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Rmpi spawning across nodes

1 message · Renaud Gaujoux

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Hi Ben,

I am not familiar with PBS but when you specify

-l nodes=4:ppn=1

I think you are asking for 4 CPUs spread over _up to_ 4 nodes with _at 
least_ 1 process per node. Depending on the state of the cluster at 
submission time, the queuing system might well give you 4 CPUs on a 
single nodes (which you are sure have have at 4 cores).
Not sure how you enforce having 4 separate physical machines with PBS. 
On SGE you can define a queue with a specific allocation rule ( 
'fill_up' if I remember well) that ensure that you get full machines.

Not sure if this is actually what you want to get though (since you 
require a single CPU on a single machine).
Do you need separate machines? If you need it due to memory usage or if 
each initial single process on the nodes will actually use all available 
CPUs on the node, then you might also want to add a memory specification 
so that other users' jobs don't take up your resources.

The strange thing here is that you say that your cluster only has 
dual-core nodes, so you should get at least 2 different machines instead 
of the 4 you expect.
Also printing/returning the process ID together with the machine name 
could possibly give you better information about how the computation is 
carried out.

Renaud