computer shuts down during autobulding with rosetta

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    • #980
      Anonymous

        Hi
        i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down.
        i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version.

        i will be grateful if some one helps me out

        the error message is as folows

        Parameters taken from: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/PARAMS_1.eff

        # mr_rosetta
        #
        # Run automr/autobuild/rosetta together

        # Type phenix.doc for help
        Values of all params:
        mr_rosetta {
        input_files {
        seq_file = “/home/khkim/kjcho/ros_st4/ha_st4.fasta”
        hhr_files = None
        alignment_files = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali”
        model_info_file = None
        data = “/home/khkim/kjcho/ros_st4/757p212121.mtz”
        labin = None
        search_models = None
        copies_in_search_models = None
        mr_rosetta_solutions = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/rosetta_rebuild_result.pkl”
        ids_to_load = None
        map_coeffs = “”
        labin_map_coeffs = None
        map = “”
        display_solutions = False
        fragment_files = “/home/khkim/kjcho/ros_st4/stem4_frag09.txt”
        fragment_files = “/home/khkim/kjcho/ros_st4/stem4_frag03.txt”
        use_dummy_fragment_files = False
        sort_fragment_files = True
        }
        output_files {
        log = “mr_rosetta.log”
        params_out = “mr_rosetta_params.eff”
        }
        directories {
        temp_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        workdir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        output_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        top_output_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2”
        rosetta_path = “/usr/local/rosetta”
        rosetta_binary_dir = “rosetta_source/bin”
        rosetta_binary_name = “mr_protocols.default.linuxgccrelease”
        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 = False
        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 = False
        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 = False
        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 = 20
        chunk_size = 1
        edit_model = True
        superpose_model = False
        }
        rosetta_rescore {
        run_rosetta_rescore = False
        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 = False
        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 = False
        percent_to_average = 100
        }
        relax_top_models {
        run_relax_top_models = False
        stage_to_relax = None
        number_to_relax = 2
        nstruct = 5
        }
        autobuild_top_models {
        run_autobuild_top_models = False
        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 = False
        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 = False
        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 = “p212121”
        chain_type = *PROTEIN DNA RNA
        ncs_copies = 2
        }
        control {
        verbose = False
        debug = False
        raise_sorry = False
        dry_run = False
        nproc = 100
        group_run_command = “sh”
        condor = None
        single_run_command = “sh “
        background = True
        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 = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/INFO_FILE_1”
        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 = False
        highest_id = 15
        is_sub_process = True
        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
        }
        }

        Starting mr_rosetta
        Date: Tue Jul 19 13:40:23 2011
        Directory: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1

        Changing to work directory: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1

        Log file will be /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/mr_rosetta.log
        Splitting output to /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/mr_rosetta.log
        Checking rosetta paths:
        rosetta binary: /usr/local/rosetta/rosetta_source/bin/mr_protocols.default.linuxgccrelease
        database_dir: /usr/local/rosetta/rosetta_database
        script_dir: /usr/local/rosetta/rosetta_source/src/apps/public/electron_density
        pilot_script_dir: /usr/local/rosetta/rosetta_source/src/apps/pilot/frank/

        ================================================================================
        Setting up reflection file and labels
        ================================================================================
        FP=F_757p212121 SIGFP=SIGF_757p212121 FreeR_flag=FreeR_flag:

        ================================================================================
        LOADING EXISTING SOLUTIONS
        ================================================================================
        Loading solutions from /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/rosetta_rebuild_result.pkl
        RESULTS:
        ID: 7 Model: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/ha1.p_mr.1.pdb Single chain: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/ha1.p_mr.1_one.pdb
        Stage: rescored_mr_solution MR_LLG: 741.77 Target NCS copies: 2
        NCS copies found: 2
        Group: None
        CRYST1 73.527 90.035 237.980 90.00 90.00 90.00 P 21 21 21
        map_coeffs: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/cycle_best_2.mtz labin:FP=FP PHIB=PHIM FOM=FOMM
        map: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/cycle_best_2_nf.map
        Placed model: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/ha1.p_mr.1.pdb
        component_solutions: None

        Loaded 1 previous solutions:
        (list is in /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/solutions_loaded.log)
        SET CRYSTAL SYMMETRY FROM INPUT SOLUTION: CRYST1 73.527 90.035 237.980 90.00 90.00 90.00 P 21 21 21

        Methods to be run:

        place_model : False
        rescore_mr : False
        rosetta_rebuild : True
        rosetta_rescore : False
        similarity : False
        refine_top_models : False
        average_density_top_models : False
        relax_top_models : False
        autobuild_top_models : False
        setup_repeat_mr_rosetta : False
        repeat_mr_rosetta : False

        ================================================================================
        REBUILDING BEST MR SOLUTIONS WITH ROSETTA

        ================================================================================

        Choosing 1 MR solutions for Rosetta rebuilding

        Rebuilding MR model (ID:7) by generating 20 rosetta models and choosing
        the best using rosetta scoring

        # mr_rosetta_rebuild
        #
        # Run automr mr_rosetta_rebuild with rosetta

        # Type phenix.doc for help
        Values of all params:
        mr_rosetta_rebuild {
        input_files {
        model = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/ha1.p_mr.1_one.pdb”
        map = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/cycle_best_2_nf.map”
        seq_file = “/home/khkim/kjcho/ros_st4/ha_st4.fasta”
        hhr_files = None
        alignment_files = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali”
        model_info_file = “”
        fragment_files = “/home/khkim/kjcho/ros_st4/stem4_frag09.txt”
        fragment_files = “/home/khkim/kjcho/ros_st4/stem4_frag03.txt”
        use_dummy_fragment_files = False
        sort_fragment_files = True
        }
        output_files {
        log = “mr_rosetta_rebuild.log”
        params_out = “mr_rosetta_rebuild_params.eff”
        }
        directories {
        temp_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        workdir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        output_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1”
        top_output_dir = “/home/khkim/kjcho/ros_st4/MR_ROSETTA_2”
        rosetta_path = “/usr/local/rosetta”
        rosetta_binary_dir = “rosetta_source/bin”
        rosetta_binary_name = “mr_protocols.default.linuxgccrelease”
        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”
        }
        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 = 20
        chunk_size = 1
        edit_model = True
        superpose_model = False
        }
        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 = “P 21 21 21 “
        chain_type = *PROTEIN DNA RNA
        ncs_copies = 2
        }
        control {
        verbose = False
        debug = False
        raise_sorry = False
        dry_run = False
        nproc = 100
        group_run_command = “sh”
        condor = None
        single_run_command = “sh “
        background = True
        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 = “ha1.p_mr.1”
        print_citations = False
        highest_id = 15
        is_sub_process = True
        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
        }
        }

        Starting mr_rosetta_rebuild
        Date: Tue Jul 19 13:40:24 2011
        Directory: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1

        USER = root
        USERNAME = khkim
        PID = 16462
        Checking rosetta paths:
        rosetta binary: /usr/local/rosetta/rosetta_source/bin/mr_protocols.default.linuxgccrelease
        database_dir: /usr/local/rosetta/rosetta_database
        script_dir: /usr/local/rosetta/rosetta_source/src/apps/public/electron_density
        pilot_script_dir: /usr/local/rosetta/rosetta_source/src/apps/pilot/frank/

        Sequence rewritten to /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_ha_st4.fasta :
        >ha1
        CKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCY
        PGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGA
        KSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSL
        YQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKIT
        FEATGNLVVPRYAFAMERNAGKVDDGFLDIWTYNAELLVLLENERTLDYHDSNV

        Changing to work directory: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1

        Rebuilding the model /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/ha1.p_mr.1_one.pdb
        with rosetta
        ================================================================================

        Splitting generation of rebuilt models into 20 jobs
        with 1 structures generated per job

        ================================================================================
        ==============================================================================
        Starting sub-processes Rebuild in sets…
        ==============================================================================

        Splitting work into 20 jobs and running with 100 processors using sh
        background=True in /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1

        Starting job 1…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log
        Starting job 2…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_2.log
        Starting job 3…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_3.log
        Starting job 4…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_4.log
        Starting job 5…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_5.log
        Starting job 6…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_6.log
        Starting job 7…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_7.log
        Starting job 8…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_8.log
        Starting job 9…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_9.log
        Starting job 10…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_10.log
        Starting job 11…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_11.log
        Starting job 12…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_12.log
        Starting job 13…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_13.log
        Starting job 14…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_14.log
        Starting job 15…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_15.log
        Starting job 16…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_16.log
        Starting job 17…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_17.log
        Starting job 18…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_18.log
        Starting job 19…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_19.log
        Starting job 20…Log will be: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_20.log

      • #5873
        Anonymous

          Do you mean the computer literally turns itself off and/or reboots? Rosetta shouldn’t have a way to do that; I’ve certainly never heard of it. The only way I’ve ever seen Rosetta affect the stability of the computer overall is when Rosetta is trying to use more RAM than is available; even then it should just get sluggish until it throws a bad allocation error.

          Is it possible it is time-related (it’s shutting down overnight after a certain amount of idle time?) or heat-related (faulty heatsink, Rosetta heats up the processor till it fries and shuts down?)?

        • #5883
          Anonymous

            yes the computer hangs and process is stoppped and no response overnight. We were using a memeory of 2GB which we increased to 3GB.
            The specifications of our system are as follows:
            Ubuntu 9.04
            GCC 4.2
            RAM 3GB
            Rosetta 3.2
            Phenix 1.7.1
            the command line test using “phenix_regression.wizards.test_command_line_rosetta_quick_tests
            test_rosetta_rebuild” works well .

          • #5886
            Anonymous

              3 GB sounds like an awful lot for Rosetta to be using. Is there any tool you can use to track how much memory it has? You could set up a cron job to save “ps aux” every 5 minutes or something to see if it’s using a ton of memory before it crashes. There are probably good tools out there for this that I’m not aware of.

              I don’t know if the MR protocol does much repacking. The normal way for Rosetta to gobble up TONS of memory is during protein design; generally repacking only can’t get that many rotamers. How many residues are in the problem you’re trying to solve? (I mean how many are in the Rosetta pose, not necessarily how many are in the biological protein). If that number is more than a thousand then maybe we should consider ways to pare down the rotamer memory usage.

            • #5888
              Anonymous

                Splitting work into 20 jobs and running with 100 processors using sh

                I’m not familiar with the MR protocol, but this line concerns me. Is this on a single box or a cluster? If it’s a single 8-core, shared memory machine, trying to launch 100 copies of Rosetta or Phenix is very likely to hang/kill your box as they all compete for the same 8 cores and the same memory.

                Try changing the “nproc = 100” line to something more reasonable for your system and see if that helps.

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