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

templedf daniel.templeton at oracle.com
Fri Mar 26 04:53:17 GMT 2010


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Is there a reason you don't want to use qrsh?

Daniel

On 3/25/10 1:30 PM, fansn wrote:
> 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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