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From Ognen Duzlevski <og...@nengoiksvelzud.com>
Subject Spark job failing on cluster
Date Sat, 18 Jan 2014 13:49:41 GMT
I am trying to run a simple job on a 3-machine Spark cluster. All three
machines are Amazon instances within the VPC (xlarge size instances). All I
am doing is reading a (rather large - about 20GB) file from an S3 bucket
and doing some basic filtering on each line.

Here I start the spark shell:

sparkuser@spark-master:~$ MASTER=spark://10.10.0.200:7077 spark-shell
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in
[jar:file:/home/sparkuser/spark/tools/target/scala-2.9.3/spark-tools-assembly-0.8.1-incubating.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/home/sparkuser/spark/assembly/target/scala-2.9.3/spark-assembly-0.8.1-incubating-hadoop1.0.4.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 0.8.1
      /_/

Using Scala version 2.9.3 (OpenJDK 64-Bit Server VM, Java 1.6.0_27)
Initializing interpreter...
14/01/18 13:29:53 WARN Utils: Your hostname, spark-master resolves to a
loopback address: 127.0.0.1; using 10.10.0.200 instead (on interface eth0)
14/01/18 13:29:53 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to
another address
Creating SparkContext...
Spark context available as sc.
Type in expressions to have them evaluated.
Type :help for more information.

Here is relevant stuff:

scala> val f = sc.textFile("s3n://data-pipeline/large_data/2013-11-30.json")
f: org.apache.spark.rdd.RDD[String] = MappedRDD[1] at textFile at
<console>:12

scala> val events = f.filter(_.split(",")(0).split(":")(1).replace("\"","")
== "Sign Up").map(line =>
(line.split(",")(2).split(":")(1).replace("\"",""),0)).cache
events: org.apache.spark.rdd.RDD[(java.lang.String, Int)] = MappedRDD[3] at
map at <console>:14

scala> events.count
14/01/18 13:30:13 WARN NativeCodeLoader: Unable to load native-hadoop
library for your platform... using builtin-java classes where applicable
14/01/18 13:30:13 WARN LoadSnappy: Snappy native library not loaded

Here 5 minutes later the failure happens (see below). A few questions: 1.
in order for spark to talk to S3 - do I actually have to have a hadoop
installation somewhere or does Spark do all the talking (once provided with
the AWS credentials) and 2. Is there something I am missing in terms of
open ports, pings and other checks that I may be banning through the
instance security group mask? Thanks! Ognen

14/01/18 13:35:12 ERROR Client$ClientActor: Master removed our application:
FAILED; stopping client
14/01/18 13:35:12 WARN SparkDeploySchedulerBackend: Disconnected from Spark
cluster! Waiting for reconnection...
14/01/18 13:35:12 ERROR ClusterScheduler: Lost an executor 1 (already
removed): remote Akka client shutdown
14/01/18 13:36:01 WARN BlockManagerMasterActor: Removing BlockManager
BlockManagerId(1, 10.10.0.200, 33179, 0) with no recent heart beats:
56653ms exceeds 45000ms
14/01/18 13:36:14 WARN RestUtils: Retried connection 6 times, which exceeds
the maximum retry count of 5
org.apache.commons.httpclient.ConnectTimeoutException: The host did not
accept the connection within timeout of 60000 ms
        at
org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:155)
        at
org.apache.commons.httpclient.protocol.SSLProtocolSocketFactory.createSocket(SSLProtocolSocketFactory.java:130)
        at
org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
        at
org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
        at
org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
        at
org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
        at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
        at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:323)
        at
org.jets3t.service.impl.rest.httpclient.RestS3Service.performRequest(RestS3Service.java:342)
        at
org.jets3t.service.impl.rest.httpclient.RestS3Service.performRestHead(RestS3Service.java:718)
        at
org.jets3t.service.impl.rest.httpclient.RestS3Service.getObjectImpl(RestS3Service.java:1599)
        at
org.jets3t.service.impl.rest.httpclient.RestS3Service.getObjectDetailsImpl(RestS3Service.java:1535)
        at
org.jets3t.service.S3Service.getObjectDetails(S3Service.java:1987)
        at
org.jets3t.service.S3Service.getObjectDetails(S3Service.java:1332)
        at
org.apache.hadoop.fs.s3native.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:111)
        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:622)
        at
org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:82)
        at
org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:59)
        at org.apache.hadoop.fs.s3native.$Proxy8.retrieveMetadata(Unknown
Source)
        at
org.apache.hadoop.fs.s3native.NativeS3FileSystem.getFileStatus(NativeS3FileSystem.java:326)
        at
org.apache.hadoop.fs.FileSystem.getFileStatus(FileSystem.java:1337)
        at
org.apache.hadoop.fs.FileSystem.globStatusInternal(FileSystem.java:1045)
        at org.apache.hadoop.fs.FileSystem.globStatus(FileSystem.java:987)
        at
org.apache.hadoop.mapred.FileInputFormat.listStatus(FileInputFormat.java:177)
        at
org.apache.hadoop.mapred.FileInputFormat.getSplits(FileInputFormat.java:208)
        at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:141)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:199)
        at scala.Option.getOrElse(Option.scala:108)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:199)
        at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:26)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:199)
        at scala.Option.getOrElse(Option.scala:108)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:199)
        at
org.apache.spark.rdd.FilteredRDD.getPartitions(FilteredRDD.scala:27)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:199)
        at scala.Option.getOrElse(Option.scala:108)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:199)
at org.apache.spark.rdd.FilteredRDD.getPartitions(FilteredRDD.scala:27)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:199)
        at scala.Option.getOrElse(Option.scala:108)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:199)
        at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:26)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
        at
org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:199)
        at scala.Option.getOrElse(Option.scala:108)
        at org.apache.spark.rdd.RDD.partitions(RDD.scala:199)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:886)
        at org.apache.spark.rdd.RDD.count(RDD.scala:698)
        at <init>(<console>:17)
        at <init>(<console>:22)
        at <init>(<console>:24)
        at <init>(<console>:26)
        at <init>(<console>:28)
        at .<init>(<console>:32)
        at .<clinit>(<console>)
        at .<init>(<console>:11)
        at .<clinit>(<console>)
        at $export(<console>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:622)
        at
org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:629)
        at
org.apache.spark.repl.SparkIMain$Request$$anonfun$10.apply(SparkIMain.scala:897)
        at
scala.tools.nsc.interpreter.Line$$anonfun$1.apply$mcV$sp(Line.scala:43)
        at scala.tools.nsc.io.package$$anon$2.run(package.scala:25)
        at java.lang.Thread.run(Thread.java:701)
Caused by: java.net.SocketTimeoutException: connect timed out
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at
java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
        at
java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
        at
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:385)
        at java.net.Socket.connect(Socket.java:546)
        at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:590)
        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:622)
        at
org.apache.commons.httpclient.protocol.ReflectionSocketFactory.createSocket(ReflectionSocketFactory.java:140)
        ... 68 more

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