MPCOTool

The Multi-Purposes Calibration and Optimization Tool. A software to perform calibrations or optimizations of empirical parameters.

VERSIONS

4.12.0: Stable and recommended version.

AUTHORS

Javier Burguete Tolosa (jburguete@eead.csic.es)
Borja Latorre Garcés (borja.latorre@csic.es)

WINDOWS EXECUTABLE FILES

This repository contains source and example files with the latest version of MPCOTool. Stable versions with executable files and manuals for Microsoft Windows systems can be downloaded in digital.csic

TOOLS AND LIBRARIES REQUIRED TO BUILD THE EXECUTABLE

gcc or clang (to compile the source code)
make (to build the executable file)
autoconf (to generate the Makefile in different operative systems)
automake (to check the operative system)
pkg-config (to find the libraries to compile)
gsl (to generate random numbers)
libxml (to deal with XML files)
glib (extended utilities of C to work with data, lists, mapped files, regular expressions, using multicores in shared memory machines, ...)
json-glib (to deal with JSON files)
genetic (genetic algorithm)

OPTIONAL TOOLS AND LIBRARIES

gettext (to work with different locales)
gtk+3 (to create the interactive GUI tool)
openmpi or mpich (to run in parallelized tasks on multiple computers)
doxygen (standard comments format to generate documentation)
latex (to build the PDF manuals)

FILES

The source code has to have the following files:

4.12.0/configure.ac: configure script generator.
4.12.0/Makefile.in: Makefile generator.
4.12.0/config.h.in: config header generator.
4.12.0/*.c: C-source code files.
4.12.0/*.h: C-header code files.
4.12.0/mpcotool.ico: icon file.
4.12.0/build.sh: shell script to build all.
4.12.0/logo.png: logo figure.
4.12.0/Doxyfile: configuration file to generate doxygen documentation.
TODO: tasks to do.
README*.md: README files.
license.md: license file.
tests/testX/*: several tests to check the program working.
locales/*/LC_MESSAGES/mpcotool.po: translation files.
manuals/*.eps: manual figures in EPS format.
manuals/*.png: manual figures in PNG format.
manuals/*.tex: documentation source files.
applications/*/*: several practical application cases.
check_errors/*.xml: several mistaken files to check error handling.

BUILDING INSTRUCTIONS

On Microsoft Windows systems you have to install MSYS2 and the required libraries and utilities. You can follow detailed instructions in install-unix. Optional Windows binary package can be built doing in the terminal:

$ make windist

On NetBSD 9.3, to compile with last GCC version you have to do first on the building terminal:

$ export PATH=/usr/pkg/gcc8/bin:$PATH"

On OpenBSD 7.6 you have to do first on the building terminal to select adequate versions and deactivate OpenMPI (does not link) building with CLang:

$ export AUTOCONF_VERSION=2.69 AUTOMAKE_VERSION=1.16 CC=clang

On OpenIndiana Hipster, in order to enable OpenMPI compilation, do in a terminal:

$ export PATH=$PATH:/usr/lib/openmpi/gcc/bin

On OpenSUSE Leap, in order to enable OpenMPI compilation, in 64 bits version do in a terminal (OpenMPI configure script does not work in last OpenSUSE versions then does not apply this step):

$ export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin

This software has been built and tested in the following operative systems:

Arch Linux
Debian Linux 12
Devuan Linux 4
DragonFly BSD 6.4
Fedora Linux 38
FreeBSD 13.2
Gentoo Linux
Linux Mint DE 5
MacOS Monterey + Homebrew
Manjaro Linux
Microsoft Windows 10 + MSYS2
NetBSD 9.3
OpenBSD 7.6
OpenInidiana Hipster
OpenSUSE Linux Leap 15.5
Ubuntu Linux 23.04

Probably, it can be built in other systems, distributions, or versions but it has not been tested.

Download the latest genetic doing on a terminal:

$ git clone https://github.com/jburguete/genetic.git

Build the genetic library:

$ cd genetic/3.0.1

$ sh build.sh

Download this repository:

$ cd ../..

$ git clone https://github.com/jburguete/mpcotool.git

Link the latest genetic version to genetic:

$ cd mpcotool/4.12.0

$ ln -s ../../genetic/3.0.1 genetic

$ ln -s genetic/libgenetic.so (or .dll in Windows systems)

Build doing on a terminal:

$ sh build.sh

Building no-GUI version on servers

On servers or clusters, where no-GUI with MPI parallelization is desirable, replace the 5th step of the previous section by:

$ sh build_without_gui.sh

Linking as an external library

MPCOTool can also be used as an external library:

First copy the dynamic libraries (libmpcotool.so and libgenetic.so on Unix systems or libmpcotool.dll and libgenetic.dll on Windows systems) to your program directory.
Include the function header in your source code:

extern int mpcotool (int argn, char **argc);

Build the executable file with the linker and compiler flags:

$ gcc -L. -Wl,-rpath=. -lmpcotool -lgenetic ... `pkg-config --cflags --libs gsl glib-2.0 json-glib-1.0 ...'

Calling to this function is equivalent to command line order (see next chapter USER INSTRUCTIONS):

argn: number of arguments
argc[0]: "mpcotool"
argc[1]: first command line argument.

...

argc[argn-1]: last argument.

FINAL VERSIONS

Optionally, final compact versions without debug information can be built doing on the terminal:

$ make strip

MAKING MANUALS INSTRUCTIONS

On UNIX type systems you need texlive installed. On Windows systems you need MiKTeX. In order to compile the manuals you can type on a terminal:

$ make manuals

MAKING TESTS INSTRUCTIONS

In order to build the tests follow the next instructions:

Link some tests that needs genetic library doing in a terminal (assuming that you are in the directory mpcotool/4.12.0):

$ cd ../tests/test2

$ ln -s ../../../genetic/3.0.1 genetic

$ ln -s genetic/libgenetic.so (or .dll on Windows systems)

$ cd ../test3

$ ln -s ../../../genetic/3.0.1 genetic

$ ln -s genetic/libgenetic.so (or .dll on Windows systems)

$ cd ../test4

$ ln -s ../../../genetic/3.0.1 genetic

$ ln -s genetic/libgenetic.so (or .dll on Windows systems)

Build all tests doing in the same terminal:

$ cd ../../4.12.0

$ make tests

USER INSTRUCTIONS

Optional arguments are typed in square brackets.

Command line in sequential mode (where X is the number of threads to execute and S is a seed for the pseudo-random numbers generator):

$ ./mpcotoolbin [-nthreads X] [-seed S] input_file.xml [result_file] [variables_file]

Command line in parallelized mode (where X is the number of threads to open for every node and S is a seed for the pseudo-random numbers generator):

$ mpirun [MPI options] ./mpcotoolbin [-nthreads X] [-seed S] input_file.xml [result_file] [variables_file]

The syntax of the simulator has to be:

$ ./simulator_name input_file_1 [input_file_2] [input_file_3] [input_file_4] output_file

The syntax of the program to evaluate the objetive function has to be (where the first data in the results file has to be the objective function value):

$ ./evaluator_name simulated_file data_file results_file

On UNIX type systems the GUI application can be open doing on a terminal:

$ ./mpcotool

INPUT FILE FORMAT

The format of the main input file is as:

<?xml version="1.0"?>
<optimize simulator="simulator_name" evaluator="evaluator_name" algorithm="algorithm_type" nsimulations="simulations_number" niterations="iterations_number" tolerance="tolerance_value" nbest="best_number" npopulation="population_number" ngenerations="generations_number" mutation="mutation_ratio" reproduction="reproduction_ratio" adaptation="adaptation_ratio" direction="direction_search_type" nsteps="steps_number" relaxation="relaxation_parameter" nestimates="estimates_number" threshold="threshold_parameter" norm="norm_type" p="p_parameter" seed="random_seed" result_file="result_file" variables_file="variables_file">
    <experiment name="data_file_1" template1="template_1_1" template2="template_1_2" ... weight="weight_1"/>
    ...
    <experiment name="data_file_N" template1="template_N_1" template2="template_N_2" ... weight="weight_N"/>
    <variable name="variable_1" minimum="min_value" maximum="max_value" precision="precision_digits" nsweeps="sweeps_number" nbits="bits_number" step="step_size"/>
    ...
    <variable name="variable_M" minimum="min_value" maximum="max_value" precision="precision_digits" nsweeps="sweeps_number" nbits="bits_number" step="step_size"/>
</optimize>

with:

simulator: simulator executable file name.
evaluator: optional. When needed is the evaluator executable file name.
seed: optional. Seed of the pseudo-random numbers generator (default value is 7007).
result_file: optional. It is the name of the optime result file (default name is "result").
variables_file: optional. It is the name of all simulated variables file (default name is "variables").
precision: optional, defined for each variable. Number of precision digits to evaluate the variable. 0 apply for integer numbers (default value is 14).
weight: optional, defined for each experiment. Multiplies the objective value obtained for each experiment in the final objective function value (default value is 1).
threshold: optional, to stop the simulations if objective function value less than the threshold is obtained (default value is 0).
algorithm: optimization algorithm type.
norm: error norm type.

Implemented algorithms are:

sweep: Sweep brute force algorithm. It requires for each variable:
- nsweeps: number of sweeps to generate for each variable in every experiment.
  
  The total number of simulations to run is:

(number of experiments) x (variable 1 number of sweeps) x ... x (variable n number of sweeps) x (number of iterations)

Monte-Carlo: Monte-Carlo brute force algorithm. It requires on calibrate:
- nsimulations: number of simulations to run in every experiment.
  
  The total number of simulations to run is:

(number of experiments) x (number of simulations) x (number of iterations)

orthogonal: Orthogonal sampling brute force algorithm. It requires for each variable:
- nsweeps: number of sweeps to generate for each variable in every experiment.
  
  The total number of simulations to run is:

(number of experiments) x (variable 1 number of sweeps) x ... x (variable n number of sweeps) x (number of iterations)

Three former brute force algorithms can be iterated to improve convergence by using the following parameters:
- nbest: number of best simulations to calculate convergence interval on next iteration (default 1).
- tolerance: tolerance parameter to increase convergence interval (default 0).
- niterations: number of iterations (default 1).
  
  It multiplies the total number of simulations:

x (number of iterations)

Moreover, brute force algorithms can be coupled with a direction search method by using:
- direction: method to estimate the optimal direction. Two options are currently available:
  - coordinates: coordinates descent method.
    
    It increases the total number of simulations by:

(number of experiments) x (number of iterations) x (number of steps) x 2 x (number of variables) * random: random method. It requires: * nestimates: number of random checks to estimate the optimal direction.

  It increases the total number of simulations by:

(number of experiments) x (number of iterations) x (number of steps) x (number of estimates)

Former methods require also: * nsteps: number of steps to perform the direction search method, * relaxation: relaxation parameter,

and for each variable: * step: initial step size for the direction search method.

genetic: Genetic algorithm. It requires the following parameters:
- npopulation: number of population.
- ngenerations: number of generations.
- mutation: mutation ratio.
- reproduction: reproduction ratio.
- adaptation: adaptation ratio.
and for each variable:
- nbits: number of bits to encode each variable.
The total number of simulations to run is:

(number of experiments) x (npopulation) x [1 + (ngenerations - 1) x (mutation + reproduction + adaptation)]

Implemented error noms are:

euclidian: Euclidian norm.
maximum: maximum norm.
p: p-norm. It requires the parameter:
- p: p exponent.
taxicab: Taxicab norm.

Alternatively, the input file can be also written in JSON format as:

{
	"simulator": "simulator_name",
	"evaluator": "evaluator_name",
	"algorithm": "algorithm_type",
	"nsimulations": "simulations_number",
	"niterations": "iterations_number",
	"tolerance": "tolerance_value",
	"nbest": "best_number",
	"npopulation": "population_number",
	"ngenerations": "generations_number",
	"mutation": "mutation_ratio",
	"reproduction": "reproduction_ratio",
	"adaptation": "adaptation_ratio",
	"direction": "direction_search_type",
	"nsteps": "steps_number",
	"relaxation": "relaxation_parameter",
	"nestimates": "estimates_number",
	"threshold": "threshold_parameter",
	"norm": "norm_type",
	"p": "p_parameter",
	"seed": "random_seed",
	"result_file": "result_file",
	"variables_file": "variables_file",
	"experiments":
	[
		{
			"name": "data_file_1",
			"template1": "template_1_1",
			"template2": "template_1_2",
			...
			"weight": "weight_1",
		},
		...
		{
			"name": "data_file_N",
			"template1": "template_N_1",
			"template2": "template_N_2",
			...
			"weight": "weight_N",
		}
	],
	"variables":
	[
		{

			"name": "variable_1",
			"minimum": "min_value",
			"maximum": "max_value",
			"precision": "precision_digits",
			"nsweeps": "sweeps_number",
			"nbits": "bits_number",
			"step": "step_size",
		},
		...
		{
			"name": "variable_M",
			"minimum": "min_value",
			"maximum": "max_value",
			"precision": "precision_digits",
			"nsweeps": "sweeps_number",
			"nbits": "bits_number",
			"step": "step_size",
		}
	]
}

SOME EXAMPLES OF INPUT FILES

Example 1

The simulator program name is: pivot
The syntax is:

$ ./pivot input_file output_file

The program to evaluate the objective function is: compare
The syntax is:

$ ./compare simulated_file data_file result_file

The calibration is performed with a sweep brute force algorithm.
The experimental data files are:

27-48.txt

42.txt

52.txt

100.txt

Templates to get input files to simulator for each experiment are:

template1.js

template2.js

template3.js

template4.js

The variables to calibrate, ranges, precision and sweeps number to perform are:

alpha1, [179.70, 180.20], 2, 5

alpha2, [179.30, 179.60], 2, 5

random, [0.00, 0.20], 2, 5

boot-time, [0.0, 3.0], 1, 5

Then, the number of simulations to run is: 4x5x5x5x5=2500.
The input file is:

<?xml version="1.0"?>
<optimize simulator="pivot" evaluator="compare" algorithm="sweep">
    <experiment name="27-48.txt" template1="template1.js"/>
    <experiment name="42.txt" template1="template2.js"/>
    <experiment name="52.txt" template1="template3.js"/>
    <experiment name="100.txt" template1="template4.js"/>
    <variable name="alpha1" minimum="179.70" maximum="180.20" precision="2" nsweeps="5"/>
    <variable name="alpha2" minimum="179.30" maximum="179.60" precision="2" nsweeps="5"/>
    <variable name="random" minimum="0.00" maximum="0.20" precision="2" nsweeps="5"/>
    <variable name="boot-time" minimum="0.0" maximum="3.0" precision="1" nsweeps="5"/>
</optimize>

A template file as template1.js:

    {
      "towers" :
      [
        {
          "length"      : 50.11,
          "velocity"    : 0.02738,
          "@variable1@" : @value1@,
          "@variable2@" : @value2@,
          "@variable3@" : @value3@,
          "@variable4@" : @value4@
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.02824,
          "@variable1@" : @value1@,
          "@variable2@" : @value2@,
          "@variable3@" : @value3@,
          "@variable4@" : @value4@
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.03008,
          "@variable1@" : @value1@,
          "@variable2@" : @value2@,
          "@variable3@" : @value3@,
          "@variable4@" : @value4@
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.03753,
          "@variable1@" : @value1@,
          "@variable2@" : @value2@,
          "@variable3@" : @value3@,
          "@variable4@" : @value4@
        }
      ],
      "cycle-time"     : 71.0,
      "plot-time"     : 1.0,
      "comp-time-step": 0.1,
      "active-percent" : 27.48
    }

produces simulator input files to reproduce the experimental data file 27-48.txt as:

    {
      "towers" :
      [
        {
          "length"      : 50.11,
          "velocity"    : 0.02738,
          "alpha1" : 179.95,
          "alpha2" : 179.45,
          "random" : 0.10,
          "boot-time" : 1.5
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.02824,
          "alpha1" : 179.95,
          "alpha2" : 179.45,
          "random" : 0.10,
          "boot-time" : 1.5
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.03008,
          "alpha1" : 179.95,
          "alpha2" : 179.45,
          "random" : 0.10,
          "boot-time" : 1.5
        },
        {
          "length"    : 50.11,
          "velocity"  : 0.03753,
          "alpha1" : 179.95,
          "alpha2" : 179.45,
          "random" : 0.10,
          "boot-time" : 1.5
        }
      ],
      "cycle-time"     : 71.0,
      "plot-time"     : 1.0,
      "comp-time-step": 0.1,
      "active-percent" : 27.48
    }

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MPCOTool

VERSIONS

AUTHORS

WINDOWS EXECUTABLE FILES

TOOLS AND LIBRARIES REQUIRED TO BUILD THE EXECUTABLE

OPTIONAL TOOLS AND LIBRARIES

FILES

BUILDING INSTRUCTIONS

MAKING MANUALS INSTRUCTIONS

MAKING TESTS INSTRUCTIONS

USER INSTRUCTIONS

INPUT FILE FORMAT

SOME EXAMPLES OF INPUT FILES

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Name		Name	Last commit message	Last commit date
Latest commit History 739 Commits
4.12.0		4.12.0
applications		applications
check_errors		check_errors
manuals		manuals
tests		tests
README.es.md		README.es.md
README.md		README.md
TODO		TODO
license.md		license.md
update_version.sh		update_version.sh
update_version_bsd.sh		update_version_bsd.sh

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WINDOWS EXECUTABLE FILES

TOOLS AND LIBRARIES REQUIRED TO BUILD THE EXECUTABLE

OPTIONAL TOOLS AND LIBRARIES

FILES

BUILDING INSTRUCTIONS

MAKING MANUALS INSTRUCTIONS

MAKING TESTS INSTRUCTIONS

USER INSTRUCTIONS

INPUT FILE FORMAT

SOME EXAMPLES OF INPUT FILES

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