[torqueusers] qsub and mpiexec -f machinefile

Tiago Silva (Cefas) tiago.silva at cefas.co.uk
Wed Feb 19 05:40:09 MST 2014


Hi,

My MPI code is normally executed across a set of nodes with something like:

mpiexec -f machinefile -np 6 ./bin

where the machinefile has 6 entries with node names, for instance:
n01
n01
n02
n02
n02
n02


Now the issue here is that this list has been optimised to balance the load between nodes and to reduce internode communication. So for instance model domain tiles 0 and 1 will run on n01 while tiles 2 to 5 will run on n02.

Is there a way to integrate this into qsub since I don't know which nodes will be assigned before submission? Or in other words can I control grouping processes in one node?

In my example I used 6 processes for simplicity but normally I parallelise across 4-16 nodes and >100 processes.

Thanks,
tiago
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