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openmpisungridenginesupercomputers

Submit multiple mpirun programs in sun grid engine

I would like to know how to submit several mpirun programs in one job script file in Sun Grid Engine.

Suppose I have compiled program1, program2, program3 .. program100 and want to run them simultaneously such that each use 16 cpus in one job script without making 100 job scripts.

mpirun -np 16 program1 &
mpirun -np 16 program2 &
mpirun -np 16 program3 ....

How can I distribute nodes to each programs in Sun Grid engine? (Can I split hostfile of SGE into 100 and supply them into each mpirun? )

Thank you.

Solution

  • The proper way to implement that use case with SGE is to use array jobs:

    #$ -cwd
#$ -pe mpi 16
#$ -t 100

mpirun -np $NSLOTS ./program${SGE_TASK_ID}

    The -t 100 parameter creates an array job of 100 tasks and each one receives a different value in the SGE_TASK_ID environment variable ranging from 1 to 100.

    Splitting the hostfile is undesirable since that could interfere with the integration between the MPI library and the SGE execution and job monitoring mechanisms.