I needed to submit some jobs to SGE today that use pthreads to take advantage of SMP systems. From the attribute/resource list visible with qconf -sc all.q, you might think a qsub -l cpu=4 would work, but it doesn’t. It submits the job, but lets other jobs that don’t specify the number of CPUs needed to be allocated to the same exec host. Next, I tried qsub -l slots=4 and got the error message Unable to run job: denied: use parallel environments instead of requesting slots explicitly..
A quick google search for the error message turned up This discussion on the ROCKS mailing list that specifies how to set up a parallel environment, so I followed the instructions. I don’t fully understand the what this incantation means yet, but now qsub -pe serial 4 causes the job to fill 4 slots on a single exec host, which is what I needed.
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