[GE users] pthread job killed by SGE

Ravi Chandra Nallan Ravichandra.Nallan at Sun.COM
Mon Nov 26 12:50:18 GMT 2007


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I assume job.ini is a binary which is very big, check your qmaster 
messages .

If you run qsub <binary>, by default qsub  assumes the file is a script 
and hence tries to stage to the exec host where it has to run.
The file might be bigger than <some value> not sure how much, but 
essentially it was not possible to move the file.
try the -b y option with qsub (man qsub) and make sure this binary is 
accessible across the exec hosts.
hope that  helps!

regards,
~Ravi
 

Alois Dirnaichner wrote:
> Hello,
>
> one of our scientists wrote a program with a single worker-pthread
> (started from the main thread) to do his calculations (he wants to scale
> it for multiprocessors later).
> If he submits using qsub job.ini.sge, the binary is started but the
> memory for the worker-pthread cannot be allocated. (error 12)
> job.ini.sge:
>
> #$ -l h_vmem=1G
> #$ -l s_rt=6:0:0
> ./job.ini
>
> Our grid (sge 6.1) runs with two forced flags, s_rt and h_vmem, h_vmem
> is set on each exechost to RAM-500MB.
> SGE regards the job as completed, and no error is reported neither a
> limit seems to be exceeded.
>
> If he uses qsub -l h_vmem=1G,s_rt=6:0:0 job.ini
> he gets
>
> Unable to run job: Script length does not match declared length.
> Exiting
>
> What is happening? And how can I enable jobs like this?
> Thanks in advance,
>
> Alois Dirnaichner
> Computing Maintenance Group, ASC
>
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