ProteinInterfaceMS

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    • October 24, 2018 at 6:31 pm #3042
      Anonymous

        Hello,

        I have been running the ProteinInterfaceMS mover with rosettascripts. It runs successfully, though one single design seems to take about 5 days to complete. This is on one cpu. I was wondering if ProteinInterfaceMS mover is capable of making use of MPI? If so how does it split the calculations? And how would you submit the command?

         

        Thanks

      • November 21, 2018 at 11:10 pm #14502
        Anonymous

          Unfortunately, the ProteinInterfaceMS mover is intrinsically single threaded, and you can’t spread the genetic algorithm across multiple processors with MPI or threading. (At least for a single run through. If you’re asking about having multiple -nstruct or multiple input structures, those can be split trivially or with MPI. But for a single run-through, it’s strictly single threaded.)

          If you are looking for an MPI-capable multistate design protocol, you might want to look at the mpi_msd application: https://www.rosettacommons.org/docs/latest/application_documentation/design/mpi-msd and https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020937 — this approach does distribute the genetic algorithm out across multiple processors.

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