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

Question

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

You can do it by creating a queue in which you can define the queue uses only only 2 processors out of 12 processors in each node.

You can see configuration of current queue by using the command

 qconf -sq queuename

you will see following in the queue configuration. This queue named in such a way that it uses only 5 execution hosts and 4 slots (processors) each.

....
slots                 1,[master=4],[slave1=4],[slave2=4],[slave3=4],[slave4=4]
....

use following command to change the queue configuration

qconf -mq queuename

then change those 4 into 2.