I am attempting to run rosettadock in 8 parallel processes on an 8-core machine. After building using the extras=mpi flag in scons, I am able to successfully execute 8 processes using mpirun -np 8 dockingexecutable @flags. Unfortunately, when the process goes to write the output files, it returns errors because it is trying to write to "outdir_1", "outdir_2"..."outdir_8".
Because I would like to be able to retrieve the structure of the lowest scoring docking complex I have my flags set to write the fullatom pdb of the results. Adjusting the output file name, prefix, or path does not solve the error. If I create the directories "outdir_1"...etc in my working directory, the problem is solved and the output pdb files are distributed among the directories.
While this solution suffices for the small parallel task I am doing now, I would soon like to upgrade to a larger cluster. If I am using say 300 processors, will I have to create 300 directories (outdir_1....outdir_300) to collect my results? Please let me know if I am doing something wrong or missing something. Thank you.
-dock_pert 3 8