Hi Dan -

You do not need to specify a number of threads at build time. In theory, you need to enable support for multi-threading and OpenMP, but since these default to "on", there's really nothing to do.

At runtime, by default, a CMTK tool will use all available CPU cores. Obviously you'd want to reduce the number of threads if you're sharing a machine etc. For that, every CMTK tool accepts the "--threads N" command line argument, where N is the number of threads. Maybe Greg can comment on if/how that is exposed by munger.

Re qsub - I think that very much depends on how your cluster is configured, but I can definitely say, that CMTK does not use MPI. So the only option on your list that makes any sense is "SMP". But I don't think that's a predefined configuration of your cluster management software (what is it anyway, OpenPBS, SGE, ...?). More likely something your admins have set up to mean something specific. In that case, you'd want to consult with them.

And regarding mpirun - the answer is, no, absolutely not. No MPI support in CMTK, so no point in using mpirun.

Hope this helps.

Torsten