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From Robert Evans <ev...@yahoo-inc.com>
Subject Re: Hadoop-streaming using binary executable c program
Date Fri, 22 Jul 2011 19:39:08 GMT
I would suggest that you do the following to help you debug.

hadoop fs -cat /user/yehdego/RNAData/RF00028_B.bpseqL3G5_seg_Centered_Method.txt | head -2
| /data/yehdego/hadoop-0.20.2/pknotsRG-1.3/src/pknotsRG -

This is simulating what hadoop streaming is doing.  Here we are taking the first 2 lines out
of the input file and feeding them to the stdin of pknotsRG.  The first step is to make sure
that you can get your program to run correctly with something like this.  You may need to
change the command line to pknotsRG to get it to read the data it is processing from stdin,
instead of from a file.  Alternatively you may need to write a shell script that will take
the data coming from stdin.  Write it to a file and then call pknotsRG on that temporary file.
 Once you have this working then you should try it again with streaming.

--Bobby Evans

On 7/22/11 12:31 PM, "Daniel Yehdego" <dtyehdego@miners.utep.edu> wrote:



Hi Bobby, Thanks for the response.

After I tried the following comannd:

bin/hadoop jar $HADOOP_HOME/hadoop-0.20.2-streaming.jar -mapper /data/yehdego/hadoop-0.20.2/pknotsRG-1.3/src/pknotsRG
-  -file /data/yehdego/hadoop-0.20.2/pknotsRG-1.3/src/pknotsRG  -reducer NONE -input /user/yehdego/RNAData/RF00028_B.bpseqL3G5_seg_Centered_Method.txt
-output /user/yehdego/RF-out - verbose

I got a stderr logs :

java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 139
        at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:311)
        at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:545)
        at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:132)
        at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
        at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
        at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:358)
        at org.apache.hadoop.mapred.MapTask.run(MapTask.java:307)
        at org.apache.hadoop.mapred.Child.main(Child.java:170)



syslog logs

2011-07-22 13:02:27,467 INFO org.apache.hadoop.metrics.jvm.JvmMetrics: Initializing JVM Metrics
with processName=MAP, sessionId=
2011-07-22 13:02:27,913 INFO org.apache.hadoop.mapred.MapTask: numReduceTasks: 0
2011-07-22 13:02:28,149 INFO org.apache.hadoop.streaming.PipeMapRed: PipeMapRed exec [/data/yehdego/hadoop_tmp/dfs/local/taskTracker/jobcache/job_201107181535_0079/attempt_201107181535_0079_m_000000_0/work/./pknotsRG]
2011-07-22 13:02:28,242 INFO org.apache.hadoop.streaming.PipeMapRed: R/W/S=1/0/0 in:NA [rec/s]
out:NA [rec/s]
2011-07-22 13:02:28,267 INFO org.apache.hadoop.streaming.PipeMapRed: MROutputThread done
2011-07-22 13:02:28,267 INFO org.apache.hadoop.streaming.PipeMapRed: MRErrorThread done
2011-07-22 13:02:28,267 INFO org.apache.hadoop.streaming.PipeMapRed: PipeMapRed failed!
2011-07-22 13:02:28,361 WARN org.apache.hadoop.mapred.TaskTracker: Error running child
java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 139
        at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:311)
        at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:545)
        at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:132)
        at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
        at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
        at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:358)
        at org.apache.hadoop.mapred.MapTask.run(MapTask.java:307)
        at org.apache.hadoop.mapred.Child.main(Child.java:170)
2011-07-22 13:02:28,395 INFO org.apache.hadoop.mapred.TaskRunner: Runnning cleanup for the
task



Regards,

Daniel T. Yehdego
Computational Science Program
University of Texas at El Paso, UTEP
dtyehdego@miners.utep.edu

> From: evans@yahoo-inc.com
> To: common-user@hadoop.apache.org; dtyehdego@miners.utep.edu
> Date: Fri, 22 Jul 2011 09:12:18 -0700
> Subject: Re: Hadoop-streaming using binary executable c program
>
> It looks like it tried to run your program and the program exited with a 1 not a 0. 
What are the stderr logs like for the mappers that were launched, you should be able to access
them through the Web GUI?  You might want to add in some stderr log messages to you c program
too. To be able to debug how far along it is going before exiting.
>
> --Bobby Evans
>
> On 7/22/11 9:19 AM, "Daniel Yehdego" <dtyehdego@miners.utep.edu> wrote:
>
> I am trying to parallelize some very long RNA sequence for the sake of
> predicting their RNA 2D structures. I am using a binary executable c
> program called pknotsRG as my mapper. I tried the following bin/hadoop
> command:
>
> HADOOP_HOME$ bin/hadoop
> jar /data/yehdego/hadoop-0.20.2/hadoop-0.20.2-streaming.jar
> -mapper /data/yehdego/hadoop-0.20.2/pknotsRG
> -file /data/yehdego/hadoop-0.20.2/pknotsRG
> -input /user/yehdego/RF00028_B.bpseqL3G5_seg_Centered_Method.txt
> -output /user/yehdego/RF-out -reducer NONE -verbose
>
> but i keep getting the following error message:
>
> java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess
> failed with code 1
>         at
> org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:311)
>         at
> org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:545)
>         at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:132)
>         at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
>         at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
>         at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:358)
>         at org.apache.hadoop.mapred.MapTask.run(MapTask.java:307)
>         at org.apache.hadoop.mapred.Child.main(Child.java:170)
>
> FYI: my input file is RF00028_B.bpseqL3G5_seg_Centered_Method.txt which
> is a chunk of RNA sequences and the mapper is expected to get the input
> and execute the input file line by line and out put the predicted
> structure for each line of sequence for a specified number of maps. Any
> help on this problem is really appreciated. Thanks.
>
>



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