I have no idea how to use the broker code either. I think it obeys the same flags as abinitiorelax, but its author has declined to comment. Perhaps smg3d figured it out…
The option is specifically
“I tried the abinitiorelax.script that smg3d posted above. It worked except that the output file has multiple entry of the same tag, e.g. I have multiple S_0000001.pdb structure in my silent file.”
This is what is expected to happen when you run non-MPI code in an MPI setup. The MPI in rosetta only communicates to prevent the outputs from overlapping – one processor takes S_001, one takes S_002, etc. With no MPI, there’s no communication, so all N processors create S_001 and overwrite each others’ work.