TOM,
What the HADOOP script do is ...read each line from the STDIN and execute the
program pknotsRG. tmp.txt is a temporary file.
the script is like this:
#!/bin/sh
rm -f temp.txt; while read line
do echo $line >> temp.txt; done exec
/data/yehdego/hadoop-0.20.2/PKNOTSRG/src/pknotsRG -k 0 -F temp.txt;
> Date: Sat, 3 Dec 2011 19:49:46 -0800
> Subject: Re: Hadoop Streaming
> From: t...@supertom.com
> To: common-user@hadoop.apache.org
>
> Hi Daniel,
>
> I see from your other thread that your HADOOP script has a line like:
>
> #!/bin/shrm -f temp.txt
>
> I'm not sure what that is, exactly. I suspect the -f is reading from
> some file and the while loop you had listed read from stdin it seems.
>
> What does your input look like? I think what's happening is that you
> might be expecting lines of input and you're getting splits. What
> does your input look like?
>
> You might want to try this:
> -inputformat org.apache.hadoop.mapred.lib.NLineInputFormat
>
> Thanks,
>
> Tom
>
>
>
>
> On Sat, Dec 3, 2011 at 7:22 PM, Daniel Yehdego
> <dtyehd...@miners.utep.edu> wrote:
> >
> > Thanks Tom for your reply,
> > I think my code is reading from stdin. Because I tried it locally using the
> > following command and its running:
> > $ bin/hadoop fs -cat
> > /user/yehdego/Hadoop-Data-New/RF00171_A.bpseqL3G1_seg_Optimized_Method.txt
> > | head -2 | ./HADOOP
> >
> > But when I tried streaming , it failed and gave me the error code 126.
> >
> >> Date: Sat, 3 Dec 2011 19:14:20 -0800
> >> Subject: Re: Hadoop Streaming
> >> From: t...@supertom.com
> >> To: common-user@hadoop.apache.org
> >>
> >> So that code 126 should be kicked out by your program - do you know
> >> what that means?
> >>
> >> Your code can read from stdin?
> >>
> >> Thanks,
> >>
> >> Tom
> >>
> >> On Sat, Dec 3, 2011 at 7:09 PM, Daniel Yehdego
> >> <dtyehd...@miners.utep.edu> wrote:
> >> >
> >> > I have the following error in running hadoop streaming,
> >> > PipeMapRed\.waitOutputThreads(): subprocess failed with code 126
> >> > 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)
> >> > I couldn't find out any other error information.
> >> > Any help ?
> >> >
> >
