How to allow multithreading in PyRosetta?

[yc-lu05]

in Rosetta, multithreading is easily accomplished by adding option '-total_threads: int'
By running ./rosetta/main/source/bin/relax.cxx11thread.linuxgccrelease -s 1ubq.pdb -out:suffix _relaxed @general_relax_flags -total_threads 30 the following can be seen in the terminal

core.pack.pack_rotamers: {0} Requesting all available threads for interaction graph computation.
core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
basic.thread_manager.RosettaThreadManager: {?} Creating a thread pool of 30 threads.
basic.thread_manager.RosettaThread: {?} Launching thread 1.
basic.random.init_random_generator: {?} 'RNG device' seed mode, using '/dev/urandom', seed=681666408 seed_offset=0 real_seed=681666409 thread_index=1
basic.random.init_random_generator: {?} RandomGenerator:init: Normal mode, seed=681666409 RG_type=mt19937
basic.thread_manager.RosettaThread: {?} Launching thread 3.
basic.thread_manager.RosettaThread: {?} Launching thread 4.

But how to accomplish this in PyRosetta? A similar code for relax is executed:

r=relax.ClassicRelax()
r.set_scorefxn(pyrosetta.get_fa_scorefxn())
r.apply(pose)

but it only launch 1 thread

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_RSF
core.pack.pack_rotamers: built 11596 rotamers at 339 positions.
core.pack.pack_rotamers: Requesting all available threads for interaction graph computation.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
basic.thread_manager.RosettaThreadManager: Creating a thread pool of 1 threads.
basic.thread_manager.RosettaThreadPool: Launched 0 new threads.
core.pack.rotamer_set.RotamerSets: Completed interaction graph pre-calculation in 1 available threads (1 had been requested).

[roccomoretti]

First off, you need a version of (Py)Rosetta which was compiled with threading support. You have that with the cxx11thread "extras" tagged version of the Rosetta binary, but depending on how you installed PyRosetta, you may or may not have it. (That said, I believe the 'default' version of the PyRosetta install should come with threading support these days -- this probably isn't your issue, but I mention it for completeness.)

Otherwise, to enable the RosettaThreadManager, all you need to do is set the -multithreading:total_threads command line option (as you mention). This applies to both the command line and PyRosetta versions. To set the command line options for PyRosetta, just pass them to the init() function (as a single command line string) when you first call it.

P.S. Unless you're trying to exactly replicate an old protocol or have specialized needs, I don't think there's a reason to use ClassicRelax -- I don't think anyone in the Rosetta developer community is still using ClassicRelax -- FastRelax is now the "default" relax, and has supplanted ClassicRelax for pretty much all uses. (Just because it's faster, doesn't mean it's any less quality.)