[gmx-developers] mpi and thread command line options

Berk Hess hess at kth.se
Tue Jul 10 23:15:41 CEST 2012


We are working on the final part of the 4.6 release, which is making the MPI
and OpenMP thread setup automated, fully checked and user friendly.
We have to decide on the naming of the options.
Roland has an implementation of mpi spawn ready. This would allow to do
mdrun -np #processes instead of using mpirun (at least with openmpi).
The question now is how to name the (thread-)mpi option and the openmp
thread option. I suggested -np and -nt, but I now think we should not change
the functionality of -nt.
So I would suggest -np and -nth (or -ntsm for shared memory threads).
Then -nt can be kept in 4.6 for backward compatibility, with a warning.
I think we don't want to use -ntomp as we might move away from OpenMP.
Another question is if the processes MPI and thread-mpi option should
have the same name. An inexperienced user might submit a thread-mpi mdrun
job on multiple nodes and get unwanted effects. A way to catch this could
be to give a fatal error when you ask for more threads then there are cores
in the node, with the hint that you shoud compile with MPI to run over 
nodes and a hint that you can set an env.var. if you really want to use
more threads than cores.

So in short, my suggestion is: -np and -nth

If you think you have a better suggestion, please tell me.



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