PGAPy: Python Wrapper for PGAPack Parallel Genetic Algorithm Library

Author:	Ralf Schlatterbeck <rsc@runtux.com>

News

News Oct 2023:

• Add Differential Evolution for integer
• Add Negative Assortative Mating option

News 04-2023:

• The last build on PyPi was broken for serial installs, it was missing the mpi_stub.c needed for the serial version. Parallel installs were still possible so I didn't notice, sorry!

• Add MPI_Abort to the wrapper, it is called with:

  pga.MPI_Abort (errcode)
  

  See below in secion Running with MPI how this can be used to abort the MPI run in case of exception in the evaluate method.

News 12-2022: Add regression test and update to new upstream with several bug-fixes. Includes also some bug fixes in wrapper.

News 10-2022: Add user defined datatypes. Example in examples/gp use user defined data types to implement genetic programming (we represent expressions by a tree data structure). This uses the new serialization API in pgapack to transfer a Python pickle representation to peer MPI processes. Also incorporate the latest changes in pgapack which optimizes duplicate checking. This is of interest for large population sizes in the genetic programming examples. Note that the gene_difference method has been renamed to gene_distance.

News 08-2022: Epsilon-constrained optimization and a crossover variant that preserves permutations (so with integer genes the gene can represent a permutation).

News 03-2022: Attempt to make this installable on Windows. This involves some workaround in the code because the visual compiler does not support certain C99 constructs.

News 01-2022: This version wraps multiple evaluation with NSGA-III (note the additional 'I').

News 12-2021: This version wraps multiple evaluation values from your objective function: Now you can return more than one value to either use it for constraints (that must be fulfilled before the objective is optimized) or for multi-objective optimization with the Nondominated Sorting Genetic Algorithm V.2 (NSGA-II). You can combine both, multi-objective optimization and constraints.

News: This version wraps the Differential Evolution method (that's quite an old method but is newly implemented in pgapack).

Introduction

PGAPy is a wrapper for PGAPack, the parallel genetic algorithm library (see PGAPack Readme), a powerfull genetic algorithm library by D. Levine, Mathematics and Computer Science Division Argonne National Laboratory. The library is written in C. PGAPy wraps this library for use with Python. The original PGAPack library is already quite old but is one of the most complete and accurate (and fast, although this is not my major concern when wrapping it to python) genetic algorithm implementations out there with a lot of bells and whistles for experimentation. It also has shown a remarkably small number of bugs over the years. It supports parallel execution via the message passing interface MPI in addition to a normal "serial" version. That's why I wanted to use it in Python, too.

To get started you need the PGAPack library, although it now comes bundled with PGApy, to install a parallel version you currently need a pre-installed PGAPack compiled for the MPI library of choice. See Installation section for details.

There currently is not much documentation for PGAPy. You really, absolutely need to read the documentation that comes with PGAPack. The PGAPack user guide is now shipped together with PGAPy. It is installed together with some examples in share/pgapy, wherever the Python installer decides to place this in the final installation (usually /usr/local/share on Linux).

The original PGAPack library can still be downloaded from the PGAPack ftp site, it is written in ANSI C but will probably not compile against a recent version of MPI. It will also not work with recent versions of PGAPy. Note that this version is not actively maintained. I've started a PGAPack fork on github where I've ported the library to the latest version of the MPI standard and have fixed some minor inconsistencies in the documentation. I've also implemented some new features, notably enhancements in selection schemes, a new replacement strategy called restricted tournament replacement [1], [2], [4] and, more recently, the differential evolution strategy [5], [6]. In addition this version now supports multi objective optimization with NSGA-II [7] and many-objective optimization with NSGA-III [8], [9]. It also supports the Epsilon Constraint method [10].

Note: When using NSGA_III replacement for multi (or many-) objective optimization you need to either

• set reference points on the hyperplane intersecting all axes at offset 1. These reference points can be obtained with the convenience function pga.das_dennis, it creates a regular set of reference points using an algorithm originally publised by I. Das and J. E. Dennis [12]. These points are then passed as the parameter reference_points to the PGA constructor.

  See examples/dtlz2.py for a usage example and the user guide for the bibliographic reference. The function gets the dimensionality of the objective space (num_eval minus num_constraint) and the number of partition to use.

• Or set reference directions (in the objective space) with the reference_directions parameter, number of partitions for these directions with the refdir_partitions parameter (see das_dennis above, this uses Das/Dennis points internally), and a scale factor with the parameter refdir_scale.

You can set both, these parameters are not mutually exclusive.

I'm mainly testing pgapy on Linux. But I've recently made it run on Windows, too but I'm not very actively testing on Windows. Let me know if you run it on Windows, sucessfully or not sucessfully.

As mentioned above, you can find my PGAPack fork on github, this repository has the three upstream releases as versions in git and contains some updates concerning support of newer MPI versions and documentation updates. I've also included patches in the git repository of the Debian maintainer of the package, Dirk Eddelbuettel. I'm actively maintaining that branch, adding new features and bug-fixes.

To get you started, I've included some very simple examples in examples, e.g., one-max.py implements the "Maxbit" example similar to one in the PGAPack documentation. The examples were inspired by the book "Genetic Algorithms in Python" but are written from scratch and don't include any code from the book. The examples illustrates several points:

• Your class implementing the genetic algorithm needs to inherit from pga.PGA (pga is the PGAPy wrapper module).
• You need to define an evaluation function called evaluate that returns a sequence of numbers indicating the fitness of the gene given. It gets the parameters p and pop that can be used to fetch allele values from the gene using the get_allele method, for more details refer to the PGAPack documentation. The number of evaluations returned by your function is defined with the constructor parameter num_eval, the default for this parameter is 1. If your evaluation function does not return multiple evaluations (with the default setting of num_eval) you can either return a one-element sequence or a single return value.
• When using multiple evaluations, these can either be used for constraints (the default) or for multi-objective optimization. In the latter case, the number of constraints (which by default is one less than the number of evaluations set with the parameter num_eval) must be set to a number that leaves at least two evaluations for objectives. The number of constraints can be set with the parameter num_constraint. When using multi-objective optimization, you need one of the two replacement-types PGA_POPREPL_NSGA_II or PGA_POPREPL_NSGA_III, set this with the pop_replace_type parameter.
• You can define additional functions overriding built-in functions of the PGAPack library, illustrated by the example of print_string. Note that we could call the original print_string method of our PGA superclass. In the same way you can implement, e.g., your own crossover method.
• The constructor of the class needs to define the Gene type, in the examples we use int and bool built-in datatypes.
• The length of the gene needs to be given in the constructor.
• We often want to maximize the numbers returned by our evaluation function, set the parameter maximize to False if you want to minimize.
• For non-binary genes we can define an array of init values, each entry containing a sequence with lower and upper bound. The array has to have the length of the gene. Note that the upper bound is included in the range of possible values (unlike the python range operator but compatible with the PGAPack definition).
• In the constructor of the class we can add parameters of the genetic algorithm. Not all parameters of PGAPack are wrapped yet, currently you would need to consult the sourcecode of PGAPy to find out which parameters are wrapped. In the example we define several print options.
• Finally the genetic algorithm is started with the run method.

Naming conventions in PGAPy

When you extend PGAPy – remember not all functions of PGAPack are wrapped yet and you may need additional functions – you should stick to my naming conventions when making changes. The following naming conventions were used for the wrapper:

• Constants of PGAPack like PGA_REPORT_STRING are used as-is in uppercase. These constants can be directly imported from the wrapper module. Not all constants are wrapped so far, if you need more, add them to the constdef array in pgamodule.c and send me a patch.
• For methods of the pga.PGA class I've removed the PGA prefix used throughout PGAPack and converted the method to lowercase with underscores between uppercase words in the original function name, so PGARun becomes run, PGACheckStoppingConditions becomes check_stopping_conditions. An exception of the lowercase-rule is whenever a name contains "GA" (for "genetic algorithm"), So PGASetMaxGAIterValue becomes max_GA_iter.
• Where possible I've made a single class method where PGAPack needs a separate function for each datatype, so PGAGetBinaryAllele, PGAGetCharacterAllele, PGAGetIntegerAllele, PGAGetRealAllele all become get_allele. Same holds true for set_allele.
• Whenever a name in PGAPack has a "Value" or "Flag" suffix, I've left this out, so PGAGetFitnessCmaxValue becomes fitness_cmax and PGAGetMutationAndCrossoverFlag becomes mutation_and_crossover, the only exception to this rule is for the two functions PGAGetMutationRealValue and PGAGetMutationIntegerValue which become mutation_value not just mutation.
• Some fields can take multiple values (they are implemented by ORing integer constants, in python they are specified as a list or tuple of constants). These are converted to plural (if not already plural in PGAPack), e.g., PGASetStoppingRuleType becomes stopping_rule_types.
• Internal method names in the wrapper program have a leading PGA_ – so the class method set_allele is implemented by the C-function PGA_set_allele in pgamodule.c.

Constructor Parameters

PGAPack has a lot of PGASet and PGAGet functions for setting parameters. These are reflected in constructor parameters on the one hand and in (typically read-only, but see below) properties of a PGA object on the other hand. The following table gives an overview of all the original PGAPack names and the names of the python wrapper. For the PGAPack name I've only listed the PGASet function, in many cases there is a corresponding PGAGet function. If a corresponding read-only property exists for a constructor parameter this is indicated in the "Prop" column. In some cases properties are missing because no corresponding PGAGet function is implemented in PGAPack, in other cases returning a numeric value that has a symbolic constant in PGApy doesn't make much sense.

The properties have the same name as the constructor parameter. There are Properties that don't have a corresponding constructor parameter, namely the eval_count property (returning the count of function evaluations), the GA_iter property that returns the current GA generation, and the mpi_rank property that returns the MPI rank of the current process (this is sorted under PGAGetRank).

In the type column I'm listing the Python type. If the type is followed by a number, more than one item of that type is specified (a sequence in Python). Some entries contain "sym", these are integer values with a symbolic constant, the value "msym" indicates that several values denoted by a list of symbolic constants can be given. A special case are the PGASetRealInitRange, PGASetRealInitPercent, PGASetIntegerInitRange functions. These take two values for each allele of the gene. In python this is a sequence of 2-tuples. Note that this means that you can have different ranges of allowed values for each allele.

The num_eval property is special: Due to limitations of the C programming language, for multiple evaluations in C the first evaluation is returned as the function return-value of the evaluate function and all other parameters are returned in an auxiliary array. PGAPack specifies the number of auxiliary evaluations to be returned. In Python the evaluation function can always return a sequence of evaluation values and the num_eval is one more than PGAGetNumAuxEval would return. The default for num_eval is 1.

The first two (mandatory) constructor parameters are the type of the gene (this takes a Python type, e.g., bool for a binary genome or int for an integer genome) and the length. Note that the string_length is implicitly set with the length parameter. The string_length is also available as the length of the PGA object using the Python built-in len function.

Some properties can now also be set during the run of the optimizer. These currently are crossover_prob, epsilon_exponent, multi_obj_precision, p_tournament_prob, and uniform_crossover_prob. Just assign to the member variable of the optimizer (child of PGA.pga) object.

PGAPack name	Constructor parameter	Type	Prop
PGASetCrossoverBoundedFlag	crossover_bounded	int	yes
PGASetCrossoverBounceBackFlag	crossover_bounce_back	int	yes
PGASetCrossoverSBXEta	crossover_SBX_eta	float	yes
PGASetCrossoverSBXOncePerString	crossover_SBX_once_per_string	int	yes
PGASetCrossoverProb	crossover_prob	float	yes
PGASetCrossoverType	crossover_type	sym	no
PGASetDEAuxFactor	DE_aux_factor	double	yes
PGASetDECrossoverProb	DE_crossover_prob	double	yes
PGASetDECrossoverType	DE_crossover_type	sym	no
PGASetDEDither	DE_dither	double	yes
PGASetDEDitherPerIndividual	DE_dither_per_individual	bool	yes
PGASetDEJitter	DE_jitter	double	yes
PGASetDENumDiffs	DE_num_diffs	int	yes
PGASetDEProbabilityEO	DE_probability_EO	double	yes
PGASetDEScaleFactor	DE_scale_factor	double	yes
PGASetDEVariant	DE_variant	sym	yes
PGASetEpsilonExponent	epsilon_exponent	float	yes
PGASetEpsilonGeneration	epsilon_generation	int	yes
PGASetEpsilonTheta	epsilon_theta	int	yes
PGAGetEvalCount	eval_count	int	yes
PGASetFitnessCmaxValue	fitness_cmax	float	yes
PGASetFitnessMinType	fitness_min_type	sym	yes
PGASetFitnessType	fitness_type	sym	yes
PGAIntegerSetFixedEdges	fixed_edges		no
PGAIntegerSetFixedEdges	fixed_edges_symmetric	bool	no
PGAGetGAIterValue	GA_iter	int	yes
PGASetIntegerInitPermute	integer_init_permute	int2	no
PGASetIntegerInitRange	init		no
PGASetMaxFitnessRank	max_fitness_rank	float	yes
PGASetMaxGAIterValue	max_GA_iter	int	yes
PGASetMaxNoChangeValue	max_no_change	int	no
PGASetMaxSimilarityValue	max_similarity	int	yes
PGASetMixingType	mixing_type	sym	no
PGASetMultiObjPrecision	multi_obj_precision	int	yes
PGASetMutationAndCrossoverFlag	mutation_and_crossover	int	yes
PGASetMutationBounceBackFlag	mutation_bounce_back	int	yes
PGASetMutationBoundedFlag	mutation_bounded	int	yes
PGASetMutationIntegerValue	mutation_value	int	yes
PGASetMutationOrCrossoverFlag	mutation_or_crossover	int	yes
PGASetMutationPolyEta	mutation_poly_eta	float	yes
PGASetMutationPolyValue	mutation_poly_value	float	yes
PGASetMutationProb	mutation_prob	float	yes
PGASetMutationRealValue	mutation_value	float	yes
PGASetMutationType	mutation_type	sym	no
PGASetNAMWindowSize	nam_window_size	int	yes
PGASetNoDuplicatesFlag	no_duplicates	int	no
PGASetNumAuxEval	num_eval	int	yes
PGASetNumConstraint	num_constraint	int	yes
PGASetNumReplaceValue	num_replace	int	yes
PGASetPopSize	pop_size	int	yes
PGASetPopReplaceType	pop_replace_type	sym	no
PGASetPrintFrequencyValue	print_frequency	int	yes
PGASetPrintOptions	print_options	msym	no
PGASetPTournamentProb	p_tournament_prob	float	yes
PGASetRandomizeSelect	randomize_select	int	yes
PGASetRandomSeed	random_seed	int	yes
PGAGetRank	mpi_rank	int	yes
PGASetRealInitRange	init		no
PGASetRealInitPercent	init_percent		no
PGASetReferenceDirections	refdir_partitions	int	no
PGASetReferenceDirections	refdir_scale	double	no
PGASetReferenceDirections	reference_directions		no
PGASetReferencePoints	reference_points		no
PGASetRestartFlag	restart	int	yes
PGASetRestartFrequencyValue	restart_frequency	int	yes
PGASetRTRWindowSize	rtr_window_size	int	yes
PGASetSelectType	select_type	sym	no
PGASetStoppingRuleType	stopping_rule_types	msym	no
PGASetStringLength	string_length	int	yes
PGASetSumConstraintsFlag	sum_constraints	int	yes
PGASetTournamentSize	tournament_size	int	yes
PGASetTournamentWithReplacement	tournament_with_replacement	int	yes
PGASetTruncationProportion	truncation_proportion	float	yes
PGASetUniformCrossoverProb	uniform_crossover_prob	float	yes

Note: The mutation_or_crossover and mutation_and_crossover parameters are deprecated, use mixing_type instead!

PGA Object Methods

The following are the methods that can be used during the run of the genetic search. The run method is used to start the search. This can be used, to, e.g., set an allele during hill-climbing in a custom endofgen method. Note that some methods only apply to certain gene types, e.g. the encode_int_ methods can only be used on binary alleles (they encode an integer value as a binary or gray code representation into the gene). Other methods take or return different types depending on the type of gene, e.g. get_allele or set_allele, they call different backend functions depending on the gene type. With the set_random_seed method, the random number generator can be re-seeded. It is usually best to seed the generator once at (before) the beginning by specifying random_seed in the constructor. For further details consult the user guide. The method get_evaluation will return a double for a single evaluation and a tuple of double for multiple evaluations (when num_eval is >1)

Method	Parameters	Return
check_stopping_conditions		True if stop should occur
encode_int_as_binary	p, pop, frm, to, val	None
encode_int_as_gray_code	p, pop, frm, to, val	None
encode_real_as_binary	p, pop, frm, to l, u, val	None
encode_real_as_gray_code	p, pop, frm, to l, u, val	None
euclidian_distance	p1, pop1 p2, pop2	float
fitness	pop	None
get_allele	p, pop, index	allele value
get_best_index	pop	index of best string
get_best_report_index	pop, idx	index of best eval with idx
get_evaluation	p, pop	evaluation of p
get_evaluation_up_to_date	p, pop	True if up-to-date
get_fitness	p, pop	fitness of p (float)
get_gene	p, pop	get gene (user data types)
get_int_from_binary	p, pop, frm, to	int
get_int_from_gray_code	p, pop, frm, to	int
get_iteration		deprecated, use GA_iter
get_real_from_binary	p, pop, frm, to, l, u	float
get_real_from_gray_code	p, pop, frm, to, l, u	float
random01		float between 0 and 1
random_flip	probability	0 or 1
random_gaussian	mean, stddev	float
random_interval	l, r	int between l, r
random_uniform	l, r	float between l, r
run		None
select_next_index	pop	index selected individual
set_allele	p, pop, i, value	None
set_evaluation	p, pop, value	None
set_evaluation_up_to_date	p, pop, status	None
set_gene	p, pop, gen	set gene (user data types)
set_random_seed	seed	None (use constructor!)

User-Methods

PGAPack has the concept of user functions. These allow customization of different areas of a genetic algorihm. In Python they are implemented as methods that can be changed in a derived class. One of the methods that must be implemented in a derived class is the evaluate function (although technically it is not a user function in PGAPack). It interprets the gene and returns an evaluation value or a sequence of evaluation values if you set the num_eval constructor parameter. PGAPack computes a fitness from the raw evaluation value. For some methods an up-call into the PGA class is possible, for some methods this is not possible (and in most cases not reasonable). Note that for the stop_cond method, the standard check for stopping conditions can be called with:

self.check_stopping_conditions()

The following table lists the overridable methods with their parameters (for the function signature the first parameter self is omitted). Note that in PGAPack there are additional user functions that are needed for user-defined data types which are currently not exposed in Python. In the function signatures p denotes the index of the individual and pop denotes the population. If more than one individual is specified (e.g., for crossover) these can be followed by a number. For crossover c1 and c2 denote the destination individuals (children). The propability for the mutation method is a floating-point value between 0 and 1. Remember to count the number of mutations that happen, and return that value for the mutation method!

Method	Call Signature	Return Value	Up-Call
check_duplicate	p1, pop1, p2, pop2	True if dupe	no
stop_cond		True to stop	no
crossover	p1, p2, p_pop, c1, c2, c_pop	None	no
endofgen		None	no
evaluate	p, pop	sequence of float	no
gene_distance	p1, pop1, p2, pop2	float	no
hash	p, pop	int	no
initstring	p, pop	None	no
mutation	p, pop, propability	#mutations	no
pre_eval	pop	None	no
print_string	file, p, pop	None	yes

Constants

The following PGAPack constants are available:

Constant	Description
PGA_CROSSOVER_EDGE	Edge crossover for permutations
PGA_CROSSOVER_ONEPT	One-point Crossover
PGA_CROSSOVER_SBX	Simulated Binary Crossover
PGA_CROSSOVER_TWOPT	Two-point Crossover
PGA_CROSSOVER_UNIFORM	Uniform Crossover
PGA_FITNESSMIN_CMAX	Map fitness by subtracting worst
PGA_FITNESSMIN_RECIPROCAL	Map fitness via reciprocal
PGA_FITNESS_NORMAL	Linear normalization of fitness
PGA_FITNESS_RANKING	Linear fitness ranking
PGA_FITNESS_RAW	Identity fitness function
PGA_MUTATION_CONSTANT	Mutation by adding/subtracting constant
PGA_MUTATION_GAUSSIAN	Mutation by selecting from Gaussian distribution
PGA_MUTATION_PERMUTE	Mutation swaps two random genes
PGA_MUTATION_POLY	Polynomial Mutation
PGA_MUTATION_RANGE	Replace gene with uniform selection from init range
PGA_MUTATION_UNIFORM	Mutation uniform from interval
PGA_NEWPOP	Symbolic constant for new population
PGA_OLDPOP	Symbolic constant for old population
PGA_POPREPL_BEST	Population replacement best strings
PGA_POPREPL_NSGA_II	Use NSGA-II replacement for multi-objective opt.
PGA_POPREPL_NSGA_III	Use NSGA-III replacement for multi-objective opt.
PGA_POPREPL_PAIRWISE_BEST	Compare same index in old and new population
PGA_POPREPL_RANDOM_NOREP	Population replacement random no replacement
PGA_POPREPL_RANDOM_REP	Population replacement random with replacement
PGA_POPREPL_RTR	Restricted Tournament Replacement
PGA_REPORT_AVERAGE	Report average evaluation
PGA_REPORT_HAMMING	Report hamming distance
PGA_REPORT_OFFLINE	Report offline
PGA_REPORT_ONLINE	Report online
PGA_REPORT_STRING	Report the string
PGA_REPORT_WORST	Report the worst evaluation
PGA_SELECT_LINEAR	Return individuals in population order
PGA_SELECT_PROPORTIONAL	Fitness-proportional selection
PGA_SELECT_PTOURNAMENT	Binary probabilistic tournament selection
PGA_SELECT_SUS	Stochastic universal selection
PGA_SELECT_TOURNAMENT	Tournament selection
PGA_SELECT_TRUNCATION	Truncation selection
PGA_STOP_MAXITER	Stop on max iterations
PGA_STOP_NOCHANGE	Stop on max number of generations no change
PGA_STOP_TOOSIMILAR	Stop when individuals too similar

User Defined Data Types

The latest version of PGAPy features user defined data types. Just define your data type and pass it as the second parameter to the PGA constructor. The framework will take care of serializing the data when transmitting via MPI (if you're running a parallel version).

If duplicate checking is enabled via the no_duplicates constructor parameter, your data type needs to define a __hash__ method (unless the python default hash method fulfills your requirements).

User defined data types do not use alleles, so the normal get_allele (and set_allele) methods are not available. Instead the full individual can be retrieved with the get_gene method and set with the set_gene method.

With user data types you need to define the following methods:

• check_duplicate (self, p1, pop1, p2, pop2) if you enable duplicate checking with the crossover parameter no_duplicates. This should return True when the two individuals are duplicates. Use get_gene to retrieve the genes for the individuals p1 and p2 in populations pop1 and pop2.
• crossover (self, p1, p2, ppop, c1, c2, cpop) for crossover operation, use get_gene for getting the parent genes for the parents p1 and p2 in generation ppop and use set_gene for setting the child genes c1 and c2 in generation cpop.
• initstring (self, p, pop) for initializing the given string, use set_gene in that method for setting your object as a gene.
• mutation (self, p, pop, pm) for the mutation operation. This should return the number of mutations performed. If duplicate checking is enabled, the framework will repeatedly call the mutation operator for mutating a duplicate individual into another individual that is no duplicate. This uses the return value of your mutation method. You will enter an endless loop if your mutation operator does not occasionally return an non-zero number of mutatations performed when duplicate checking is enabled. The pm parameter gives the mutation probability. Use get_gene for retrieving the individual to be mutated and use set_gene to update this individual after mutation.
• print_string (self, file, p, pop) to print a gene object, use get_gene for retrieving the individual to be printed.

For these methods it is generally a good idea to never modify an individual in-place: This individual may be repeatedly used in genetic operations (e.g. mutation and crossover), so when modifying it you will produce erroneous results for later genetic operations. To copy a data structure, python's deepcopy function in the module copy is usually used.

In addition to the methods above you may want to define a stopping rule with a stop_cond method or override the way a hash is computed using a hash method. The default for computing a hash is to call hash (gene) where gene is an object of the user defined data type. Other methods that may be used is an endofgen method, a gene_distance method (e.g., when using Restricted Tournament Replacement, with PGA_POPREPL_RTR), or a pre_eval method.

An example with user defined data types is in examples/gp: This implements Genetic Programming with a tree data structure. Note that the Node class in gp.py has a __hash__ method that builds a hash over the serialization of the tree (which is the same for individuals with the same tree structure).

Missing Features

As already mentioned, not all functions and constants of PGAPack are wrapped yet – still for many applications the given set should be enough. If you need additional functions, you may want to wrap these and send me a patch.

Reporting Bugs

Please use the Sourceforge Bug Tracker or the Github Bug Tracker and

• give a short description of what you think is the correct behaviour
• give a description of the observed behaviour
• tell me exactly what you did.
• if you can publish your source code this makes it a lot easier to debug for me

Resources

Project information and download from Sourceforge main page

or checkout from Github

or directly install via pypi.

Installation

PGApy, as the name suggests, supports parallelizing the evaluation function of the genetic algorithm. This uses the Message Passing Interface (MPI) standard.

To install a serial version (without parallel programming using MPI) you can simply install from pypi using pip. Alternatively when you have unpacked or checked out from sources you can install with:

python3 setup.py install --prefix=/usr/local

If you want a parallel version using an MPI (Message-Passing Interface) library you will have to install a parallel version of PGAPack first. The easiest way to do this is to use my pgapack debian package builder from github. Clone this repository, check out the branch master, install the build dependencies, they're listed in the file debian/control and build the debian packages using:

dpkg-buildpackage -rfakeroot

This builds pgapack debian packages for all supported MPI libraries in debian, currently these are mpich, openmpi, and lam. In addition to the MPI libraries a serial version of the pgapack library is also built. Proceed by installing the package pgapack and the MPI backend library of choice. If you don't have a preference for an MPI library, libpgapack-openmpi is the package that uses the Debians default preferences of an MPI library.

Once a parallel version of PGAPack is installed, you can install PGApy as follows: You set environment variables for the PGA_PARALLEL_VARIANT (one of mpich, openmpi, or lam) and set the PGA_MODULE to module_from_parallel_install. Finally you envoke the setup, e.g.:

export PGA_PARALLEL_VARIANT=openmpi
export PGA_MODULE=module_from_parallel_install
python3 setup.py install --prefix=/usr/local

Note that the same works with pip install, i.e., after installation of a parallel version of PGAPack you can directly install with pip:

export PGA_PARALLEL_VARIANT=openmpi
export PGA_MODULE=module_from_parallel_install
pip install pgapy

or alternatively depending on how pip is installed on your system:

python3 -m pip install pgapy

If your MPI library is installed in a different place you should study the Extension configurations in setup.py to come up with an Extension definition that fits your installation. If your installation is interesting to more people, feel free to submit a patch that adds your Extension-configuration to the standard setup.py.

Note on newer python versions

Newer python versions have deprecated installing into the system python version, even in /usr/local. You can still build the pgapy package locally and install using the installer. On Debian Linux you need the following packages installed:

apt-get install python3-pip python3-dev python3-toml \
    python3-build python3-installer python3-venv python3-sphinx
    netpbm

Then you can build locally and install:

python3 -m build
python3 -m installer dist/*.whl

Better yet, clone my releasetool package from github:

git clone https://github.com/schlatterbeck/releasetool.git

into a directory parallel to pgapy and build using:

make dist

This also will generate a Version.py file with the correct version number from git. If you want to install a parallel version you should set the environment variables:

export PGA_PARALLEL_VARIANT=openmpi
export PGA_MODULE=module_from_parallel_install

before building.

Running with MPI

To run a parallel version with MPI, a parallel version must be installed, see above in section Installation.

For a serial version, PGAPy makes sure that the otimization is aborted if an exception occurs in the evaluate function. This is currently not the case for MPI, because the framework currently does not support returning information to the rank-0 MPI leader process. A workaround is as follows: Rename your evaluate method to _evaluate and catch exceptions in a new evaluate method that wraps _evaluate. Call MPI_Abort if an exception occurs:

import traceback
import sys

...

def evaluate (self, p, pop):
    try:
        return self._evaluate (p, pop)
    except Exception:
        # Optionally log exception here
        print (traceback.format_exc ())
        pga.MPI_Abort (1)
        sys.exit (1)

Testing

For testing – preferrably before installation you can build locally:

python3 setup.py build_ext --inplace

After this you have a pga.*.so file in the local directory. Now you can run the tests with:

python3 -m pytest test

This runs all the tests and can take a while. Note that the tests run most of the examples in the examples directory with different command line parameters where available. To perform several optimization runs in a single (Python-) process, we must call MPI_Init explicitly (and not relying on PGAPack to call it implicitly). This is because MPI_Init may be called only once per process. Calling of MPI_Init and MPI_Finalize is handled in a fixture in test/conftest.py

Coverage

For the python examples, the coverage can be computed with:

python3 -m pytest --cov examples test

or more verbose including untested lines with:

python3 -m pytest --cov-report term-missing --cov examples test

Performing a coverage analysis for the C code in pgamodule.c is currently possible only on Linux – at least, since I'm developing on Linux this is the architecture where I've found out how to perform coverage analysis including the C code. To compile for coverage analysis:

export CFLAGS=-coverage
python3 setup.py build_ext --inplace

This will create a file ending in .gcno under the build directory, typically something like build/temp.linux-x86_64-3.9 when using python3.9 on the x86_64 architecture. Running the tests will create statistics data files with ending .gcda. These are data files for the GNU profiler gcov. From these, .html files can be generated that can be inspected with a browser:

lcov --capture --directory . --output-file coverage.info
genhtml coverage.info --output-directory coverage_out

Note that the lcov program is part of the linux distribution.

Running under MPI

The tests can be directly run under MPI. Note that currently the --with-mpi option of pytest is not supported. This option asumes that the package mpi4py is used. But pgapy uses only calls from pgapack, which in turn calls MPI.

Running under MPI is done using:

mpirun $MPI_OPTIONS python3 -m pytest test

The MPI_OPTIONS can be, e.g.:

MPI_OPTIONS=--machinefile ~/.mpi-openmpi --np 8

which would use a machine definition file for openmpi in your home directory and eight processes.

Running under MPI is especially useful for determining C code coverage. Asuming a parallel version of openmpi is installed, the code can be compiled with:

PGA_PARALLEL_VARIANT=openmpi
PGA_MODULE=module_from_parallel_install
export CFLAGS=-coverage
python3 setup.py build_ext --inplace

Note that the coverage analysis uses files in the build directory which need to be present before a parallel version can be started. Otherwise each parallel instance would try to create the coverage files resulting in race conditions. Once the coverage files are in place, the coverage framework ensures proper locking so that no two processes write concurrently to the same coverage files.

Creating the coverage files is best achieved by running the tests without MPI first and then running the same version with a number of processes under MPI. Running under MPI shows that the serialization and deserialization code in pgamodule.c is called.

As of this writing we get:

Lines:      1423    1475    96.5 %
Functions:   131     133    98.5 %

References

[1]	Georges Harik. Finding multiple solutions in problems of bounded difficulty. IlliGAL Report 94002, Illinois Genetic Algorithm Lab, May 1994.

[2]	Georges R. Harik. Finding multimodal solutions using restricted tournament selection. In Eshelman [3], pages 24–31.

[3]	Larry J. Eshelman, editor. Proceedings of the 6th International Conference on Genetic Algorithms (ICGA). Morgan Kaufmann, July 1995.

[4]	Martin Pelikan. Hierarchical Bayesian Optimization Algorithm: Toward a New Generation of Evolutionary Algorithms, volume 170 of Studies in Fuzziness and Soft Computing. Springer, 2005.

[5]	Rainer Storn and Kenneth Price. Differential evolution – a simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization, 11(4):341–359, December 1997.

[6]	Kenneth V. Price, Rainer M. Storn, and Jouni A. Lampinen. Differential Evolution: A Practical Approach to Global Optimization. Springer, Berlin, Heidelberg, 2005.

[7]	Kalyanmoy Deb, Amrit Pratap, Sameer Agarwal, and T. Meyarivan. A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Transactions on Evolutionary Computation, 6(2):182–197, April 2002.

[8]	Kalyanmoy Deb and Himanshu Jain. An evolutionary many-objective optimization algorithm using reference-point-based nondominated sorting approach, part I: Solving problems with box constraints. IEEE Transactions on Evolutionary Computation, 18(4):577–601, August 2014.

[9]	Himanshu Jain and Kalyanmoy Deb. An evolutionary many-objective optimization algorithm using reference-point-based nondominated sorting approach, part II: Handling constraints and extending to an adaptive approach. IEEE Transactions on Evolutionary Computation, 18(4):602–622, August 2014.

[10]	Tetsuyuki Takahama and Setsuko Sakai. Constrained optimization by the ε constrained differential evolution with an archive and gradient-based mutation. In [11].

[11]	IEEE Congress on Evolutionary Computation (CEC). Barcelona, Spain, July 2010.

[12]	Indraneel Das and J. E. Dennis. Normal-boundary intersection: A new method for generating the pareto surface in nonlinear multicriteria optimization problems. SIAM Journal on Optimization, 8(3):631–657, August 1998.

Changes

Version 2.4: New upstream

• Wrap Negative Assortative Mating
• Allow Differential Evolution for integer genes
• Upstream fixes feature interaction bugs with duplicate avoidance and Differential Evolution and RTR population replacement
• Add option to use Negative Assortative Mating in Royal Road example

Version 2.2.2: Add pyproject.toml

• Add pyproject.toml -- unfortunately it seems that binary modules cannot currently be described in the pyproject.toml, especially not the variant selection via the environment that is currently implemented in setup.py

Version 2.2.1: MPI_Abort

• Add MPI_Abort to the wrapper
• Include mpi_stub.c in the release (this is missing if some env variables are set, see above in Installation)

Version 2.2: Module directory

• Put the pga C-module inside a pga module
• Add several python-only modules to pga
• pga.__init__ exports everything to this is compatible
• pga.random includes a python Random class based on the pgapack random number generator

Version 2.1: Regression test

• PGAPack bug-fixes discovered during testing
• Bug-fixes of python wrapper
• Lots of tests with coverage of wrapper C-code > 90%

Version 2.0: User defined data types

• Implement user defined data types, note that your data type can be variable-size, e.g., a tree data structure. The framework takes care of serializing the data type and transmitting it to a remote MPI process if using a parallel version.
• When duplicate checking is enabled with the constructor parameter no_duplicates, the underlying pgapack code now uses a hash table. This means the effort is no longer quadratic in the population size but linear.
• Example of Genetic Programming (GP) in the examples/gp directory
• Rename the gene_difference method to gene_distance

Version 1.8: Epsilon-constrained optimization

• Epsilon-constrained optimization
• Precision for printing evals in multi-objective optimization, use this feature for making regression-test work on AMD where a floating-point difference in the 16th or so decimal place made a test fail
• Crossover for permutations
• Version-numbers: try to match pgapack, we might still diverge in the last digit, though

Version 1.2: Many-objective optimization with NSGA-III

• Implement NSGA-III

Version 1.1.6: Polynomial mutation and simulated binary crossover (SBX)

• Simulated binary crossover (SBX)
• Polynomial mutation

Version 1.1.1-1.1.5: Small PGAPack updates, fixes for non-debian

• Fix setup.py for non-debian systems
• Update to latest PGAPack with small changes

Version 1.1: Add multi-objective optimization with NSGA-II

• Wrap latest pgapack version 1.4
• This add multi-objective optimization using the Nondominated Sorting Genetic Algorithm version 2 (NSGA-II) by Deb et. al. This makes use of the previously-introduced option to return more than one value in the objective function. To use the feature you need to set the num_constraint parameter to a value that leave some of the function values returned by your evaluation function as objective function values (and not as constraints). See example in examples/multi.py.

Version 1.0: Add constraint handling

• Wrap latest pgapack version 1.3
• This adds auxiliary evaluations. Now your evaluation function can return multiple floating-point values as a sequence if you set the num_eval parameter >1 in the constructor. Currently additional evaluation values are used for constraint handling. Constraint values are minimized. Once they reach zero or a negative value they no longer count: The sum of all positive constraints is the overall constraint violation. For details see paper by Deb, 2000, see user guide for citation. If you're not using constraints, nothing in your code needs changes.
• This release may change the path an optimization takes. So for the same seed of the random number generator you will get a different result, at least if during the search there are individuals with the same evaluation (and different genetic material). This is due to a change of the sort function in pgapack (it switched to a stable sort from the C standard library).

Version 0.9: Allow installation of parallel version

• Pass argv (or sys.argv) to PGACreate
• Add a stanza to setup.py to allow a parallel installation with a given pgapack variant compiled for an MPI library. This currently needs a pre-installed pgapack debian package.

Version 0.8: Bugfix in real mutation

• Fix a core-dump in the latest pgapack

Version 0.7: Major changes in wrapping

• Now Differential Evolution is implemented, see the minfloat example and the user guide of pgapack.

Version 0.6: Major changes in wrapping

• Now the wrapping uses the standard Python recommendations on how to create a custom class.
• Update documentation
• Rename fitness_cmax (from fitness_cmax_value)
• Better error checking of parameters

Version 0.5: Bug-fix release

• Now the setup.py works, previous version had an encoding problem
• Wrap some minor new methods
• Bug-fix in PGAPack truncation selection

Version 0.4: Bundle PGAPack

• The PGAPack package is now included as a git submodule. By default we build against this library
• License fixes: The module long shipped a COPYING file that includes the 2-clause BSD license. But the headers of setup.py and pgamodule.c still included another license. This has been corrected.

Version 0.3: Feature enhancements, Bug fixes

Port to Python3, Python2 is still supported, license change.

• C-Code of wrapper updated to support both, Python2 and Python3
• Update documentation
• Fix some memory leaks that could result when errors occurred during some callback methods
• License change: We now have the 2-clause BSD license (similar to the MPICH license of PGAPack), this used to be LGPL.

Version 0.2: Feature enhancements, Bug fixes

64 bit support, more PGAPack functions and attributes wrapped, Readme-update: Sourceforge logo, Changes chapter.

• Bug-fixes for 64 bit architectures
• More functions and attributes of PGAPack wrapped
• Add a build-rule to setup.py to allow building for standard-install of PGAPack – this currently needs editing of setup.py – should use autodetect here but this would require that I set up a machine with standard install of PGAPack for testing.
• Add Sourceforge logo as required
• Add Changes chapter for automagic releases
• Add the __module__ string to class PGA in module pga. Now calling:: help (pga) in python works as expected, previously no help-text was given for the included module

Version 0.1: Initial freshmeat announcement

PGAPy is a wrapper for PGAPack, the parallel genetic algorithm library, a powerful genetic algorithm library. PGAPy wraps this library for use with Python. Pgapack is one of the most complete and accurate genetic algorithm implementations out there with a lot of features for experimentation.

• Initial Release