The scheduler places jobs based on the PBS vnodes of the system. From your post it sounds like you only have one vnode. The scheduler will look at the entire system as one large pool of resources instead of smaller chunks of resources.
While SGI systems provide a topology file we create vnodes from, you don't have one. You'll have to create vnodes yourself. Create yourself a vnode def file with one vnode per NUMA node.
You can go further if you want and create placement sets. This will allow the scheduler to place jobs closer together.
I hope this helps,