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I'm running Torque with Open MPI on a cluster with 30 nodes and 360 cores. I have found that the wall time of mpirun -np N ~./myjob and qsub -l nodes=1:ppn=N mpirun -np N ~./myjob differs many times. For small jobs it grows from 1.2 s to 20 s, from 2 s to 37 s and so on.
For larger jobs the difference becomes important. How to overcome it?

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  • The clustering software is GridEngine? I'm assuming this based on the command qsub ....
    – slm
    Jun 2, 2014 at 16:25

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Apparently, it depends on the stuffing of ./myjob. If this script includes the creation and reading of files then they are created N times and their reading causes interference. The slow down is absent if ./myjob is just binary, then the execution time is more or less the same.

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