[gmx-developers] mpi and thread command line options

Berk Hess hess at kth.se
Wed Jul 11 09:12:39 CEST 2012

Hi all,

Thanks for all the feedback.

What I forgot to say is that most users will not have to look and 
probably will not look
at all these options, as we will automate things as much as possible.
Furthermore, with the group cut-off scheme (the only scheme pre-4.6) openmp
threads are not even supported, so there is not much option. With the 
Verlet scheme
combining MPI processes/threads with openmp threads is slower, except at
the scaling limit. Within a single CPU openmp threads might be faster 
than mpi.
We can handle all these cases, except for optimization at the scaling limit,
automatically when using all available cores.

While thinking of this, and if we don't add mpi spawn, I came up with a 
new proposal:
-nt total number of threads (effectively the same functionality as in 4.5)
-ntmpi number of MPI threads (advanced option)
-ntomp number of OpenMP threads (advanced option)
In this way the user would not have to worry/know about MPI and openmp 
and would not have to set anything, or only -nt when using part of a node;
mdrun can choose the optimal number of MPI and openmp threads.
We might move away from openmp in the next release, but if users would 
never use -ntomp, renaming that option later is not problematic.



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