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As you can see that shows the number of cpus (NCPU), the number of CPU sockets (NSOC), the number of cores (NCOR) and the number of threads (NTHR). This information could be important as you plan jobs but it essentially reflects what was said in regard to HT cores. Note that all argon nodes have the same processor topology. SGE uses the concept of job slots which serve as a proxy for the number of cores as well as the amount of memory on a machine. Job slots are one of the resources that is requested when submitting a job to the system. As a general rule, the number of job slots requested should be equal to or greater than the number of processes/threads that will actually consume resources. The parallel environment to request an entire node on Argon is called Xcpn where X=number of slots. For example, to request one node from the 56 slot machines you would request
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qsub -pe 56cpn 56 |
More nodes would be requested by specifying a slot count that is a multiple of 56. So for 2 nodes
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qsub -pe 56cpn 112 |
and so on.
The available Xcpn parallel environments on Argon are:
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You will need to be aware of the approximate amount of memory per job slot when setting up jobs if your job uses a significant amount of memory. The actual amount will vary due to OS overhead but the values below can be used for planning purposes.
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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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