it have been placed, after installation? Should I now download it - since we appear to be missing it - from here? http://code.google.com/p/guava-libraries/downloads/list I Googled and found issue HBASE-2714 (Remove Guava as a client dependency, June 11 2010) here http://www.mail-archive.com/[email protected]/msg00950.html (see below, where I've included the text) which appears to say that Hbase (at least *some* release of Hbase - does this include 0.89?) has a dependency on Guava, in order to run a MapReduce job over Hbase. But nothing on Guava is mentioned at http://hbase.apache.org/docs/r0.20.4/api/org/apache/hadoop/hbase/mapreduce/package-summary.html#classpath (I cannot find anything in the Hbase 0.89 online documents on Guava or in how to set CLASSPATH or in what *.jar files to include so I can use MapReduce with Hbase; the best guidance I can find is in this earlier document.) So - I could really use further clarification in regard to Guava as to what I should be doing to set up Hbase-MapReduce work. Regards, Ron %%%%%%%%%%%%%%%%%%%%%%%% From http://www.mail-archive.com/[email protected]/msg00950.html Todd Lipcon commented on HBASE-2714: ------------------------------------ Why not? In theory, the new TableMapReduceUtil.addDependencyJars should take care of shipping it in the distributedcache. Apparently it's not working? ryan rawson commented on HBASE-2714: ------------------------------------ not everyone uses that mechanism to run map reduce jobs on hbase. The standard for a long time was to add hbase.jar and zookeeper-3.2.2.jar to the hadoop classpath, thus not requiring every job include the hbase jars. Todd Lipcon commented on HBASE-2714: ------------------------------------ Does this mean in general that we can't add more dependencies to the hbase client? I think instead we should make it easier to run hbase MR jobs *without* touching the Hadoop config (eg right now you have to restart MR to upgrade hbase, that's not going to fly for a lot of clusters) stack commented on HBASE-2714: ------------------------------ So, we need to change our recommendations here: http://hbase.apache.org/docs/r0.20.4/api/org/apache/hadoop/hbase/mapreduce/package-summary.html#classpath? > Remove Guava as a client dependency > ----------------------------------- > > Key: HBASE-2714 > URL: https://issues.apache.org/jira/browse/HBASE-2714 > Project: HBase > Issue Type: Improvement > Components: client > Reporter: Jeff Hammerbacher > > We shouldn't need Guava on the classpath to run a MapReduce job over HBase. %%%%%%%%%%%%%%%%%%%%%%%% -----Original Message----- From: Ryan Rawson [mailto:[email protected]] Sent: Sunday, September 19, 2010 12:45 AM To: [email protected] Cc: [email protected]; Taylor, Ronald C Subject: Re: hadoop-hbase failure - could use some help, a class is apparently not being found by Hadoop hey, looks like you've done all the right things... you might want to double check that all the 'slave' machines have the updated hadoop-env.sh and that the path referenced therein is present _on all the machines_. You also need to include the guava*.jar as well. the log4j is already included by mapred by default, so no need there. -ryan On Fri, Sep 17, 2010 at 4:19 PM, Taylor, Ronald C <[email protected]> wrote: > > Hi folks, > > Got a problem in basic Hadoop-Hbase communication. My small test > program ProteinCounter1.java - shown in full below - reports out this > error > > java.lang.RuntimeException: java.lang.ClassNotFoundException: > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > at > org.apache.hadoop.conf.Configuration.getClass(Configuration.java:809) > > The full invocation and error msgs are shown at bottom. > > We are using Hadoop 20.2 with HBase0.89.2010726 on a 24-node cluster. Hadoop > and Hbase each appears to work fine separately. That is, I've created > programs that run MapReduce on files, and programs that import data into > Hbase tables and manipulate such. Both types of programs have gone quite > smoothly. > > Now I want to combine the two - use MapReduce programs on data drawn from an > Hbase table, with results placed back into an Hbase table. > > But my test program for such, as you see from the error msg, is not > working. Apparently the > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > class is not found. > > However, I have added these paths, including the relevant Hbase *.jar, to > HADOOP_CLASSPATH, so the missing class should have been found, as you can see: > > export HADOOP_CLASSPATH=/home/hbase/hbase/conf: > /home/hbase/hbase/hbase-0.89.20100726.jar: > /home/rtaylor/HadoopWork/log4j-1.2.16.jar: > /home/rtaylor/HadoopWork/zookeeper-3.3.1.jar > > This change was made in the ../hadoop/conf/hadoop-env.sh file. > > I checked the manifest of /home/hbase/hbase/hbase-0.89.20100726.jar > and > org/apache/hadoop/hbase/mapreduce/TableOutputFormat.class > is indeed present that Hbase *.jar file. > > Also, I have restarted both Hbase and Hadoop after making this change. > > Don't understand why the TableOutputFormat class is not being found. Or is > the error msg misleading, and something else is going wrong? I would very > much appreciate any advice people have as to what is going wrong. Need to get > this working very soon. > > Regards, > Ron T. > > ___________________________________________ > Ronald Taylor, Ph.D. > Computational Biology & Bioinformatics Group Pacific Northwest > National Laboratory > 902 Battelle Boulevard > P.O. Box 999, Mail Stop J4-33 > Richland, WA 99352 USA > Office: 509-372-6568 > Email: [email protected] > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%% > > contents of the "ProteinCounter1.java" file: > > > > // to compile > // javac ProteinCounter1.java > // jar cf ProteinCounterTest.jar *.class > > // to run > // hadoop jar ProteinCounterTest.jar ProteinCounter1 > > > import org.apache.hadoop.hbase.HBaseConfiguration; > import org.apache.hadoop.conf.Configuration; > import org.apache.hadoop.hbase.filter.FirstKeyOnlyFilter; > import org.apache.hadoop.mapreduce.Job; import > org.apache.hadoop.io.IntWritable; > > import java.util.*; > import java.io.*; > import org.apache.hadoop.hbase.*; > import org.apache.hadoop.hbase.client.*; import > org.apache.hadoop.hbase.io.*; import org.apache.hadoop.hbase.util.*; > import org.apache.hadoop.hbase.mapreduce.*; > > > // %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > /** > * counts the number of times each protein appears in the proteinTable > * > */ > public class ProteinCounter1 { > > > static class ProteinMapper1 extends > TableMapper<ImmutableBytesWritable, IntWritable> { > > private int numRecords = 0; > private static final IntWritable one = new IntWritable(1); > > @Override > public void map(ImmutableBytesWritable row, Result values, > Context context) throws IOException { > > // retrieve the value of proteinID, which is the row key > for each protein in the proteinTable > ImmutableBytesWritable proteinID_Key = new > ImmutableBytesWritable(row.get()); > try { > context.write(proteinID_Key, one); > } catch (InterruptedException e) { > throw new IOException(e); > } > numRecords++; > if ((numRecords % 100) == 0) { > context.setStatus("mapper processed " + numRecords + " > proteinTable records so far"); > } > } > } > > public static class ProteinReducer1 extends > TableReducer<ImmutableBytesWritable, > IntWritable, > ImmutableBytesWritable> { > > public void reduce(ImmutableBytesWritable proteinID_key, > Iterable<IntWritable> values, > Context context) > throws IOException, InterruptedException { > int sum = 0; > for (IntWritable val : values) { > sum += val.get(); > } > > Put put = new Put(proteinID_key.get()); > put.add(Bytes.toBytes("resultFields"), > Bytes.toBytes("total"), Bytes.toBytes(sum)); > System.out.println(String.format("stats : proteinID_key : > %d, count : %d", > > Bytes.toInt(proteinID_key.get()), sum)); > context.write(proteinID_key, put); > } > } > > public static void main(String[] args) throws Exception { > > org.apache.hadoop.conf.Configuration conf; > conf = org.apache.hadoop.hbase.HBaseConfiguration.create(); > > Job job = new Job(conf, "HBaseTest_Using_ProteinCounter"); > job.setJarByClass(ProteinCounter1.class); > > org.apache.hadoop.hbase.client.Scan scan = new Scan(); > > String colFamilyToUse = "proteinFields"; > String fieldToUse = "Protein_Ref_ID"; > > // retreive this one column from the specified family > scan.addColumn(Bytes.toBytes(colFamilyToUse), > Bytes.toBytes(fieldToUse)); > > org.apache.hadoop.hbase.filter.FirstKeyOnlyFilter > filterToUse = > new > org.apache.hadoop.hbase.filter.FirstKeyOnlyFilter(); > scan.setFilter(filterToUse); > > TableMapReduceUtil.initTableMapperJob("proteinTable", scan, > ProteinMapper1.class, > ImmutableBytesWritable.class, > IntWritable.class, job); > TableMapReduceUtil.initTableReducerJob("testTable", > ProteinReducer1.class, job); > System.exit(job.waitForCompletion(true) ? 0 : 1); > } > } > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%% > > > session output: > > [rtay...@h01 Hadoop]$ javac ProteinCounter1.java > > [rtay...@h01 Hadoop]$ jar cf ProteinCounterTest.jar *.class > > [rtay...@h01 Hadoop]$ hadoop jar ProteinCounterTest.jar > ProteinCounter1 > > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.job.tracker; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.local.dir; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.system.dir; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.map.tasks.maximum; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.reduce.tasks.maximum; Ignoring. > 10/09/17 15:46:18 WARN mapred.JobClient: Use GenericOptionsParser for parsing > the arguments. Applications should implement Tool for the same. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.job.tracker; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.local.dir; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.system.dir; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.map.tasks.maximum; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.reduce.tasks.maximum; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.name.dir; Ignoring. > 10/09/17 15:46:18 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.data.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.job.tracker; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.local.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.system.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.map.tasks.maximum; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.reduce.tasks.maximum; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.name.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.data.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.job.tracker; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.local.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.system.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.map.tasks.maximum; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: mapred-default.xml:a attempt to > override final parameter: mapred.tasktracker.reduce.tasks.maximum; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.name.dir; Ignoring. > 10/09/17 15:46:19 WARN conf.Configuration: hdfs-default.xml:a attempt to > override final parameter: dfs.data.dir; Ignoring. > 10/09/17 15:46:19 INFO zookeeper.ZooKeeperWrapper: Reconnecting to > zookeeper > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:zookeeper.version=3.3.1-942149, built on 05/07/2010 17:14 > GMT > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:host.name=h01.emsl.pnl.gov > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.version=1.6.0_21 > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.vendor=Sun Microsystems Inc. > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.home=/usr/java/jdk1.6.0_21/jre > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.class.path=/home/hadoop/hadoop/bin/../conf:/usr/java/ > default/lib/tools.jar:/home/hadoop/hadoop/bin/..:/home/hadoop/hadoop/b > in/../hadoop-0.20.2-core.jar:/home/hadoop/hadoop/bin/../lib/commons-cl > i-1.2.jar:/home/hadoop/hadoop/bin/../lib/commons-codec-1.3.jar:/home/h > adoop/hadoop/bin/../lib/commons-el-1.0.jar:/home/hadoop/hadoop/bin/../ > lib/commons-httpclient-3.0.1.jar:/home/hadoop/hadoop/bin/../lib/common > s-logging-1.0.4.jar:/home/hadoop/hadoop/bin/../lib/commons-logging-api > -1.0.4.jar:/home/hadoop/hadoop/bin/../lib/commons-net-1.4.1.jar:/home/ > hadoop/hadoop/bin/../lib/core-3.1.1.jar:/home/hadoop/hadoop/bin/../lib > /hsqldb-1.8.0.10.jar:/home/hadoop/hadoop/bin/../lib/jasper-compiler-5. > 5.12.jar:/home/hadoop/hadoop/bin/../lib/jasper-runtime-5.5.12.jar:/hom > e/hadoop/hadoop/bin/../lib/jets3t-0.6.1.jar:/home/hadoop/hadoop/bin/.. > /lib/jetty-6.1.14.jar:/home/hadoop/hadoop/bin/../lib/jetty-util-6.1.14 > .jar:/home/hadoop/hadoop/bin/../lib/junit-3.8.1.jar:/home/hadoop/hadoo > p/bin/../lib/kfs-0.2.2.jar:/home/hadoop/hadoop/bin/../lib/log4j-1.2.15 > .jar:/home/hadoop/hadoop/bin/../lib/mockito-all-1.8.0.jar:/home/hadoop > /hadoop/bin/../lib/oro-2.0.8.jar:/home/hadoop/hadoop/bin/../lib/servle > t-api-2.5-6.1.14.jar:/home/hadoop/hadoop/bin/../lib/slf4j-api-1.4.3.ja > r:/home/hadoop/hadoop/bin/../lib/slf4j-log4j12-1.4.3.jar:/home/hadoop/ > hadoop/bin/../lib/xmlenc-0.52.jar:/home/hadoop/hadoop/bin/../lib/jsp-2 > .1/jsp-2.1.jar:/home/hadoop/hadoop/bin/../lib/jsp-2.1/jsp-api-2.1.jar: > /home/hbase/hbase/conf:/home/hbase/hbase/hbase-0.89.20100726.jar:/home > /rtaylor/HadoopWork/log4j-1.2.16.jar:/home/rtaylor/HadoopWork/zookeepe > r-3.3.1.jar > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.library.path=/home/hadoop/hadoop/bin/../lib/native/Li > nux-i386-32 > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.io.tmpdir=/tmp > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:java.compiler=<NA> > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:os.name=Linux > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:os.arch=i386 > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:os.version=2.6.18-194.11.1.el5 > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:user.name=rtaylor > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:user.home=/home/rtaylor > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Client > environment:user.dir=/home/rtaylor/HadoopWork/Hadoop > 10/09/17 15:46:19 INFO zookeeper.ZooKeeper: Initiating client > connection, > connectString=h05:2182,h04:2182,h03:2182,h02:2182,h10:2182,h09:2182,h0 > 8:2182,h07:2182,h06:2182 sessionTimeout=60000 > watcher=org.apache.hadoop.hbase.zookeeper.zookeeperwrap...@dcb03b > 10/09/17 15:46:19 INFO zookeeper.ClientCnxn: Opening socket connection > to server h04/192.168.200.24:2182 > 10/09/17 15:46:19 INFO zookeeper.ClientCnxn: Socket connection > established to h04/192.168.200.24:2182, initiating session > 10/09/17 15:46:19 INFO zookeeper.ClientCnxn: Session establishment > complete on server h04/192.168.200.24:2182, sessionid = > 0x22b21c04c330002, negotiated timeout = 60000 > 10/09/17 15:46:20 INFO mapred.JobClient: Running job: > job_201009171510_0004 > 10/09/17 15:46:21 INFO mapred.JobClient: map 0% reduce 0% > > 10/09/17 15:46:27 INFO mapred.JobClient: Task Id : > attempt_201009171510_0004_m_000002_0, Status : FAILED > java.lang.RuntimeException: java.lang.ClassNotFoundException: > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > at > org.apache.hadoop.conf.Configuration.getClass(Configuration.java:809) > at > org.apache.hadoop.mapreduce.JobContext.getOutputFormatClass(JobContext > .java:193) > at org.apache.hadoop.mapred.Task.initialize(Task.java:413) > at org.apache.hadoop.mapred.MapTask.run(MapTask.java:288) > at org.apache.hadoop.mapred.Child.main(Child.java:170) > > Caused by: java.lang.ClassNotFoundException: > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > at java.net.URLClassLoader$1.run(URLClassLoader.java:202) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:190) > at java.lang.ClassLoader.loadClass(ClassLoader.java:307) > at > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) > at java.lang.ClassLoader.loadClass(ClassLoader.java:248) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:247) > at > org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java > :762) > at > org.apache.hadoop.conf.Configuration.getClass(Configuration.java:807) > ... 4 more > > 10/09/17 15:46:33 INFO mapred.JobClient: Task Id : > attempt_201009171510_0004_r_000051_0, Status : FAILED > java.lang.RuntimeException: java.lang.ClassNotFoundException: > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > at > org.apache.hadoop.conf.Configuration.getClass(Configuration.java:809) > at > org.apache.hadoop.mapreduce.JobContext.getOutputFormatClass(JobContext > .java:193) > at org.apache.hadoop.mapred.Task.initialize(Task.java:413) > at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:354) > at org.apache.hadoop.mapred.Child.main(Child.java:170) > Caused by: java.lang.ClassNotFoundException: > org.apache.hadoop.hbase.mapreduce.TableOutputFormat > at java.net.URLClassLoader$1.run(URLClassLoader.java:202) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:190) > at java.lang.ClassLoader.loadClass(ClassLoader.java:307) > at > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) > at java.lang.ClassLoader.loadClass(ClassLoader.java:248) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:247) > at > org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java > :762) > at > org.apache.hadoop.conf.Configuration.getClass(Configuration.java:807) > ... 4 more > > I terminated the program here via <Control><C>, since the error msgs were > simply repeating. > > [rtay...@h01 Hadoop]$ >
