GROMACS

mdrun employs a number of heuristics for picking defaults at runtime in order to optimize out-of-the-box performance behavior or to advise users about their choice of options/parameters. These heuristics need regular revision and maintenance so we should facilitate finding/tracking these in order to plan for revising and updating them to the changing code and external conditions.

The aim is two-fold:

• gather the heuristics (will keep adding them below with pointers to the source roughly around v2018-b1)
• come up with a way to track them (e.g. mark them with GMX_HEURISTIC)

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• OpenMP recommended #threads/rank
  source:src/gromacs/taskassignment/resourcedivision.cpp#L115

• Minimum number of atoms per thread-MPI rank w/wo GPU
  source:src/gromacs/taskassignment/resourcedivision.cpp#L89

• Using OpenMP-only vs MPI+OpenMP parallelizaiton with GPUs
  source:src/gromacs/taskassignment/resourcedivision.cpp#L125 and nthreads_omp_faster()

• Automation of tMPI rank count and rank to OpenMP thread division
  get_tmpi_omp_thread_d ivision() in source:src/gromacs/taskassignment/resourcedivision.cpp#L201 and
  get_nthreads_mpi() in source:src/gromacs/taskassignment/resourcedivision.cpp#L335
  and efficency check in check_resource_division_efficiency()

• #atoms per code for SMT on/of threshold
  source:src/gromacs/taskassignment/resourcedivision.cpp#L868

• thread pinning stride (with/without topolgy info
  NOTE: the comment on the no topology available case is outdated (now there are 2 existing arch where it's not true)
  source:src/gromacs/mdrunutility/threadaffinity.cpp#L221

• switch to MPMD / separate PME rank mode

• Target NB list size per GPU multiprocessor; gpu_min_ci_balanced_factor in
  source:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu#L78
  and
  source:src/gromacs/mdlib/nbnxn_ocl//nbnxn_ocl_data_mgmt.cpp#L85

• GPU API wait overhead margin (gpuWaitApiOverheadMargin)
  source:src/gromacs/mdlib/sim_util.cpp#L1436

• Tabulated VS analytical nonbonded Ewald kernels per arch (both CPU and GPU)

TODO:

• add SIMD heuristics (kernel flavor choice / CPU arch)?
• DD heuristics?