The History Array

libEnsemble uses a NumPy structured array H to store corresponding output from each gen_f and sim_f. Similarly, gen_f and sim_f are expected to return output as NumPy structured arrays. The names of the input fields for gen_f and sim_f must be output from gen_f or sim_f. In addition to the user-function output fields, the final history from libEnsemble will include the following:

  • sim_id [int]: Each unit of work output from gen_f must have an associated sim_id. The generator can assign this, but users must be careful to ensure that points are added in order. For example, if alloc_f allows for two gen_f instances to be running simultaneously, alloc_f should ensure that both don’t generate points with the same sim_id.

  • given [bool]: Has this gen_f output been given to a libEnsemble worker to be evaluated yet?

  • given_time [float]: At what time (since the epoch) was this gen_f output first given to a worker?

  • last_given_time [float]: At what time (since the epoch) was this gen_f output last given to a worker?

  • sim_worker [int]: libEnsemble worker that output was given to for evaluation

  • gen_worker [int]: libEnsemble worker that generated this sim_id

  • gen_time [float]: At what time (since the epoch) was this entry (or collection of entries) first put into H by the manager

  • last_gen_time [float]: At what time (since the epoch) was this entry (or collection of entries) first put into H by the manager

  • returned [bool]: Has this worker completed the evaluation of this unit of work?

History and Log Files

The history array H and persis_info dictionary are returned to the user by libEnsemble. If libEnsemble aborts on an exception, these structures are dumped automatically to the respective files:

  • libE_history_at_abort_<sim_count>.npy

  • libE_history_at_abort_<sim_count>.pickle

where sim_count is the number of points evaluated. To suppress libEnsemble from producing these two files, set libE_specs['save_H_and_persis_on_abort'] to False.

Two other libEnsemble files produced by default:

  • libE_stats.txt: This contains one-line summaries for each user calculation. Each summary is sent by workers to the manager and logged as the run progresses.

  • ensemble.log: This contains logging output from libEnsemble. The default logging level is INFO. In order to gain additional diagnostics, the logging level can be set to DEBUG. If this file is not removed, multiple runs will append output. Messages at or above MANAGER_WARNING are also copied to stderr to alert the user promptly. For more info, see Logging.

To suppress libEnsemble from producing these two files, set libE_specs['disable_log_files'] to True.

Output Working Directory Structure

libEnsemble features configurable output and working directory structuring for storing results at every step of a calculation, or directing workers to perform calculations on separate filesystems or in other directories. This is helpful for users performing simulations or using high-resource generator functions who want to take advantage of high-speed scratch spaces or disks, or organize their I/O by application run.

With these features enabled, each time a worker initiates a user function routine (gen_f or sim_f) it automatically enters a configurable directory, either a new directory specific to that worker and function instance or a shared directory for all workers. Where these directories are created or what files they contain is configurable through settings in libE_specs. Defining any compatible settings initiates this system with default settings for unspecified options. Each setting will be described in detail here:

  • 'sim_dirs_make': Boolean. Enables per-simulation directories with default settings. Directories are labeled in the form 'sim0-worker1', by sim ID and initiating worker. Without further configuration, directories are placed in the ensemble directory ./ensemble, relative to where libEnsemble was launched. Default: True with other sim_dir options enabled. If False, all workers will operate within the ensemble directory without producing per-simulation directories.

  • 'gen_dirs_make': Boolean. Enabled per-generator instance directories with default settings. Directories are labeled in the form 'gen1-worker1'. by initiating worker and how many times that worker has initiated the generator. These behave similarly to simulation directories. Default: True with other gen_dir options enabled.

  • 'ensemble_dir_path': This location, typically referred to as the ensemble directory, is where each worker places its calculation directories. If not specified, calculation directories are placed in ./ensemble, relative to where libEnsemble was launched. If 'sim_dirs_make' is False, workers initiating simulation instances will run within this directory. This behavior is similar when 'gen_dirs_make' is False. On supported systems, writing to local-node storage is possible and recommended for increased performance.:

    libE_specs['ensemble_dir_path'] = "/scratch/my_ensemble"
    
  • 'use_worker_dirs': Boolean. Sorts calculation directories into per-worker directories at runtime. Particularly useful for organization when running with multiple workers on global scratch spaces or the same node, and may produce performance benefits. Default: False.

    Default structure with 'use_worker_dirs' unspecified:

    - /ensemble_dir
        - /sim0-worker1
        - /gen1-worker1
        - /sim1-worker2
        ...
    

    Structure with libE_specs['use_worker_dirs'] = True:

    - /ensemble_dir
        - /worker1
            - /sim0
            - /gen1
            - /sim4
            ...
        - /worker2
        ...
    
  • 'sim_dir_copy_files': A list of paths for files to copy into simulation directories. If 'sim_dirs_make' is False, these files are copied to the ensemble directory. If using the Executor to launch an application, this may be helpful for copying over configuration files for each launch.

  • 'gen_dir_copy_files': A list of paths for files to copy into generator directories. If 'gen_dirs_make' is False, these files are copied to the ensemble directory.

  • 'sim_dir_symlink_files': A list of paths for files to symlink into simulation directories.

  • 'gen_dir_symlink_files': A list of paths for files to symlink into generator directories.

  • 'ensemble_copy_back': Boolean. Instructs the manager to create an empty directory where libEnsemble was launched where workers copy back their calculation directories when a run concludes or an exception occurs. Especially useful when 'ensemble_dir_path' has been set to some scratch space or another temporary location. Default: False.

  • 'sim_input_dir': A path to a directory to copy for simulation directories. This directory and its contents are copied to form the base of new simulation directories. If 'sim_dirs_make' is False, this directory’s contents are copied into the ensemble directory.

  • 'gen_input_dir': A path to a directory to copy for generator directories. This directory and its contents are copied to form the base of new generator directories. If 'gen_dirs_make' is False, this directory’s contents are copied into the ensemble directory.

See the regression tests test_sim_dirs_per_calc.py and test_use_worker_dirs.py for examples of many of these settings. See test_sim_input_dir_option.py for examples of using these settings without simulation-specific directories.

Note

The postproc_scripts directory, in the libEnsemble project root directory, contains scripts to compare outputs and create plots based on the ensemble output.

Timing analysis scripts

Note that all plotting scripts produce a file rather than opening a plot interactively.

The following scripts must be run in the directory with the libE_stats.txt file. They extract and plot information from that file.

  • plot_libe_calcs_util_v_time.py: Extracts worker utilization vs. time plot (with one-second sampling). Shows number of workers running user sim or gen functions over time.

  • plot_libe_runs_util_v_time.py: Extracts launched task utilization v time plot (with one second sampling). Shows number of workers with active tasks, launched via the executor, over time.

  • plot_libe_histogram.py: Creates histogram showing the number of completed/killed/failed user calculations binned by run time.

Results analysis scripts

  • print_npy.py: Prints to screen from a given *.npy file containing a NumPy structured array. Use done to print only the lines containing 'returned' points. Example:

    ./print_npy.py run_libe_forces_results_History_length=1000_evals=8.npy done
    
  • print_fields.py: Prints to screen from a given *.npy file containing a NumPy structured array. This is a more versatile version of print_npy.py that allows the user to select fields to print and boolean conditions determining which rows are printed (see ./print_fields.py -h for usage).

  • compare_npy.py: Compares either two provided *.npy files or one provided *.npy file with an expected results file (by default located at ../expected.npy). A tolerance is given on floating-point results, and NANs are compared as equal. Variable fields (such as those containing a time) are ignored. These fields may need to be modified depending on the user’s history array.

  • plot_pareto_2d.py: Loop through objective points in f and extract the Pareto front. Arguments are an *.npy file and a budget.

  • plot_pareto_3d.py: Loop through objective points in f and extract the Pareto front. Arguments are an *.npy file and a budget.

  • print_pickle.py: Prints to screen from a given *.pickle file. Example:

    ./print_pickle.py persis_info_length=1000_evals=1000_workers=2.pickle
    

Balsam analysis scripts

These scripts require an activated Balsam database and create plots as png files.

  • plot_util_v_time.py: Shows number of active Balsam launched tasks over time

  • plot_tasks_v_time.py: Shows completed Balsam launched tasks over time

  • plot_waiting_v_time.py: Shows number of tasks waiting in Balsam database over time