SSGE 8.1.9 : how to pass a "-pe mpi xx" option into submit file?

When you want to launch a parallel job with SSGE, you have to do something like that : “qsub -N MYJOB -pe mpi 12 myjob”. the parallel environment “mpi” alllows to book slots and to create a PE_HOSTFILE filled with the list of the allocated nodes, as you know. You can use this PE_HOSTFILE to create a machinefile to use with mpiexec.

for the moment, i have tried the field native: “-pe mpi <%= num_cores %>” inside the submit file without success and i get this error message : "qsub: invalid option argument “-pe mpi 12"”

some ideas, please ?



To generalize, what are the options supported by the «native:» field for the «sge» adaptor ?

It could be that the native field is an array and that’s being passed as a string. That is, in shell it’s likely being interpreted as 1 token instead of 3 - hence the error message complaining about one grouped token.

This may work instead.

  native: [ "-pe", "mpi", "<%= num_cores %>" ]

   # or if you prefer this format
   - "-pe"
   - "mpi"
   - "<%= num_cores %>"

As to what’s supported, we naively pass it along in most cases. Sometimes the formatting is different (like torque uses native: headers where headers is a map - just as an example) but mostly native is just an array that we pass as arguments to the command. SGE falls into this category where we just add native directly.

Thanks a lot. it runs at you say.

have a nice day