Hi All,
I have been contemplating at this problem and couldn't figure out what is
missing in the configuration. I traced the script and try to look for
CLASSPATH and see what is included, however, I couldn't find any place that
is honoring/inheriting HADOOP_CLASSPATH (or pulling in any map-reduce
JARs). The only thing I saw was bringing in the HADOOP_CONF_DIR and
YARN_CONF_DIR folders and other JARs, but not the mapred compression JARs.
spark-shell => spark-class => compute-classpath.sh => spark-env.sh(empty)
This is the command I execute to run the spark-shell:
CLASSPATH=/opt/hadoop/share/hadoop/mapreduce/lib/hadoop-lzo-0.4.18-201403101806.jar:${CLASSPATH}
SPARK_JAR=./assembly/target/scala-2.10/spark-assembly-0.9.0-incubating-hadoop2.2.0.jar
SPARK_YARN_APP_JAR=examples/target/scala-2.10/spark-examples-assembly-0.9.0-incubating.jar
MASTER=yarn-client ./bin/spark-shell
and try to run the LinearRegression examples from (
http://docs.sigmoidanalytics.com/index.php/MLlib), however, every time when
I try to generate the model, it runs into LzoCodec not found exception.
Does anyone have any clue why this is happening? I see reflection applied
from the API stack, but I'm wondering why it isn't bringing in the correct
lzo libs? My assumptions are:
1. It looks like when Spark launched Yarn application, it override the
original classpath for Hadoop on the NodeManager machine? I'm not sure what
happened here behind the scene?
2. By running other MR apps, or program, they worked fine, including
examples SparkPi, and KMean.
3. Wondering what are the command/tools/places I can look into to figure
out why the lib is missing from the remote classpath?
4. On YARN log, I only see 2 JARs were deployed to HDFS in the
.sparkStaging folder.
hdfs@alexie-dt ~/spark-0.9.0-incubating $ hdfs dfs -ls
/user/hdfs/.sparkStaging/application_1395091699241_0019/
Found 2 items
-rw-r--r-- 3 hdfs hdfs 99744537 2014-03-17 23:52
/user/hdfs/.sparkStaging/application_1395091699241_0019/spark-assembly-0.9.0-incubating-hadoop2.2.0.jar
-rw-r--r-- 3 hdfs hdfs 135645837 2014-03-17 23:52
/user/hdfs/.sparkStaging/application_1395091699241_0019/spark-examples-assembly-0.9.0-incubating.jar
Any insights and feedback are welcome and appreciated. Guess I probably
overlooked something in the doc.
I copied/pasted the console here for reference.
==============================================
14/03/17 23:30:30 INFO spark.HttpServer: Starting HTTP Server
14/03/17 23:30:30 INFO server.Server: jetty-7.x.y-SNAPSHOT
14/03/17 23:30:30 INFO server.AbstractConnector: Started
[email protected]:43720
Welcome to
____ __
/ __/__ ___ _____/ /__
_\ \/ _ \/ _ `/ __/ '_/
/___/ .__/\_,_/_/ /_/\_\ version 0.9.0
/_/
Using Scala version 2.10.3 (Java HotSpot(TM) 64-Bit Server VM, Java
1.7.0_45)
Type in expressions to have them evaluated.
Type :help for more information.
14/03/17 23:30:34 INFO slf4j.Slf4jLogger: Slf4jLogger started
14/03/17 23:30:34 INFO Remoting: Starting remoting
14/03/17 23:30:34 INFO Remoting: Remoting started; listening on addresses
:[akka.tcp://[email protected]:47469]
14/03/17 23:30:34 INFO Remoting: Remoting now listens on addresses:
[akka.tcp://[email protected]:47469]
14/03/17 23:30:34 INFO spark.SparkEnv: Registering BlockManagerMaster
14/03/17 23:30:34 INFO storage.DiskBlockManager: Created local directory at
/tmp/spark-local-20140317233034-81b8
14/03/17 23:30:34 INFO storage.MemoryStore: MemoryStore started with
capacity 294.9 MB.
14/03/17 23:30:34 INFO network.ConnectionManager: Bound socket to port
43255 with id = ConnectionManagerId(alexie-dt.local.altiscale.com,43255)
14/03/17 23:30:34 INFO storage.BlockManagerMaster: Trying to register
BlockManager
14/03/17 23:30:34 INFO storage.BlockManagerMasterActor$BlockManagerInfo:
Registering block manager alexie-dt.local.altiscale.com:43255 with 294.9 MB
RAM
14/03/17 23:30:34 INFO storage.BlockManagerMaster: Registered BlockManager
14/03/17 23:30:34 INFO spark.HttpServer: Starting HTTP Server
14/03/17 23:30:34 INFO server.Server: jetty-7.x.y-SNAPSHOT
14/03/17 23:30:34 INFO server.AbstractConnector: Started
[email protected]:33611
14/03/17 23:30:34 INFO broadcast.HttpBroadcast: Broadcast server started at
http://10.10.10.4:33611
14/03/17 23:30:34 INFO spark.SparkEnv: Registering MapOutputTracker
14/03/17 23:30:34 INFO spark.HttpFileServer: HTTP File server directory is
/tmp/spark-9abcbe38-ef79-418d-94af-20979b1083fc
14/03/17 23:30:34 INFO spark.HttpServer: Starting HTTP Server
14/03/17 23:30:34 INFO server.Server: jetty-7.x.y-SNAPSHOT
14/03/17 23:30:34 INFO server.AbstractConnector: Started
[email protected]:53963
14/03/17 23:30:35 INFO server.Server: jetty-7.x.y-SNAPSHOT
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/storage/rdd,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/storage,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/stages/stage,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/stages/pool,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/stages,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/environment,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/executors,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/metrics/json,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/static,null}
14/03/17 23:30:35 INFO handler.ContextHandler: started
o.e.j.s.h.ContextHandler{/,null}
14/03/17 23:30:35 INFO server.AbstractConnector: Started
[email protected]:4040
14/03/17 23:30:35 INFO ui.SparkUI: Started Spark Web UI at
http://alexie-dt.local.altiscale.com:4040
14/03/17 23:30:35 WARN util.NativeCodeLoader: Unable to load native-hadoop
library for your platform... using builtin-java classes where applicable
14/03/17 23:30:35 INFO client.RMProxy: Connecting to ResourceManager at
alexie-rm.local.altiscale.com/10.10.10.6:8032
14/03/17 23:30:36 INFO yarn.Client: Got Cluster metric info from
ApplicationsManager (ASM), number of NodeManagers: 3
14/03/17 23:30:36 INFO yarn.Client: Queue info ... queueName: default,
queueCurrentCapacity: 0.0, queueMaxCapacity: 1.0,
queueApplicationCount = 10, queueChildQueueCount = 0
14/03/17 23:30:36 INFO yarn.Client: Max mem capabililty of a single
resource in this cluster 8192
14/03/17 23:30:36 INFO yarn.Client: Preparing Local resources
14/03/17 23:30:36 INFO yarn.Client: Uploading
file:/home/hdfs/spark-0.9.0-incubating/examples/target/scala-2.10/spark-examples-assembly-0.9.0-incubating.jar
to hdfs://
alexie-nn.local.altiscale.com:8020/user/hdfs/.sparkStaging/application_1395091699241_0018/spark-examples-assembly-0.9.0-incubating.jar
14/03/17 23:30:37 INFO yarn.Client: Uploading
file:/home/hdfs/spark-0.9.0-incubating/assembly/target/scala-2.10/spark-assembly-0.9.0-incubating-hadoop2.2.0.jar
to hdfs://
alexie-nn.local.altiscale.com:8020/user/hdfs/.sparkStaging/application_1395091699241_0018/spark-assembly-0.9.0-incubating-hadoop2.2.0.jar
14/03/17 23:30:38 INFO yarn.Client: Setting up the launch environment
14/03/17 23:30:39 INFO yarn.Client: Setting up container launch context
14/03/17 23:30:39 INFO yarn.Client: Command for starting the Spark
ApplicationMaster: $JAVA_HOME/bin/java -server -Xmx512m
-Djava.io.tmpdir=$PWD/tmp org.apache.spark.deploy.yarn.WorkerLauncher
--class notused --jar
examples/target/scala-2.10/spark-examples-assembly-0.9.0-incubating.jar
--args 'alexie-dt.local.altiscale.com:47469' --worker-memory 1024
--worker-cores 1 --num-workers 2 1> <LOG_DIR>/stdout 2> <LOG_DIR>/stderr
14/03/17 23:30:39 INFO yarn.Client: Submitting application to ASM
14/03/17 23:30:39 INFO impl.YarnClientImpl: Submitted application
application_1395091699241_0018 to ResourceManager at
alexie-rm.local.altiscale.com/10.10.10.6:8032
14/03/17 23:30:39 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: ACCEPTED
14/03/17 23:30:40 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: ACCEPTED
14/03/17 23:30:41 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: ACCEPTED
14/03/17 23:30:42 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: ACCEPTED
14/03/17 23:30:43 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: ACCEPTED
14/03/17 23:30:44 INFO cluster.YarnClientSchedulerBackend: Application
report from ASM:
appMasterRpcPort: 0
appStartTime: 1395113439042
yarnAppState: RUNNING
14/03/17 23:30:46 INFO cluster.YarnClientClusterScheduler:
YarnClientClusterScheduler.postStartHook done
Created spark context..
Spark context available as sc.
scala> 14/03/17 23:30:47 INFO cluster.YarnClientSchedulerBackend:
Registered executor: Actor[akka.tcp://
[email protected]:36752/user/Executor#-560732716]
with ID 1
14/03/17 23:30:48 INFO storage.BlockManagerMasterActor$BlockManagerInfo:
Registering block manager alexie-s3.local.altiscale.com:43611 with 589.2 MB
RAM
14/03/17 23:30:49 INFO cluster.YarnClientSchedulerBackend: Registered
executor: Actor[akka.tcp://
[email protected]:36292/user/Executor#395229219]
with ID 2
14/03/17 23:30:50 INFO storage.BlockManagerMasterActor$BlockManagerInfo:
Registering block manager alexie-s1.local.altiscale.com:50270 with 589.2 MB
RAM
scala>
scala> import org.apache.spark.mllib.regression.LinearRegressionWithSGD
import org.apache.spark.mllib.regression.LinearRegressionWithSGD
scala> import org.apache.spark.mllib.regression.LabeledPoint
import org.apache.spark.mllib.regression.LabeledPoint
scala>
scala> // Load and parse the data
scala> val data = sc.textFile("mllib/data/ridge-data/lpsa.data")
14/03/17 23:31:05 INFO storage.MemoryStore: ensureFreeSpace(181512) called
with curMem=0, maxMem=309225062
14/03/17 23:31:05 INFO storage.MemoryStore: Block broadcast_0 stored as
values to memory (estimated size 177.3 KB, free 294.7 MB)
data: org.apache.spark.rdd.RDD[String] = MappedRDD[1] at textFile at
<console>:14
scala> val parsedData = data.map { line =>
| val parts = line.split(',')
| LabeledPoint(parts(0).toDouble, parts(1).split(' ').map(x =>
x.toDouble).toArray)
| }
parsedData:
org.apache.spark.rdd.RDD[org.apache.spark.mllib.regression.LabeledPoint] =
MappedRDD[2] at map at <console>:16
scala>
scala> // Building the model
scala> val numIterations = 20
numIterations: Int = 20
scala> val model = LinearRegressionWithSGD.train(parsedData, numIterations)
java.lang.RuntimeException: Error in configuring object
at
org.apache.hadoop.util.ReflectionUtils.setJobConf(ReflectionUtils.java:109)
at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:75)
at
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:133)
at org.apache.spark.rdd.HadoopRDD.getInputFormat(HadoopRDD.scala:123)
at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:136)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:207)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:205)
at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:207)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:205)
at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:207)
at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.partitions(RDD.scala:205)
at org.apache.spark.rdd.RDD.take(RDD.scala:824)
at org.apache.spark.rdd.RDD.first(RDD.scala:856)
at
org.apache.spark.mllib.regression.GeneralizedLinearAlgorithm.run(GeneralizedLinearAlgorithm.scala:121)
at
org.apache.spark.mllib.regression.LinearRegressionWithSGD$.train(LinearRegression.scala:118)
at
org.apache.spark.mllib.regression.LinearRegressionWithSGD$.train(LinearRegression.scala:154)
at $iwC$$iwC$$iwC$$iwC.<init>(<console>:20)
at $iwC$$iwC$$iwC.<init>(<console>:25)
at $iwC$$iwC.<init>(<console>:27)
at $iwC.<init>(<console>:29)
at <init>(<console>:31)
at .<init>(<console>:35)
at .<clinit>(<console>)
at .<init>(<console>:7)
at .<clinit>(<console>)
at $print(<console>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:772)
at
org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1040)
at org.apache.spark.repl.SparkIMain.loadAndRunReq$1(SparkIMain.scala:609)
at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:640)
at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:604)
at org.apache.spark.repl.SparkILoop.reallyInterpret$1(SparkILoop.scala:788)
at
org.apache.spark.repl.SparkILoop.interpretStartingWith(SparkILoop.scala:833)
at org.apache.spark.repl.SparkILoop.command(SparkILoop.scala:745)
at org.apache.spark.repl.SparkILoop.processLine$1(SparkILoop.scala:593)
at org.apache.spark.repl.SparkILoop.innerLoop$1(SparkILoop.scala:600)
at org.apache.spark.repl.SparkILoop.loop(SparkILoop.scala:603)
at
org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply$mcZ$sp(SparkILoop.scala:926)
at
org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply(SparkILoop.scala:876)
at
org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply(SparkILoop.scala:876)
at
scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:876)
at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:968)
at org.apache.spark.repl.Main$.main(Main.scala:31)
at org.apache.spark.repl.Main.main(Main.scala)
Caused by: java.lang.reflect.InvocationTargetException
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.util.ReflectionUtils.setJobConf(ReflectionUtils.java:106)
... 56 more
Caused by: java.lang.IllegalArgumentException: Compression codec
com.hadoop.compression.lzo.LzoCodec not found.
at
org.apache.hadoop.io.compress.CompressionCodecFactory.getCodecClasses(CompressionCodecFactory.java:135)
at
org.apache.hadoop.io.compress.CompressionCodecFactory.<init>(CompressionCodecFactory.java:175)
at
org.apache.hadoop.mapred.TextInputFormat.configure(TextInputFormat.java:45)
... 61 more
Caused by: java.lang.ClassNotFoundException: Class
com.hadoop.compression.lzo.LzoCodec not found
at
org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:1626)
at
org.apache.hadoop.io.compress.CompressionCodecFactory.getCodecClasses(CompressionCodecFactory.java:128)
... 63 more
