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"”
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
native:
- "-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.