pdi/example/timer.yml at d7c01e88bb152ec9ae24484d1ce0f3ed1b851222 · pdidev/pdi · GitHub

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# duration in seconds
duration: 0.75
# global [height, width] (excluding boundary conditions or ghosts)
datasize: [60, 12]
# degree of parallelism
parallelism: { height: 3, width: 1 }

# only the following config is passed to PDI
pdi:
  metadata: # type of small values for which PDI keeps a copy
    iter:   int                    # current iteration id
    dsize:  { size: 2, type: array, subtype: int } # local data size including ghosts/boundary
    psize:  { size: 2, type: array, subtype: int } # number of processes in each dimension
    pcoord: { size: 2, type: array, subtype: int } # coordinate of the process
  data: # type of values for which PDI does not keep a copy
    main_field: { size: [ '$dsize[0]', '$dsize[1]' ], type: array, subtype: double }
  timer: true
  plugins:
    trace: debug
    timer:
      - timer_h5: "decl_hdf5"
      - timer_nc:
          start: "decl_netcdf_start_timer"
          stop: "decl_netcdf_stop_timer"
      - timer_python: [pycall, user_code]
      - timer_json: {start: "json_start_timer", stop: "json_stop_timer"}
      - timer_pdi: "pdi"
    mpi:
    decl_hdf5:
      file: data.h5
      communicator: $MPI_COMM_WORLD # the MPI communicator used for HDF5 parallel synchronized write
      datasets: # type of the datasets to create in file
        data:
          type: array
          subtype: double
          size: [10, '$psize[0]*($dsize[0]-2)', '$psize[1]*($dsize[1]-2)']
      write:
        main_field: # the name of the data to write
          dataset: data
          mpio: COLLECTIVE # or INDEPENDENT
          when: '$iter<10'   # do only write the first 10 iterations (0...9)
          memory_selection:  # exclude ghosts from the data in memory
            size:  ['$dsize[0]-2', '$dsize[1]-2']
            start: [1, 1]
          dataset_selection: # only write into a single slice in time
            size:  [1, '$dsize[0]-2', '$dsize[1]-2']
            start: [$iter, '($dsize[0]-2)*$pcoord[0]', '($dsize[1]-2)*$pcoord[1]']
    decl_netcdf:
      file: data.nc
      communicator: $MPI_COMM_WORLD # the MPI communicator used for HDF5 parallel synchronized write
      variables: # type of the datasets to create in file
        v_data:
          type: array
          subtype: double
          size: [10, '$psize[0]*$dsize[0]', '$psize[1]*$dsize[1]']
      write:
        main_field: # the name of the data to write
          variable: v_data
          when: '$iter<10'   # do only write the first 10 iterations (0...9)
          variable_selection: # only write into a single slice in time
            subsize:  [1, '$dsize[0]', '$dsize[1]']
            start: [$iter, '$dsize[0]*$pcoord[0]', '$dsize[1]*$pcoord[1]']
    json:
      file: data_${pcoord[0]}_${pcoord[1]}.json
      when: '$iter<10'
      write: [main_field]