[torqueusers] qsub and mpiexec -f machinefile

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


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:

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.

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