Spreading a job over different nodes of a cluster in sun grid engine (SGE)

Question

Hey,

I'm tryin get sun gridending (sge) to run the separate processes of an MPI job over all of the nodes of my cluster.

What is happening is that each node has 12 processors, so SGE is assigning 12 of my 60 processes to 5 separate nodes.

I'd like it to assign 2 processes to each of the 30 nodes available, because with 12 processes (dna sequence alignments) running on each node, the nodes are running out of memory.

So I'm wondering if it's possible to explicitly get SGE to assign the processes to a given node?

Thanks,

Paul.

Answer 1

Check out "allocation_rule" in the configuration for the parallel environment; either with that or then by specifying $pe_slots for allocation_rule and then using the -pe option to qsub you should be able to do what you ask for above.