[GE users] qsub doesn't flush the standard output in the piple

fansn fansn at hotmail.com
Thu Mar 25 20:30:59 GMT 2010


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Hi Reuti,

I'm writing a wapper script for qsub, and the script will wait until the job finishes, therefore I'm using -sync yes. I have a forked sub process tailing the output(XXX.o<jobid>), as if the command was running on a local machine. So I must get the job id immediately after the job is submitted into the grid. Currently I used DRMAA to implement the functions of qsub, and it works fine(I put $|=1 in the script), but I would like to use qsub to simplify the script. Seems qsub won't flush the pipe until the pipe is closed(job finished).

Yours sincerely,


Sinong Fan 



-----Original Message-----
From: reuti [mailto:reuti at staff.uni-marburg.de] 
Sent: 25 March 2010 19:25
To: users at gridengine.sunsource.net
Subject: Re: [GE users] qsub doesn't flush the standard output in the piple

Hi,

Am 25.03.2010 um 15:36 schrieb fansn:

> I wrote a script calling qsub and getting the the job id back using pipe, but it won't work. It seems qsub won't flush the standard output until the job finished.
> 
> Here's the code I wrote for testing:
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> 
> open (TEST, "qsub -sync yes sleep.sh |");

why are you using -sync here, is it the same w/o?

-- Reuti


> while (<TEST>)
> {
>   print $_;
> }
> close TEST;
> 
> Only when the job finishes, the job number will be printed out, together with the exit information:
> 
> Your job 284190 ("sleep.sh") has been submitted
> Job 284190 exited with exit code 0.
> 
> I also wrote a DRMAA version of qsub_perl, using perl DRMAA binding. In the script I add "$|=1". Then I use the above script to call my qsub_perl, I can successfully get the job number. 
> 
> Can anyone give me some suggestion? Thanks.
> 
> Yours sincerely,
> 
> Sinong Fan  
> 
> Hotmail: ???????????????? ?????

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