[phenixbb] mr_rosetta memory usage

17 Oct 2011

      Hi,

I am currently running mr_rosetta and found that after a while the computer (running OpenSuse/linux) slows down dramatically because its memory (8 GB) is running full. I’m not sure if the program still runs or not.
Is there a way to limit the amount of memory that phenix/mr_rosetta uses ? Or should I e.g. lower the amount of models being used (currently 5) ?
(Before starting mr_rosetta I ran the regression test which was fine).

Kind regards,

Tjaard Pijning
University of Groningen

This is the parameter file :

mr_rosetta {
  input_files {
    seq_file = gEP_mature.txt"
    hhr_files = "051011_3011840.hhr"
    alignment_files = None
    model_info_file = ""
    data = "XDS_ASCII_C2221.mtz"
    labin = None
    search_models = None
    copies_in_search_models = None
    mr_rosetta_solutions = ""
    ids_to_load = None
    map_coeffs = ""
    labin_map_coeffs = None
    map = ""
    display_solutions = False
    fragment_files = "aat000_03_05.200_v1_3"
    fragment_files = "aat000_09_05.200_v1_3"
    use_dummy_fragment_files = False
    sort_fragment_files = True
  }
  output_files {
    log = "mr_rosetta.log"
    params_out = "mr_rosetta_params.eff"
  }
  directories {
    temp_dir = "mr_rosetta/MR_ROSETTA_7/WORK_1"
    workdir = "mr_rosetta/MR_ROSETTA_7"
    output_dir = "mr_rosetta"
    top_output_dir = "mr_rosetta/MR_ROSETTA_7"
    rosetta_path = ""
    rosetta_binary_dir = "rosetta_source/bin"
    rosetta_binary_name = "mr_protocols.default"
    rosetta_script_dir = "rosetta_source/src/apps/public/electron_density"
    rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/"
    rosetta_database_dir = "rosetta_database"
  }
  read_hhpred {
    number_of_models = 5
    number_of_models_to_skip = 0
    copies_to_extract = None
    only_extract_proper_symmetry = False
  }
  place_model {
    run_place_model = True
    prerefine {
      run_prerefine = False
      number_of_prerefine_models = 1000
      number_of_models_in_ensemble = 1
    }
    model_already_placed = False
    model_already_aligned = False
    number_of_output_models = 5
    align_with_sculptor = True
    identity = None
    identity_for_scoring_only = 25
    use_all_plausible_sg = True
    overlap_allowed = 300
    selection_criteria_rot_value = 75
    fast_search_mode = True
    search_down_percent = 25
    mr_resolution = 3
    refine_after_mr = True
    denmod_after_refine = True
    find_ncs_after_mr = True
    min_length_ncs = 10
    fixed_ensembles {
      fixed_ensembleID_list = None
      fixed_euler_list = 0 0 0
      fixed_frac_list = 0 0 0
      fixed_frac_list_is_fractional = True
    }
    copies_of_search_model_to_place = None
  }
  rescore_mr {
    run_rescore_mr = True
    nstruct = 5
    relax = False
    include_unrelaxed_in_scoring = False
    align = True
    edit_model = False
    stage_to_rescore = "mr_solution"
  }
  rosetta_rebuild {
    run_rosetta_rebuild = True
    stage_to_rebuild = "rescored_mr_solution"
    max_solutions_to_rebuild = 5
    min_solutions_to_rebuild = 1
    llg_percent_of_max_to_keep = 50
    rosetta_models = 100
    chunk_size = 1
    edit_model = True
    superpose_model = False
  }
  rosetta_rescore {
    run_rosetta_rescore = True
    percentage_to_rescore = 20
    min_solutions_to_rescore = 2
  }
  similarity {
    run_similarity = False
    required_cc = 0.2
    number_of_required_cc = 5
  }
  refine_top_models {
    run_refine_top_models = True
    stage_to_refine = None
    sort_score_type = None
    percent_to_refine = 20
    denmod_after_refine = True
  }
  average_density_top_models {
    run_average_density_top_models = True
    percent_to_average = 100
  }
  relax_top_models {
    run_relax_top_models = True
    stage_to_relax = None
    number_to_relax = 2
    nstruct = 5
  }
  autobuild_top_models {
    run_autobuild_top_models = True
    number_to_autobuild = 2
    quick = False
    phase_and_build = False
    macro_cycles = None
    morph = False
    edit_model = True
    use_map_coeffs = True
  }
  setup_repeat_mr_rosetta {
    run_setup_repeat_mr_rosetta = True
    repeats = 1
    template_repeats = 0
    morph_repeats = 0
    number_to_repeat = 1
    acceptable_r = 0.25
    minimum_delta_r = None
  }
  repeat_mr_rosetta {
    run_repeat_mr_rosetta = True
    copies_in_new_search_group = 1
    update_map_coeffs_with_autobuild = True
  }
  rosetta_modeling {
    map_resolution = 3
    map_grid_spacing = 1.5
    map_weight = 1
    map_window = 5
    include_solvation_energy = True
    weights_file = ""
  }
  crystal_info {
    resolution = 0
    space_group = None
    chain_type = *PROTEIN DNA RNA
    ncs_copies = 2
  }
  control {
    verbose = False
    debug = False
    raise_sorry = False
    dry_run = False
    nproc = 5
    group_run_command = "sh "
    condor = None
    single_run_command = "sh "
    background = None
    ignore_errors_in_subprocess = True
    check_run_command = False
    max_wait_time = 100
    wait_between_submit_time = 1
    n_dir_max = 100000
    number_to_print = 5
    write_run_directory_to_file = None
    resolve_command_list = None
    start_point = *place_model rescore_mr rosetta_rebuild rosetta_rescore \
                  similarity refine_top_models average_density_top_models \
                  relax_top_models autobuild_top_models \
                  setup_repeat_mr_rosetta repeat_mr_rosetta
    stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \
                 similarity refine_top_models average_density_top_models \
                 relax_top_models autobuild_top_models \
                 setup_repeat_mr_rosetta repeat_mr_rosetta
  }
  non_user_params {
    file_base = None
    print_citations = True
    highest_id = 0
    is_sub_process = False
    dummy_autobuild = False
    dummy_refinement = False
    dummy_rosetta = False
    skip_clash_guard = True
    correct_special_position_tolerance = None
    comparison_mtz = ""
    labin_comparison_mtz = None
    write_local_files = False
    rosetta_fixed_seed = None
  }
}