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If your job does not use the system openmpi, or does not use MPI, then any desired core binding will need to be set up with whatever mechanism the software uses. Otherwise, there will be no core binding. Again, that may not be a major issue. If your job does not work well with HT then run on a number of cores equal to half of the number of slots requested and the OS scheduler will minimize contention.
new SGE utilities
While SoGE is very similar to previous versions of SGE there are some new utilities that people may find of interest. There are manual pages for each of these.
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Finally, there is clusterwide queue called the all.q queue. This queue encompasses all of the nodes and contains all of the available job slots. It is available to everyone with an account and there are no running job limits. However, it is a low priority queue on the same nodes as the higher priority investor and UI queues. The all.q queue is subordinate to these other queues and jobs running in it will relinquish the nodes they are running on when jobs in the high priority queues need them. The term we use for this is "job eviction". Jobs running in the all.q queue are the only ones subject to this.
Resource requests
There are many resources that SGE keeps track of and most of them can be used in job submissions. However, the resource designations for machines based on memory and GPU are more likely to be used in practice. For the most part, machines with different amounts of memory and GPU capability are segregated by queues. However, the all.q queue contains all machines and when running jobs in that queue it may be desirable to request specific machine types. The following table lists these out. They would be selected with the '-l resource' flag to qsub. These are all Booleans.
| Full Resource Name | Shortcut Resource Name |
|---|---|
| std_mem | sm |
| mid_mem | mm |
| high_mem | hm |
| gpu | gpu |
| gpu_k80 | k80 |
| gpu_p100 | p100 |
For example, if you run a job in the all.q queue and want to use a node with a GPU, but do not care which type,
qsub -l gpu=true
If you specifically wanted to use a node with a P100 GPU,
qsub -l gpu_p100=true
or use the shortcut,
qsub -l p100=true