Member Site Forums Rosetta 3 Rosetta 3 – General Parallel computing in RosettaDock3.1? Reply To: Parallel computing in RosettaDock3.1?


    A) Make the ten directories that the MPI docking executeable expects – they’re somehing along the lines of output_0 through output_9, or out_1 through out_10, I forget.

    B) use the option -nstruct 4000

    C) compile in MPI mode

    D) Submit a job to your cluster that requests 10 processors and runs via mpirun, or whatever your equivalent is.

    I believe the docking executeable’s MPI mode automatically assorts an equal number of jobs to each processor. I could be wrong; it could be a “pooling” implementation and it needs 11 processors to do this, where the 11th is a head node allocating jobs to the other processors.

    Docking has been ported to JD2 for the next release, which makes all this much simpler (no need for multiple directories, control of jobs-per-processor, etc).