In 3.1, MPI coverage is very spotty. Some applications use no job distributor, they have no MPI. Some use the “original” job distributor, some of those have MPI. Some use job distributor 2 (JD2), all of those have MPI.
I believe fixbb is the only “flagship” app using jd2 in the last release. (it’s been a year so I forget). We’re working on moving all the apps to jd2 for 3.2.
I’m reasonably certain both loop modeling and docking allow MPI. Neither work the same as Abinitio_MPI will that I’m sending to you, nor to each other, nor to fixbb. I think for loop modeling it’s all under the hood, just compile with extras=mpi and it will work. With docking you’ll need to pre-create a series of output directories for the result files to land in.
The development labs all run Rosetta in slightly different ways depending on the hardware they have available. The Kuhlman lab uses mostly MPI on a cluster held together by LSF. The Gray lab uses a not-too-huge cluster held by condor; they never use MPI but do use the -multiple_processes_in_one_directory flag – this is not precisely manual distribution but does use independent processes. The Baker lab has a larger condor cluster plus BOINC access to Rosetta@home. I don’t know what the other development labs use.