Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1

Question

Please help me to solve this issue in rmr2 (rhadoop integration)

I am using cloudera-quickstart-vm-5.4.0-0-virtualbox

version details:

Hadoop 2.6.0-cdh5.4.0
java version "1.7.0_67"
R version 3.2.0 
rmr 2.3.0

Below R code and error:

Sys.setenv("HADOOP_HOME"="/usr/lib/hadoop")
Sys.setenv("HIVE_HOME"="/usr/lib/hive")
Sys.setenv("HADOOP_CMD"="/usr/lib/hadoop/bin/hadoop")
Sys.setenv("HADOOP_STREAMING"="/usr/lib/hadoop-0.20-mapreduce/contrib/streaming/hadoop-streaming-2.6.0-mr1-cdh5.4.0.jar")
Sys.getenv("HADOOP_CMD")
[1] "/usr/lib/hadoop/bin/hadoop"
Sys.setenv("RHIVE_FS_HOME"="/home/rhive")
Sys.setenv(JAVA_HOME="/usr/java/jdk1.7.0_67-cloudera")
library(rmr2)
library(rhdfs)
hdfs.init()

## map function
map <- function(k,lines) {
  words.list <- strsplit(lines, '/t')
  words <- unlist(words.list)
  return( keyval(words, 1) )
}

## reduce function
reduce <- function(word, counts) {
  keyval(word, sum(counts))
}

wordcount <- function (input, output=NULL) {
  mapreduce(input=input, output=output, input.format="text",
  map=map, reduce=reduce)
}
## delete previous result if any
hdfs.root <- 'wordcount'
hdfs.data <- file.path(hdfs.root, 'input/d.txt')
hdfs.out <- file.path(hdfs.root, 'out')
out <- wordcount(hdfs.data, hdfs.out)

15/08/10 05:16:40 WARN streaming.StreamJob: -file option is deprecated, please use generic option -files instead.
packageJobJar: [/tmp/RtmpQRIzWy/rmr-local-env17807fd4e342, /tmp/RtmpQRIzWy/rmr-global-env17807c276b72, /tmp/RtmpQRIzWy/rmr-streaming-map17807a097c08, /tmp/RtmpQRIzWy/rmr-streaming-reduce178012121630] [/usr/lib/hadoop-mapreduce/hadoop-streaming-2.6.0-cdh5.4.0.jar] /tmp/streamjob8275237671226206531.jar tmpDir=null
15/08/10 05:16:41 INFO client.RMProxy: Connecting to ResourceManager at /0.0.0.0:8032
15/08/10 05:16:42 INFO client.RMProxy: Connecting to ResourceManager at /0.0.0.0:8032
15/08/10 05:16:42 INFO mapred.FileInputFormat: Total input paths to process : 1
15/08/10 05:16:42 INFO mapreduce.JobSubmitter: number of splits:2
15/08/10 05:16:43 INFO mapreduce.JobSubmitter: Submitting tokens for job: job_1439208338231_0002
15/08/10 05:16:43 INFO impl.YarnClientImpl: Submitted application application_1439208338231_0002
15/08/10 05:16:43 INFO mapreduce.Job: The url to track the job: http://quickstart.cloudera:8088/proxy/application_1439208338231_0002/
15/08/10 05:16:43 INFO mapreduce.Job: Running job: job_1439208338231_0002
15/08/10 05:16:49 INFO mapreduce.Job: Job job_1439208338231_0002 running in uber mode : false
15/08/10 05:16:49 INFO mapreduce.Job:  map 0% reduce 0%
15/08/10 05:16:57 INFO mapreduce.Job:  map 50% reduce 0%
15/08/10 05:16:57 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000000_0, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:16:57 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000001_0, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:16:58 INFO mapreduce.Job:  map 0% reduce 0%
15/08/10 05:17:06 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000000_1, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:17:07 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000001_1, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:17:16 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000000_2, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:17:17 INFO mapreduce.Job: Task Id : attempt_1439208338231_0002_m_000001_2, Status : FAILED
Error: java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 1
    at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:322)
    at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:535)
    at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:130)
    at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:61)
    at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:34)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:453)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
    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:1671)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)

15/08/10 05:17:25 INFO mapreduce.Job:  map 100% reduce 100%
15/08/10 05:17:25 INFO mapreduce.Job: Job job_1439208338231_0002 failed with state FAILED due to: Task failed task_1439208338231_0002_m_000000
Job failed as tasks failed. failedMaps:1 failedReduces:0

15/08/10 05:17:25 INFO mapreduce.Job: Counters: 13
    Job Counters 
        Failed map tasks=7
        Killed map tasks=1
        Launched map tasks=8
        Other local map tasks=6
        Data-local map tasks=2
        Total time spent by all maps in occupied slots (ms)=53461
        Total time spent by all reduces in occupied slots (ms)=0
        Total time spent by all map tasks (ms)=53461
        Total vcore-seconds taken by all map tasks=53461
        Total megabyte-seconds taken by all map tasks=54744064
    Map-Reduce Framework
        CPU time spent (ms)=0
        Physical memory (bytes) snapshot=0
        Virtual memory (bytes) snapshot=0
15/08/10 05:17:25 ERROR streaming.StreamJob: Job not successful!
Streaming Command Failed!
Error in mr(map = map, reduce = reduce, combine = combine, vectorized.reduce,  : 
  hadoop streaming failed with error code 1

Community · Accepted Answer · 2017-05-23 12:15:07Z

3

You can display logs for your app by running this command:

yarn logs -applicationId application_${appid}

in your case

yarn logs -applicationId application_1439208338231_0002

or you can find them in locations like:

/yarn/apps/&{user_name}/logs/application_${appid}/

or

/app-logs/&{user_name}/logs/application_${appid}/

In general, localization of logs in hadoop: https://stackoverflow.com/a/21629631/3846521

In logs you have stderr output from your code. If you'll still have problem with solution paste log here, I'll try help you.

edited May 23, 2017 at 12:15

CommunityBot

11 silver badge

answered Aug 17, 2015 at 14:04

Bartosz Kotwica

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