Member Site Forums Rosetta 3 Rosetta 3 – General mpi / jd2 with AbinitioRelax and relax (3.2) Reply To: mpi / jd2 with AbinitioRelax and relax (3.2)


    Indeed, Rosetta JD2 defaults to the WorkPool implementation, and indeed, it uses node 0 for management, and nodes 1-N for computation.

    1. I assume I am using MPIWorkPoolJobDistributor (based on documentation and the fact that I get 7 silent files with “mpirun -np 8”)

    Yes, you are, if you are using JD2.

    2. Do flags like “jd2::mpi_work_partition_job_distributor” apply to AbinitioRelax and relax?

    All JD2 applications accept this flag. I can describe how it works if you care. Relax definitely uses jd2.

    AbinitioRelax is harder to answer. I’m 100% positive that there ARE abinitio methods using JD2, because I’ve communicated regularly with their developer, but I can’t tell if any of them are in the release. It appears to me that vanilla AbinitioRelax STILL (ARGH!) uses the older job distributor (to which none of these flags or documentation applies). I don’t know how the older one works but I think it’s analogous to WorkPool.

    I think you can access the jd2 versions of abinitio via the minirosetta executeable (which is what goes out on BOINC?) None of this organization makes sense to me.

    3. If so, what are the other flags I could try ? (i.e. where do I find additional docs… no mention of available jd2 flags from “relax -help”

    The only ones I ever use are jd2::mpi_work_partition_job_distributor (because I schedule jobs such that a master node is not needed; this is less true for fast abinitio than my slow code) and mpi_tracer_to_file, which ensures that you get non-garbled output (one output log file per CPU). The job distributor itself doesn’t have too many flags. What do you want options for…?

    4. What is the fourth MPI flavour mentioned in the docs ? ( “How To Use The New Job Distributor” )

    There are a bunch of MPI job distributors specialized for ultra-large BlueGenes running super-fast-outputting abinitio. I don’t know how any of them work. It sure sounds like they’re relevant to you so I’ll try to get Oliver (their author) interested…

    5. Any suggestions for improved setting of distributed Abinitio and relax runs (I have attached my flags and mpi scripts) ?

    Same as 4), I’ll see what Oliver thinks.

    I know that his job distributors are specialized for silent-file-only output. I’m a little confused by your options files, where you seem to request both silent and PDB output. Surely you aren’t getting both?