Hi wadewei,
numthreads is only used byr a few mex modules that are multithreaded using pthread (interpolation functions primarily), you specify with numthreads how many threads you want by default. But it is NOT affecting the performance of Issm.exe in any way. This is only for a few functions that you may use in pre and post processing so don't worry too much about it. If you have a machine with 8 cores, then you can use --with-numthreads=8
I hope this helps
Mathieu