kaiju/docs/source/makeitso/engage.rst

Engage
===============


Introduction
------------

The Python script ``engage.py`` was developed to simplify the process of
configuring and running GTR MAGE (that is, the geospace application  of the ``kaiju`` software.) It
provides an interactive, prompt-driven interface to specify all of the
parameters needed for a model run.

The ``engage.py`` script is a wrapper around the ``makeitso.py`` and TIE-GCM's ``tiegcmrun``
script, which is used to prepare the necessary files for a GTR MAGE model run.

  - For more details on the ``makeitso.py`` script, see the :doc:`makeitso </makeitso/makeitso>` documentation.

  - For more details on the TIE-GCM ``tiegcmrun`` script, see the `tiegcmrun <https://tiegcm-docs.readthedocs.io/en/latest/tiegcm/quickstart>`_ documentation.

The ``engage.py`` script can operate in one of three different modes:
``BASIC``, ``INTERMEDIATE``, or ``EXPERT``. Each mode provides access to
a subset of the ``kaiju`` and ``tiegcm`` parameters. 

* The ``BASIC`` mode 
Requires the user to provide the minimum set of parameters needed to specify a model
run, such as the run ID, and the simulation time periods. 

* The ``INTERMEDIATE`` mode 
Allows the user to specify all of the 
parameters from the ``BASIC`` mode, as well as a wider set of run parameters, 
such as non-standard file locations and some MHD parameters and TIE-GCM parameters.

* The ``EXPERT`` mode 
Provides access to all of the user-adjustable 
parameters from the ``kaiju`` and ``TIE-GCM`` software. 

When finished, the script generates the files needed to run a magnetosphere model, and saves
all options in a convenient JSON file so that the run can be repeated at a
later date.


Running the ``engage.py`` script
----------------------------------

The ``engage.py`` script is provided as part of the ``kaiju`` software. It
is found at ``$KAIJUHOME/scripts/makeitso/engage.py``, where ``$KAIJUHOME``
is the location of your ``kaiju`` software tree. After configuring your
``kaiju`` software, you can get help text for the script like this:

.. code-block:: bash

    engage.py --help
    usage: engage.py [-h] [--clobber] [--debug] [--mode MODE] [--engage_options_path ENGAGE_OPTIONS_PATH] [--makeitso_options_path MAKEITSO_OPTIONS_PATH] [--tiegcm_options_path TIEGCM_OPTIONS_PATH] [--verbose]

    Interactive script to prepare a MAGE magnetosphere model run.

    options:
    -h, --help            show this help message and exit
    --clobber             Overwrite existing options file (default: False).
    --debug, -d           Print debugging output (default: False).
    --mode MODE           User mode (BASIC|INTERMEDIATE|EXPERT) (default: BASIC).
    --engage_options_path ENGAGE_OPTIONS_PATH, -eo ENGAGE_OPTIONS_PATH
                            Path to engage JSON file of options (default: None)
    --makeitso_options_path MAKEITSO_OPTIONS_PATH, -mo MAKEITSO_OPTIONS_PATH
                            Path to makeitso JSON file of options (default: None)
    --tiegcm_options_path TIEGCM_OPTIONS_PATH, -to TIEGCM_OPTIONS_PATH
                            Path to tiegcm JSON file of options (default: None)
    --verbose, -v         Print verbose output (default: False).

The ``--options_path`` option allows the user to specify an existing JSON file
from a previous run of ``engage.py`` so that the entire process of model
generation can be automated. More info on this given below.
The ``--mode`` option specifies the user mode to run in, with ``BASIC`` being the default.


An example in ``BASIC`` mode
----------------------------

This section provdes an annotated example session of ``engage.py`` running
in the default ``BASIC`` mode on the ``derecho`` supercomputer.

1. ``engage`` native parameters will be requested

.. code-block:: bash

  engage.py
  Name to use for PBS job(s) [geospace]:

Enter an identifying string to use for your model run. This name will be used
as the basis for most of the files created by ``engage.py``, the
``kaiju`` and ``TIE-GCM`` software. The default name is ``geospace``.


.. code-block:: bash

  Start date for simulation (yyyy-mm-ddThh:mm:ss) [2016-08-09T09:00:00]:
  Stop date for simulation (yyyy-mm-ddThh:mm:ss) [2016-08-09T11:00:00]:

Enter the start and stop date and time for the solar wind data you want to
use. The required data will be fetched from CDAWeb, and converted into a
format usable by the ``kaiju`` software.

.. code-block:: bash

  Do you want to split your job into multiple segments? (Y|N) [Y]:

Here ``Y`` is default and is required for the GTR run. This will
split your simulation into multiple PBS jobs that are chained together, with
each using the results of the previous job as a starting point.

.. code-block:: bash

  Segment length in simulated seconds [7200.0]: 3600

Enter the length of each segment in simulated seconds. The default is the entire length
of the simulation, but you can enter a shorter time to split the simulation into
multiple segments. For example, if you enter ``3600``, the simulation will be
split into two segments, each one hour long. The first segment will run from
``2016-08-09T09:00:00`` to ``2016-08-09T10:00:00``, and the second segment will run
from ``2016-08-09T10:00:00`` to ``2016-08-09T11:00:00``.

.. code-block:: bash

  GAMERA grid type (D|Q|O|H) [Q]:

The codes represent double- (``D``), quad- (``Q``), oct- (``O``) and
hex- (``H``) resolutions in the LFM grid used in the ``kaiju`` software.

.. code-block:: bash

  Name of HPC system (derecho|pleiades) [pleiades]: derecho

The ``engage.py`` script supports the ``derecho`` and ``pleiades``
supercomputers. The selection you make here will customize the remaining
prompts for the selected system.

.. code-block:: bash

  PBS account name [your_login_name]:

On ``pleiades``, your login name is usable here. On ``derecho``, you will need
a PBS account ID.

.. code-block:: bash

  Run directory [.]:

Specify the directory that you wish to perform the simulation in. The
directory will contain all of the files generated by ``engage.py``.

.. code-block:: bash

  Path to kaiju installation [YOUR_PATH_HERE]:
  Path to kaiju build directory [YOUR_PATH_HERE]:

Enter the paths to the location of your ``kaiju`` code, and the location of
your ``kaiju`` build directory.

.. code-block:: bash

  PBS queue name (low|normal|long|debug|devel) [normal]:

Select a PBS queue to use on the selected supercomputer.

.. code-block:: bash

  You are responsible for ensuring that the wall time is sufficient
  to run a segment of your simulation! Requested wall time for each PBS job
  segment (HH:MM:SS) [01:00:00]:

Specify the wall clock time to request for your job (or each segment, if you
split your job into multiple segments).

.. code-block:: bash

  Root directory for the simulation [<YOUR_RUN_DIRECTORY_HERE>]: 

This is the root directory for your simulation. It will be used to store all
of the files generated by ``engage.py`` and the ``kaiju`` and ``TIE-GCM``
software. The default is the current directory.

.. code-block:: bash

  Conda environment to use for the simulation [<YOUR_CONDA_ENVIRONMENT_DIRECTORY_HERE>]: 

This is the path to the conda environment that you want to use for the
simulation. This is automatically set to the conda environment that you have
activated when you run the ``engage.py`` script. 


2. ``makeitso`` parameters will be requested

.. code-block:: bash

  Extend TFIN by dtCouple - 1 seconds (T|F) [T]: 

This option allows you to extend the voltron TFIN time by one second. This is 
required for coupled runs with TIE-GCM, and is set to ``T`` by default. 

.. code-block:: bash

  (VOLTRON) Run in GCM mode (T|F) [T]: 

This option allows you to run the voltron code in GCM mode, which is required
for coupled runs with TIE-GCM. This is set to ``T`` by default.

.. code-block:: bash

  Do you have an existing boundary condition file to use? (Y|N) [N]:

If you already have a file containing solar wind data to use for the inner
boundary conditions of your simulation, enter ``Y``, and you will then be
prompted for the path top the file. If you don't have the file, enter ``N``
and you will be prompted for the date range to use.

.. code-block:: bash

  (GAMERA) Relative path to HDF5 file containing solar wind boundary conditions [bcwind.h5]:

This is the path to your existing solar wind file, or the path that
``makeitso.py`` will use to create the file.

.. code-block:: bash

  (VOLTRON) File output cadence in simulated seconds [60.0]:

How often (in simulated seconds) the ``kaiju`` software should output results
during the course of the simulation.

The script then runs several additional tools to prepare the files needed for
your simulation. 

.. code-block:: bash

  Running preprocessing steps.
  Generating Quad LFM-style grid ...

  Output: lfmQ.h5
  Size: (96,96,128)
  Inner Radius: 2.000000
  Sunward Outer Radius: 30.000000
  Tail Outer Radius: 322.511578
  Low-lat BC: 45.000000
  Ring params:
  <ring gid="lfm" doRing="T" Nr="8" Nc1="8" Nc2="16" Nc3="32" Nc4="32" Nc5="64" Nc6="64" Nc7="64" Nc8="64"/>

  Writing to lfmQ.h5
  Retrieving f10.7 data from CDAWeb
  Retrieving solar wind data from CDAWeb
          Using Bx fields
  Bx Fit Coefficients are  [-3.78792744 -0.77915822 -1.0774984 ]
  Saving "OMNI_HRO_1MIN.txt_bxFit.png"
  Converting to Gamera solar wind file
          Found 21 variables and 120 lines
          Offsetting from LFM start ( 0.00 min) to Gamera start ( 0.00 min)
  Saving "OMNI_HRO_1MIN.txt.png"
  Writing Gamera solar wind to bcwind.h5
  Reading /glade/derecho/scratch/ewinter/cgs/aplkaiju/kaipy-private/development/kaipy-private/kaipy/rcm/dktable
  Reading /glade/derecho/scratch/ewinter/cgs/aplkaiju/kaipy-private/development/kaipy-private/kaipy/rcm/wmutils/chorus_polynomial.txt
  Dimension of parameters in Chorus wave model, Kp: 6 MLT: 97 L: 41 Ek: 155
  Wrote RCM configuration to rcmconfig.h5
  Creating .ini file(s) for run.
  Converting .ini file(s) to .xml file(s).


  Template creation complete!


  Creating PBS job script(s) for run.
  The PBS job scripts ['./geospace-00.pbs'] are ready.
  The PBS scripts ['./geospace-00.pbs'] have been created, each with a corresponding XML file. To submit the jobs with the proper dependency (to ensure each segment runs in order), please run the script geospace_pbs.sh like this:
  bash geospace_pbs.sh

3. ``tiegcmrun`` parameters will be requested

.. code-block:: bash

   Instructions:
    -> Default Selected input parameter is given in GREEN
    -> Warnings and Information are given in YELLOW
    -> Errors are given in RED
    -> Valid values (if any) are given in brackets eg. (value1 | value2 | value3) 
    -> Enter '?' for any input parameter to get a detailed description


    Run Options:
    User Mode = BASIC
    Compile = False
    Execute = False
    Coupling = True
    Engage = True

.. code-block:: bash

  Directory of model [<YOUR_TIEGCMHOME_HERE>]:
  Directory of Tiegcm Data Files [<YOUR_TIEGCMDATA_HERE>]: 
This is the path to your TIE-GCM repository and TIE-GCM data directory. This is automatically set to 
to the TIEGCMHOME and TIEGCMDATA environment variables

.. code-block:: bash

  Standalone Executable [<YOUR_TIEGCM_STANDALONE_EXECUTABLE_HERE>]: 

This is the path to the TIE-GCM standalone executable. This is automatically set
to the ``tiegcm.exe`` in current directory.

.. code-block:: bash

  Coupled Executable [<YOUR_TIEGCM_COUPLED_EXECUTABLE_HERE>]: 

This is the path to the TIE-GCM coupled executable. This is automatically set
to the ``tiegcm.x`` in current directory.

.. code-block:: bash

  Low = 70, Medium = 140 , High = 200
  F107 flux level for TIEGCM spin up (low|medium|high) [low]: 

This is the F10.7 flux level to use for the TIE-GCM source file in spin-up period. The
default is ``low``, which corresponds to a value of 70. The other options are
``medium`` (140) and ``high`` (200). 

.. code-block:: bash

  SOURCE file location [/glade/campaign/hao/itmodel/tiegcm3.0/new_data/source/junsol_f70.nc]: 

This is the path to the TIE-GCM source file to use for the spin-up period. The default is
automatically selected based on the start date of your simulation.

.. code-block:: bash

  Selected date in source file Example: (173,0,0,0) [173 0 0 0]: 
  STEP number [30]: 
  NSTEP_SUB number [10]: 

These parameters are set as default by the ``tiegcmrun``

.. code-block:: bash

  Secondary Output Fields [['TN', 'UN', 'VN', 'NE', 'TEC', 'POTEN', 'Z', 'ZG']] / ENTER to go next:

These are the secondary output fields to include in the TIE-GCM output. 
The default is a set of fields that are commonly used in geospace simulations. 
You can add another filed if you wish, or just hit :kbd:`Return` to accept the default. 

.. code-block:: bash

  High-latitude potential model that is going to be used (HEELIS|WEIMER) [HEELIS]: 

This is the high-latitude potential model to use in the TIE-GCM simulation.
The default is ``HEELIS``, which is the Heelis potential model is required for
coupled runs with the ``kaiju`` software. 

.. code-block:: bash

  If GPI_NCFILE is specified, then KP and POWER/CTPOTEN are skipped. If further POTENTIAL_MODEL is WEIMER and IMF_NCFILE is specified, then the Weimer model and aurora will be driven by the IMF data, and only F107 and F107A will be read from the GPI data file.
  GPI file [/glade/campaign/hao/itmodel/tiegcm3.0/new_data/boundary_files/GPI/gpi_1960001-2024332.nc]: 

This is the path to the GPI file to use for the TIE-GCM simulation which contrains solar wind
data. The default is automatically selected based on the start date of your simulation.


After these inputs, the script interpolates source file for TIEGCM, and generates XML and
PBS files for the run, as well as a grid file for use in the model.

You should see output similar to this:

.. code-block:: bash

    /glade/derecho/scratch/nikhilr/GTR58 exitsts
    /glade/derecho/scratch/nikhilr/GTR58 exitsts
    /glade/derecho/scratch/nikhilr/GTR58 exitsts
    Interpolating primary file /glade/campaign/hao/itmodel/tiegcm3.0/new_data/source/junsol_f70.nc to create new primary file /glade/derecho/scratch/nikhilr/GTR58/tiegcm_standalone/geospace-tiegcm-standalone_prim.nc at horizontal resolution 2.5 and vertical resolution 0.25 with zitop 7.0.
    Creating new primary file:  /glade/derecho/scratch/nikhilr/GTR58/tiegcm_standalone/geospace-tiegcm-standalone_prim.nc
    pbs_scripts = ['./geospace-01.pbs', './geospace-02.pbs']
    submit_all_jobs_script = geospace_pbs.sh

When finished, the script creates the file ``runid.json``, where ``runid`` is
the identifying string for your simulation. This file contains a record of all
of the parameters used in your simulation. This file can be passed back to
``engage.py`` in a subsequent session to repeat the simulation, and also
provides a convenient starting point for minor tweaks to your simulation
parameters.

There are several types files created for each of the jobs, including:

* ``*.pbs``
    These are the PBS scripts that will be submitted to the job scheduler to run
    the segments of the simulation.
* ``*.xml``
    These are the XML files that contain the parameters for GAMERA and RAIJU of the
    segment. 
* ``*.inp``
    These are the namelist files that contain parameters for TIE-GCM of the segment.
* ``*.json``
    These are the JSON files that contain the parameters for the simulation. They
    are generated by the ``engage.py`` script with all the parameters required to run the
    simulation.

The run is divided into segments:

* ``geospace-SPINUP.*``
    This segment runs the GAMERA model to create the initial conditions for the
    simulation. It is run first, and its output is used by the next segment.
* ``geospace-WARMUP-**.*``
    These segments runs the GAMERA RAIJU model to "warm up" for for the coupled model execution.
    The ``-01``, ``-02``, etc. suffixes indicate the segment number, and the
    segments are run in order.
* ``tiegcm_standalone-**.*``
    This segment runs the TIE-GCM model to create the initial conditions for the coupled model.
    The ``-01`` to ``-02``, etc. suffixes indicate the segment number, and the
    segments are run in order.
* ``geospace-**.*``
    These segments runs the GTR coupled modele. The ``-01``, ``-02``, etc. 
    suffixes indicate the segment number, and the segments are run
    in order.

This image shows how the segments are run in order:

.. image:: ../running/GTRSegment.png


Additional parameters in ``INTERMEDIATE`` and ``EXPERT`` mode
-------------------------------------------------------------

Many more parameters are available in ``INTERMEDIATE`` and ``EXPERT`` modes.
These parameters are documented in the file ``option_descriptions.json``,
which is stored in the same directory as the ``engage.py`` script.

Using JSON files for ``engage.py``
---------------------------------
The ``engage.py`` script can also be run in a non-interactive mode, where it
reads a JSON file containing the parameters for the simulation. This allows
you to automate the process of running the simulation, and to easily repeat
the simulation with the same parameters.

The ``engage.py`` script requires three JSON files to be specified:
* ``engage_options_path``
    This is the path to the JSON file containing the parameters for the
    ``engage.py`` script. It contains the parameters that are specific to the
    ``engage.py`` script, such as the run ID, start and stop dates, and so on.
* ``makeitso_options_path``
    This is the path to the JSON file containing the parameters for the
    ``makeitso.py`` script. It contains the parameters that are specific to the
    ``makeitso.py`` script, such as the GAMERA grid type, segment length, and so on.
* ``tiegcm_options_path``
    This is the path to the JSON file containing the parameters for the
    ``tiegcmrun`` script. It contains the parameters that are specific to the
    TIE-GCM simulation, such as the source file, F10.7 flux level, and so on.


To run the ``engage.py`` script in non-interactive mode, you can use the
following command:
.. code-block:: bash

    engage.py --engage_options_path /path/to/engage_input.json --makeitso_options_path /path/to/makeitso_input.json --tiegcm_options_path /path/to/tiegcm_input.json

Here are templates for the JSON files:
  - Derecho: 

    - :download:`engage_input.json <engage_template/derecho/engage_input.json>`
    - :download:`makeitso_input.json <engage_template/derecho/makeitso_input.json>`
    - :download:`tiegcm_input.json <engage_template/derecho/tiegcmrun_input.json>`

  - Pleiades:

    - :download:`engage_input.json <engage_template/pleiades/engage_input.json>`
    - :download:`makeitso_input.json <engage_template/pleiades/makeitso_input.json>`
    - :download:`tiegcm_input.json <engage_template/pleiades/tiegcmrun_input.json>`

These JSON files can be used as a starting point for your own simulations. You will 
need to modify certain parameters in them:

  - engage_input.json:

    - start_date: The start date of your simulation.
    - stop_date: The stop date of your simulation.
    - segment_duration: The duration of each segment in simulated seconds.
    - gamera_grid_type: The GAMERA grid type to use (D, Q, O, or H).
    - kaiju_install_directory: The path to your ``kaiju`` installation directory.
    - kaiju_build_directory: The path to your ``kaiju`` build directory.

  - makeitso_input.json:

    - Automcatically generated by the ``engage.py`` script, but you can modify the
      parameters if needed. 

  - tiegcm_input.json:

    - modeldir: The path to your TIE-GCM repository.
    - tgcmdata: The path to your TIE-GCM data directory.
    - modelexe: The path to the TIE-GCM standalone executable.
    - coupled_modelexe: The path to the TIE-GCM coupled executable.
    - solar_flux_level: The F10.7 flux level to use for the TIE-GCM source file in spin-up period (low, medium, or high).
    - SECFLDS: The secondary output fields to include in the TIE-GCM output.
    - Automcatically generated by the ``engage.py`` script, but you can modify the
      parameters if needed.