Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/parmoo/parmoo

Python library for parallel multiobjective simulation optimization
https://github.com/parmoo/parmoo

blackbox-optimization mathematical-software multicriteria-optimization multiobjective multiobjective-optimization numerical-optimization python3 response-surface-methodology simulation-based-optimization simulation-optimization surrogate-based-optimization

Last synced: 26 days ago
JSON representation

Python library for parallel multiobjective simulation optimization

Lists

README 

        

.. image:: docs/img/logo-ParMOO.svg

    :align: center

    :alt: ParMOO



|



.. image:: https://img.shields.io/badge/License-BSD_3--Clause-green.svg

    :target: https://opensource.org/licenses/BSD-3-Clause

    :alt: License



.. image:: https://img.shields.io/pypi/v/parmoo.svg?color=green

    :target: https://pypi.org/project/parmoo



.. image:: https://github.com/parmoo/parmoo/actions/workflows/parmoo-ci.yml/badge.svg?/branch=main

    :target: https://github.com/parmoo/parmoo/actions



.. image:: https://readthedocs.org/projects/parmoo/badge/?maxAge=2592000

    :target: https://parmoo.readthedocs.org/en/latest

    :alt: Documentation Status



.. image:: https://joss.theoj.org/papers/10.21105/joss.04468/status.svg

   :target: https://doi.org/10.21105/joss.04468

   :alt: JOSS DOI



|



ParMOO: Python library for parallel multiobjective simulation optimization

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



ParMOO is a parallel multiobjective optimization solver that seeks to

exploit simulation-based structure in objective and constraint functions.



To exploit structure, ParMOO models *simulations* separately from

*objectives* and *constraints*. In our language:



 * a **design variable** is an input to the problem, which we can directly

   control;

 * a **simulation** is an expensive or time-consuming process, including

   real-world experimentation, which is treated as a blackbox function

   of the design variables and evaluated sparingly;

 * an **objective** is an algebraic function of the design variables

   and/or simulation outputs, which we would like to optimize; and

 * a **constraint** is an algebraic function of the design variables

   and/or simulation outputs, which cannot exceed a specified bound.



.. figure:: docs/img/des-sim-obj-space.png

    :alt: Designs, simulations, and objectives

    :align: center



|



To solve a multiobjective optimization problem (MOOP), we use surrogate

models of the simulation outputs, together with the algebraic definition of

the objectives and constraints.



ParMOO is implemented in Python. In order to achieve scalable parallelism,

we use libEnsemble_ to distribute batches of simulation evaluations across

parallel resources.



Dependencies

------------



ParMOO has been tested on Unix/Linux and MacOS systems.



ParMOO's base has the following dependencies:



 * Python_ 3.8+

 * numpy_ -- for data structures and performant numerical linear algebra

 * scipy_ -- for scientific calculations needed for specific modules

 * pyDOE_ -- for generating experimental designs

 * pandas_ -- for exporting the resulting databases



Additional dependencies are needed to use the additional features in

``parmoo.extras``:



 * libEnsemble_ -- for managing parallel simulation evaluations



And for using the Pareto front visualization library in ``parmoo.viz``:



 * plotly_ -- for generating interactive plots

 * dash_ -- for hosting interactive plots in your browser

 * kaleido_ -- for exporting static plots post-interaction



Installation

------------



The easiest way to install ParMOO is via the Python package index, PyPI

(commonly called ``pip``):



.. code-block:: bash



    pip install < --user > parmoo



where the braces around ``< --user >`` indicate that the ``--user`` flag is

optional.



To install *all* dependencies (including libEnsemble) use:



.. code-block:: bash



    pip install < --user > "parmoo[extras]"



You can also clone this project from our GitHub_ and ``pip`` install it

in-place, so that you can easily pull the latest version or checkout

the ``develop`` branch for pre-release features.

On Debian-based systems with a bash shell, this looks like:



.. code-block:: bash



   git clone https://github.com/parmoo/parmoo

   cd parmoo

   pip install -e .



Alternatively, the latest release of ParMOO (including all required and

optional dependencies) can be installed from the ``conda-forge`` channel using:



.. code-block:: bash



   conda install --channel=conda-forge parmoo



Before doing so, it is recommended to create a new conda environment using:



.. code-block:: bash



   conda create --name channel-name

   conda activate channel-name



Testing

-------



If you have pytest_ with the pytest-cov_ plugin and flake8_ installed,

then you can test your installation.



.. code-block:: bash



   python3 setup.py test



These tests are run regularly using GitHub Actions_.



Basic Usage

-----------



ParMOO uses numpy_ in an object-oriented design, based around the ``MOOP``

class. To get started, create a ``MOOP`` object.



.. code-block:: python



   from parmoo import MOOP

   from parmoo.optimizers import LocalGPS



   my_moop = MOOP(LocalGPS)



To summarize the framework, in each iteration ParMOO models each simulation

using a computationally cheap surrogate, then solves one or more scalarizations

of the objectives, which are specified by acquisition functions.

Read more about this framework at our ReadTheDocs_ page.

In the above example, ``LocalGPS`` is the class of optimizers that the

``my_moop`` will use to solve the scalarized surrogate problems.



Next, add design variables to the problem as follows using the

``MOOP.addDesign(*args)`` method. In this example, we define one continuous

and one categorical design variable.

Other options include integer, custom, and raw (using raw variables is not

recommended except for expert users).



.. code-block:: python



   # Add a single continuous design variable in the range [0.0, 1.0]

   my_moop.addDesign({'name': "x1", # optional, name

                      'des_type': "continuous", # optional, type of variable

                      'lb': 0.0, # required, lower bound

                      'ub': 1.0, # required, upper bound

                      'tol': 1.0e-8 # optional tolerance

                     })

   # Add a second categorical design variable with 3 levels

   my_moop.addDesign({'name': "x2", # optional, name

                      'des_type': "categorical", # required, type of variable

                      'levels': ["good", "bad"] # required, category names

                     })



Next, add simulations to the problem as follows using the

``MOOP.addSimulation`` method. In this example, we define a toy simulation

``sim_func(x)``.



.. code-block:: python



   import numpy as np

   from parmoo.searches import LatinHypercube

   from parmoo.surrogates import GaussRBF



   # Define a toy simulation for the problem, whose outputs are quadratic

   def sim_func(x):

      if x["x2"] == "good":

         return np.array([(x["x1"] - 0.2) ** 2, (x["x1"] - 0.8) ** 2])

      else:

         return np.array([99.9, 99.9])

   # Add the simulation to the problem

   my_moop.addSimulation({'name': "MySim", # Optional name for this simulation

                          'm': 2, # This simulation has 2 outputs

                          'sim_func': sim_func, # Our sample sim from above

                          'search': LatinHypercube, # Use a LH search

                          'surrogate': GaussRBF, # Use a Gaussian RBF surrogate

                          'hyperparams': {}, # Hyperparams passed to internals

                          'sim_db': { # Optional dict of precomputed points

                                     'search_budget': 10 # Set search budget

                                    },

                         })



Now we can add objectives and constraints using ``MOOP.addObjective(*args)``

and ``MOOP.addConstraint(*args)``. In this example, there are 2 objectives

(each corresponding to a single simulation output) and one constraint.



.. code-block:: python



   # First objective just returns the first simulation output

   def f1(x, s): return s["MySim"][0]

   my_moop.addObjective({'name': "f1", 'obj_func': f1})

   # Second objective just returns the second simulation output

   def f2(x, s): return s["MySim"][1]

   my_moop.addObjective({'name': "f2", 'obj_func': f2})

   # Add a single constraint, that x[0] >= 0.1

   def c1(x, s): return 0.1 - x["x1"]

   my_moop.addConstraint({'name': "c1", 'constraint': c1})



Finally, we must add one or more acquisition functions using

``MOOP.addAcquisition(*args)``. These are used to scalarize the surrogate

problems. The number of acquisition functions typically determines the

number of simulation evaluations per batch. This is useful to know if you

are using a parallel solver.



.. code-block:: python



   from parmoo.acquisitions import RandomConstraint



   # Add 3 acquisition functions

   for i in range(3):

      my_moop.addAcquisition({'acquisition': RandomConstraint,

                              'hyperparams': {}})



Finally, the MOOP is solved using the ``MOOP.solve(budget)`` method, and the

results can be viewed using ``MOOP.getPF()`` method.



.. code-block:: python



   import pandas as pd



   my_moop.solve(5) # Solve with 5 iterations of ParMOO algorithm

   results = my_moop.getPF(format="pandas") # Extract the results as pandas df



After executing the above block of code, the ``results`` variable points to

a pandas_ dataframe, each of whose rows corresponds to a nondominated

objective value in the ``my_moop`` object's final database.

You can reference individual columns in the ``results`` array by using the

``name`` keys that were assigned during ``my_moop``'s construction, or

plot the results by using the viz_ library.



Congratulations, you now know enough to get started solving MOOPs with

ParMOO!



Next steps:



 * Learn more about all that ParMOO has to offer (including saving and

   checkpointing, INFO-level logging, advanced problem definitions, and

   different surrogate and solver options) at our ReadTheDocs_ page.

 * Explore the advanced examples (including a ``libEnsemble`` example)

   in the ``examples`` directory.

 * Install libEnsemble_ and get started solving MOOPs in parallel.

 * See some of our pre-built solvers in the parmoo_solver_farm_.

 * To interactively explore your solutions, install its extra dependencies and

   use our built-in viz_ tool.

 * For more advice, consult our FAQs_.



Resources

---------



To seek support or report issues, e-mail:



 * ``[email protected]``



Our full documentation is hosted on:



 * ReadTheDocs_



Please read our LICENSE_ and CONTRIBUTING_ files.



Citing ParMOO

-------------



Please use one of the following to cite ParMOO.



Our JOSS paper:



.. code-block:: bibtex



    @article{parmoo,

        author={Chang, Tyler H. and Wild, Stefan M.},

        title={{ParMOO}: A {P}ython library for parallel multiobjective simulation optimization},

        journal = {Journal of Open Source Software},

        volume = {8},

        number = {82},

        pages = {4468},

        year = {2023},

        doi = {10.21105/joss.04468}

    }



Our online documentation:



.. code-block:: bibtex



    @techreport{parmoo-docs,

        title       = {{ParMOO}: {P}ython library for parallel multiobjective simulation optimization},

        author      = {Chang, Tyler H. and Wild, Stefan M. and Dickinson, Hyrum},

        institution = {Argonne National Laboratory},

        number      = {Version 0.3.1},

        year        = {2023},

        url         = {https://parmoo.readthedocs.io/en/latest}

    }



.. _Actions: https://github.com/parmoo/parmoo/actions

.. _CONTRIBUTING: https://github.com/parmoo/parmoo/blob/main/CONTRIBUTING.rst

.. _dash: https://dash.plotly.com

.. _FAQs: https://parmoo.readthedocs.io/en/latest/faqs.html

.. _flake8: https://flake8.pycqa.org/en/latest

.. _GitHub: https://github.com/parmoo/parmoo

.. _kaleido: https://github.com/plotly/Kaleido

.. _libEnsemble: https://github.com/Libensemble/libensemble

.. _LICENSE: https://github.com/parmoo/parmoo/blob/main/LICENSE

.. _numpy: https://numpy.org

.. _pandas: https://pandas.pydata.org

.. _parmoo_solver_farm: https://github.com/parmoo/parmoo-solver-farm

.. _plotly: https://plotly.com/python

.. _pyDOE: https://pythonhosted.org/pyDOE

.. _pytest: https://docs.pytest.org/en/7.0.x

.. _pytest-cov: https://pytest-cov.readthedocs.io/en/latest

.. _Python: https://www.python.org/downloads

.. _ReadTheDocs: https://parmoo.readthedocs.org

.. _scipy: https://scipy.org

.. _viz: https://parmoo.readthedocs.io/en/latest/modules/viz.html