Member Site Forums Rosetta 3 Rosetta 3 – General Rosetta dock parallel Reply To: Rosetta dock parallel


    Hi mahajan, would it be possible to share the response to your first question please. and the second one as well when you get a response.

    > 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.
    > Flags:
    > -database /home/mahajanr/Rosetta/rosetta_database
    > -s model.1.pdb
    > -nstruct 300
    > -dock_pert 3 8
    > -fake_native
    > -ex1
    > -unboundrot
    > -mute
    > -out:file:fullatom
    > -out:file:o modtest
    > -out:prefix modecoy
    > -out:path:pdb /home/username/test/