nojhan/paradiseo
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

* New tree configuration of the project:

Browse source 
.../
   ...           + -- EO
   |             |
   |             |
   +-- src ----- + -- EDO
   |             |
   |             |
   +-- test      + -- MO
   |             |
   |             |
   +-- tutorial  + -- MOEO
   |             |
   |             |
   +-- doc       + -- SMP
   |             |
   |             |
   ...           + -- EOMPI
                 |
                 |
                 + -- EOSERIAL

Question for current maintainers: ./README: new release?

Also:

* Moving out eompi & eoserial modules (issue #2).

* Correction of the errors when executing "make doc" command.

* Adding a solution for the conflicting headers problem (see the two CMake Cache
 Values: PROJECT_TAG & PROJECT_HRS_INSTALL_SUBPATH) (issue #1)

* Header inclusions:
        ** src: changing absolute paths into relative paths ('#include <...>' -> '#include "..."')
        ** test, tutorial: changing relative paths into absolute paths ('#include "..."' -> '#include <...>')

* Moving out some scripts from EDO -> to the root

* Add a new script for compilation and installation (see build_gcc_linux_install)

* Compilation with uBLAS library or EDO module: now ok

* Minor modifications on README & INSTALL files

* Comment eompi failed tests with no end

*** TODO: CPack (debian (DEB) & RedHat (RPM) packages) (issues #6 & #7) ***
This commit is contained in:
Adèle Harrissart 2014-08-04 13:40:28 +02:00
commit 490e837f7a
2359 changed files with 7688 additions and 16329 deletions
Download patch file Download diff file Expand all files Collapse all files

53
test/CMakeLists.txt Executable file
View file

@ -0,0 +1,53 @@
## EO Module
add_subdirectory(${EO_TEST_DIR})
if(NOT EO_ONLY)
## MO Module
if(MO)
add_subdirectory(${MO_TEST_DIR})
endif(MO)
## EDO Module
if(EDO)
if(EDO_USE_LIB STREQUAL "Eigen3")
find_package(Eigen3)
if(EIGEN3_FOUND) # see edoNormalAdaptive
add_subdirectory(${EDO_TEST_DIR})
else(EIGEN3_FOUND)
message(FATAL_ERROR "\n\nERROR: You asked for Eigen3 but it has not been found.\n" )
endif(EIGEN3_FOUND)
elseif(EDO_USE_LIB STREQUAL "uBLAS")
find_package(Boost)
if(Boost_FOUND)
message("Warning: EDO_USE_LIB MATCHES ${EDO_USE_LIB} but Eigen3 recommended for tests")
add_subdirectory(${EDO_TEST_DIR})
else(Boost_FOUND)
message(FATAL_ERROR "\n\nERROR: You asked for Boost::uBLAS but it has not been found.\n" )
endif(Boost_FOUND)
else()
message(FATAL_ERROR "\n\nYou must set EDO_USE_LIB to either 'uBLAS' or 'Eigen3'.\n" )
endif()
endif(EDO)
## MOEO Module
if(MOEO)
add_subdirectory(${MOEO_TEST_DIR})
endif(MOEO)
## SMP Module
if(SMP)
add_subdirectory(${SMP_TEST_DIR})
endif(SMP)
## EOMPI Module
if(EOMPI)
add_subdirectory(${EOMPI_TEST_DIR})
endif(EOMPI)
## EOSERIAL Module
#if(EOSERIAL)
# add_subdirectory(${EOSERIAL_TEST_DIR})
#endif(EOSERIAL)
endif()

59
test/edo/CMakeLists.txt Executable file
View file

@ -0,0 +1,59 @@
###############################################################################
##
## CMakeLists file for unit test
##
###############################################################################
######################################################################################
### 1) Include the sources
######################################################################################
#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
#include_directories(${CMAKE_SOURCE_DIR}/application/common)
include_directories(${EDO_TUTORIAL_DIR}/common)
#include_directories(${EO_SRC_DIR}/src)
#include_directories(${EDO_SRC_DIR}/src)
######################################################################################
### 2) Specify where CMake can find the libraries
######################################################################################
if(EDO_USE_LIB STREQUAL "Eigen3")
find_package(Eigen3)
include_directories( ${EIGEN3_INCLUDE_DIR} )
add_definitions( -DWITH_EIGEN )
elseif(EDO_USE_LIB STREQUAL "uBLAS")
find_package(Boost)
include_directories( ${Boost_INCLUDE_DIRS} )
add_definitions( -DWITH_BOOST )
else()
message(FATAL_ERROR "\n\nYou must set EDO_USE_LIB to either 'uBLAS' or 'Eigen3'.\n" )
endif()
######################################################################################
### 3) Define your targets and link the librairies
######################################################################################
set(SOURCES
#t-cholesky
t-variance
t-edoEstimatorNormalMulti
t-mean-distance
t-bounderno
t-uniform
t-continue
# t-dispatcher-round
t-repairer-modulo
t-binomial
t-binomialmulti
)
foreach(current ${SOURCES})
add_executable(${current} ${current}.cpp)
add_test(${current} ${current})
target_link_libraries(${current} eo eoutils edoutils)
install(TARGETS ${current} RUNTIME DESTINATION share/edo/test COMPONENT test)
endforeach()
######################################################################################

502
test/edo/COPYING Executable file
View file

@ -0,0 +1,502 @@
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
Licenses are intended to guarantee your freedom to share and change
free software--to make sure the software is free for all its users.
This license, the Lesser General Public License, applies to some
specially designated software packages--typically libraries--of the
Free Software Foundation and other authors who decide to use it. You
can use it too, but we suggest you first think carefully about whether
this license or the ordinary General Public License is the better
strategy to use in any particular case, based on the explanations below.
When we speak of free software, we are referring to freedom of use,
not price. Our General Public Licenses are designed to make sure that
you have the freedom to distribute copies of free software (and charge
for this service if you wish); that you receive source code or can get
it if you want it; that you can change the software and use pieces of
it in new free programs; and that you are informed that you can do
these things.
To protect your rights, we need to make restrictions that forbid
distributors to deny you these rights or to ask you to surrender these
rights. These restrictions translate to certain responsibilities for
you if you distribute copies of the library or if you modify it.
For example, if you distribute copies of the library, whether gratis
or for a fee, you must give the recipients all the rights that we gave
you. You must make sure that they, too, receive or can get the source
code. If you link other code with the library, you must provide
complete object files to the recipients, so that they can relink them
with the library after making changes to the library and recompiling
it. And you must show them these terms so they know their rights.
We protect your rights with a two-step method: (1) we copyright the
library, and (2) we offer you this license, which gives you legal
permission to copy, distribute and/or modify the library.
To protect each distributor, we want to make it very clear that
there is no warranty for the free library. Also, if the library is
modified by someone else and passed on, the recipients should know
that what they have is not the original version, so that the original
author's reputation will not be affected by problems that might be
introduced by others.
Finally, software patents pose a constant threat to the existence of
any free program. We wish to make sure that a company cannot
effectively restrict the users of a free program by obtaining a
restrictive license from a patent holder. Therefore, we insist that
any patent license obtained for a version of the library must be
consistent with the full freedom of use specified in this license.
Most GNU software, including some libraries, is covered by the
ordinary GNU General Public License. This license, the GNU Lesser
General Public License, applies to certain designated libraries, and
is quite different from the ordinary General Public License. We use
this license for certain libraries in order to permit linking those
libraries into non-free programs.
When a program is linked with a library, whether statically or using
a shared library, the combination of the two is legally speaking a
combined work, a derivative of the original library. The ordinary
General Public License therefore permits such linking only if the
entire combination fits its criteria of freedom. The Lesser General
Public License permits more lax criteria for linking other code with
the library.
We call this license the "Lesser" General Public License because it
does Less to protect the user's freedom than the ordinary General
Public License. It also provides other free software developers Less
of an advantage over competing non-free programs. These disadvantages
are the reason we use the ordinary General Public License for many
libraries. However, the Lesser license provides advantages in certain
special circumstances.
For example, on rare occasions, there may be a special need to
encourage the widest possible use of a certain library, so that it becomes
a de-facto standard. To achieve this, non-free programs must be
allowed to use the library. A more frequent case is that a free
library does the same job as widely used non-free libraries. In this
case, there is little to gain by limiting the free library to free
software only, so we use the Lesser General Public License.
In other cases, permission to use a particular library in non-free
programs enables a greater number of people to use a large body of
free software. For example, permission to use the GNU C Library in
non-free programs enables many more people to use the whole GNU
operating system, as well as its variant, the GNU/Linux operating
system.
Although the Lesser General Public License is Less protective of the
users' freedom, it does ensure that the user of a program that is
linked with the Library has the freedom and the wherewithal to run
that program using a modified version of the Library.
The precise terms and conditions for copying, distribution and
modification follow. Pay close attention to the difference between a
"work based on the library" and a "work that uses the library". The
former contains code derived from the library, whereas the latter must
be combined with the library in order to run.
GNU LESSER GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other
program which contains a notice placed by the copyright holder or
other authorized party saying it may be distributed under the terms of
this Lesser General Public License (also called "this License").
Each licensee is addressed as "you".
A "library" means a collection of software functions and/or data
prepared so as to be conveniently linked with application programs
(which use some of those functions and data) to form executables.
The "Library", below, refers to any such software library or work
which has been distributed under these terms. A "work based on the
Library" means either the Library or any derivative work under
copyright law: that is to say, a work containing the Library or a
portion of it, either verbatim or with modifications and/or translated
straightforwardly into another language. (Hereinafter, translation is
included without limitation in the term "modification".)
"Source code" for a work means the preferred form of the work for
making modifications to it. For a library, complete source code means
all the source code for all modules it contains, plus any associated
interface definition files, plus the scripts used to control compilation
and installation of the library.
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running a program using the Library is not restricted, and output from
such a program is covered only if its contents constitute a work based
on the Library (independent of the use of the Library in a tool for
writing it). Whether that is true depends on what the Library does
and what the program that uses the Library does.
1. You may copy and distribute verbatim copies of the Library's
complete source code as you receive it, in any medium, provided that
you conspicuously and appropriately publish on each copy an
appropriate copyright notice and disclaimer of warranty; keep intact
all the notices that refer to this License and to the absence of any
warranty; and distribute a copy of this License along with the
Library.
You may charge a fee for the physical act of transferring a copy,
and you may at your option offer warranty protection in exchange for a
fee.
2. You may modify your copy or copies of the Library or any portion
of it, thus forming a work based on the Library, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) The modified work must itself be a software library.
b) You must cause the files modified to carry prominent notices
stating that you changed the files and the date of any change.
c) You must cause the whole of the work to be licensed at no
charge to all third parties under the terms of this License.
d) If a facility in the modified Library refers to a function or a
table of data to be supplied by an application program that uses
the facility, other than as an argument passed when the facility
is invoked, then you must make a good faith effort to ensure that,
in the event an application does not supply such function or
table, the facility still operates, and performs whatever part of
its purpose remains meaningful.
(For example, a function in a library to compute square roots has
a purpose that is entirely well-defined independent of the
application. Therefore, Subsection 2d requires that any
application-supplied function or table used by this function must
be optional: if the application does not supply it, the square
root function must still compute square roots.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Library,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Library, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote
it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Library.
In addition, mere aggregation of another work not based on the Library
with the Library (or with a work based on the Library) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may opt to apply the terms of the ordinary GNU General Public
License instead of this License to a given copy of the Library. To do
this, you must alter all the notices that refer to this License, so
that they refer to the ordinary GNU General Public License, version 2,
instead of to this License. (If a newer version than version 2 of the
ordinary GNU General Public License has appeared, then you can specify
that version instead if you wish.) Do not make any other change in
these notices.
Once this change is made in a given copy, it is irreversible for
that copy, so the ordinary GNU General Public License applies to all
subsequent copies and derivative works made from that copy.
This option is useful when you wish to copy part of the code of
the Library into a program that is not a library.
4. You may copy and distribute the Library (or a portion or
derivative of it, under Section 2) in object code or executable form
under the terms of Sections 1 and 2 above provided that you accompany
it with the complete corresponding machine-readable source code, which
must be distributed under the terms of Sections 1 and 2 above on a
medium customarily used for software interchange.
If distribution of object code is made by offering access to copy
from a designated place, then offering equivalent access to copy the
source code from the same place satisfies the requirement to
distribute the source code, even though third parties are not
compelled to copy the source along with the object code.
5. A program that contains no derivative of any portion of the
Library, but is designed to work with the Library by being compiled or
linked with it, is called a "work that uses the Library". Such a
work, in isolation, is not a derivative work of the Library, and
therefore falls outside the scope of this License.
However, linking a "work that uses the Library" with the Library
creates an executable that is a derivative of the Library (because it
contains portions of the Library), rather than a "work that uses the
library". The executable is therefore covered by this License.
Section 6 states terms for distribution of such executables.
When a "work that uses the Library" uses material from a header file
that is part of the Library, the object code for the work may be a
derivative work of the Library even though the source code is not.
Whether this is true is especially significant if the work can be
linked without the Library, or if the work is itself a library. The
threshold for this to be true is not precisely defined by law.
If such an object file uses only numerical parameters, data
structure layouts and accessors, and small macros and small inline
functions (ten lines or less in length), then the use of the object
file is unrestricted, regardless of whether it is legally a derivative
work. (Executables containing this object code plus portions of the
Library will still fall under Section 6.)
Otherwise, if the work is a derivative of the Library, you may
distribute the object code for the work under the terms of Section 6.
Any executables containing that work also fall under Section 6,
whether or not they are linked directly with the Library itself.
6. As an exception to the Sections above, you may also combine or
link a "work that uses the Library" with the Library to produce a
work containing portions of the Library, and distribute that work
under terms of your choice, provided that the terms permit
modification of the work for the customer's own use and reverse
engineering for debugging such modifications.
You must give prominent notice with each copy of the work that the
Library is used in it and that the Library and its use are covered by
this License. You must supply a copy of this License. If the work
during execution displays copyright notices, you must include the
copyright notice for the Library among them, as well as a reference
directing the user to the copy of this License. Also, you must do one
of these things:
a) Accompany the work with the complete corresponding
machine-readable source code for the Library including whatever
changes were used in the work (which must be distributed under
Sections 1 and 2 above); and, if the work is an executable linked
with the Library, with the complete machine-readable "work that
uses the Library", as object code and/or source code, so that the
user can modify the Library and then relink to produce a modified
executable containing the modified Library. (It is understood
that the user who changes the contents of definitions files in the
Library will not necessarily be able to recompile the application
to use the modified definitions.)
b) Use a suitable shared library mechanism for linking with the
Library. A suitable mechanism is one that (1) uses at run time a
copy of the library already present on the user's computer system,
rather than copying library functions into the executable, and (2)
will operate properly with a modified version of the library, if
the user installs one, as long as the modified version is
interface-compatible with the version that the work was made with.
c) Accompany the work with a written offer, valid for at
least three years, to give the same user the materials
specified in Subsection 6a, above, for a charge no more
than the cost of performing this distribution.
d) If distribution of the work is made by offering access to copy
from a designated place, offer equivalent access to copy the above
specified materials from the same place.
e) Verify that the user has already received a copy of these
materials or that you have already sent this user a copy.
For an executable, the required form of the "work that uses the
Library" must include any data and utility programs needed for
reproducing the executable from it. However, as a special exception,
the materials to be distributed need not include anything that is
normally distributed (in either source or binary form) with the major
components (compiler, kernel, and so on) of the operating system on
which the executable runs, unless that component itself accompanies
the executable.
It may happen that this requirement contradicts the license
restrictions of other proprietary libraries that do not normally
accompany the operating system. Such a contradiction means you cannot
use both them and the Library together in an executable that you
distribute.
7. You may place library facilities that are a work based on the
Library side-by-side in a single library together with other library
facilities not covered by this License, and distribute such a combined
library, provided that the separate distribution of the work based on
the Library and of the other library facilities is otherwise
permitted, and provided that you do these two things:
a) Accompany the combined library with a copy of the same work
based on the Library, uncombined with any other library
facilities. This must be distributed under the terms of the
Sections above.
b) Give prominent notice with the combined library of the fact
that part of it is a work based on the Library, and explaining
where to find the accompanying uncombined form of the same work.
8. You may not copy, modify, sublicense, link with, or distribute
the Library except as expressly provided under this License. Any
attempt otherwise to copy, modify, sublicense, link with, or
distribute the Library is void, and will automatically terminate your
rights under this License. However, parties who have received copies,
or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.
9. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Library or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Library (or any work based on the
Library), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Library or works based on it.
10. Each time you redistribute the Library (or any work based on the
Library), the recipient automatically receives a license from the
original licensor to copy, distribute, link with or modify the Library
subject to these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties with
this License.
11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Library at all. For example, if a patent
license would not permit royalty-free redistribution of the Library by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Library.
If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply,
and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
12. If the distribution and/or use of the Library is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Library under this License may add
an explicit geographical distribution limitation excluding those countries,
so that distribution is permitted only in or among countries not thus
excluded. In such case, this License incorporates the limitation as if
written in the body of this License.
13. The Free Software Foundation may publish revised and/or new
versions of the Lesser General Public License from time to time.
Such new versions will be similar in spirit to the present version,
but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Library
specifies a version number of this License which applies to it and
"any later version", you have the option of following the terms and
conditions either of that version or of any later version published by
the Free Software Foundation. If the Library does not specify a
license version number, you may choose any version ever published by
the Free Software Foundation.
14. If you wish to incorporate parts of the Library into other free
programs whose distribution conditions are incompatible with these,
write to the author to ask for permission. For software which is
copyrighted by the Free Software Foundation, write to the Free
Software Foundation; we sometimes make exceptions for this. Our
decision will be guided by the two goals of preserving the free status
of all derivatives of our free software and of promoting the sharing
and reuse of software generally.
NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest
possible use to the public, we recommend making it free software that
everyone can redistribute and change. You can do so by permitting
redistribution under these terms (or, alternatively, under the terms of the
ordinary General Public License).
To apply these terms, attach the following notices to the library. It is
safest to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
<one line to give the library's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the library, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!

19
test/edo/boxplot.py Executable file
View file

@ -0,0 +1,19 @@
#!/usr/bin/env python
from pylab import *
FILE_LOCATIONS = 'means_distances_results/files_description.txt'
data = []
locations = [ line.split()[0] for line in open( FILE_LOCATIONS ) ]
for cur_file in locations:
data.append( [ float(line.split()[7]) for line in open( cur_file ).readlines() ] )
print locations
#print data
boxplot( data )
show()

104
test/edo/t-binomial.cpp Executable file
View file

@ -0,0 +1,104 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2013 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
#include <vector>
#include <iostream>
#include <string>
#include <cmath>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/ga.h> // for Bools
template<class T>
void print( T v, std::string sep=" " )
{
for( typename T::iterator it=v.begin(); it!=v.end(); ++it ) {
std::cout << *it << sep;
}
std::cout << std::endl;
}
int main(int ac, char** av)
{
typedef eoBit<double> Bools;
eoParser parser(ac, av);
std::string section("Algorithm parameters");
unsigned int popsize = parser.createParam((unsigned int)100000, "popSize", "Population Size", 'P', section).value(); // P
unsigned int dim = parser.createParam((unsigned int)20, "dim", "Dimension size", 'd', section).value(); // d
double proba = parser.createParam((double)0.5, "proba", "Probability to estimate", 'b', section).value(); // b
if( parser.userNeedsHelp() ) {
parser.printHelp(std::cout);
exit(1);
}
make_help(parser);
// This generate a random boolean when called...
eoBooleanGenerator flip( proba );
// ... by this initializator...
eoInitFixedLength<Bools> init( dim, flip );
// ... when building this pop.
std::cout << "Init a pop of eoBit of size " << popsize << " at random with p(x=1)=" << proba << std::endl;
eoPop<Bools> pop( popsize, init );
// print( pop, "\n" );
// EDO triplet
edoBinomial<Bools> distrib(dim,0.0);
edoEstimatorBinomial<Bools> estimate;
edoSamplerBinomial<Bools> sample;
std::cout << "Estimate a distribution from the init pop" << std::endl;
distrib = estimate(pop);
print( distrib );
// std::cout << std::endl;
std::cout << "Sample a new pop from the init distrib" << std::endl;
pop.clear();
for( unsigned int i=0; i<popsize; ++i ) {
pop.push_back( sample( distrib ) );
}
// print( pop, "\n" );
std::cout << "Estimate a distribution from the sampled pop" << std::endl;
distrib = estimate(pop);
print( distrib );
// std::cout << std::endl;
double sum=0;
for( unsigned int i=0; i<distrib.size(); ++i ) {
sum += distrib[i];
}
double e = sum / dim;
std::cout << "Estimated initial proba = " << e << std::endl;
}

95
test/edo/t-binomialmulti.cpp Executable file
View file

@ -0,0 +1,95 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2013 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
#include <vector>
#include <iostream>
#include <string>
#include <cmath>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/ga.h> // for Bools
#ifdef WITH_EIGEN
#include <Eigen/Dense>
#endif // WITH_EIGEN
#ifdef WITH_EIGEN
// NOTE: a typedef on eoVector does not work, because of readFrom on a vector AtomType
// typedef eoVector<eoMinimizingFitness, std::vector<bool> > Bools;
class Bools : public std::vector<std::vector<bool> >, public EO<double>
{
public:
typedef std::vector<bool> AtomType;
};
#endif
int main(int ac, char** av)
{
#ifdef WITH_EIGEN
eoParser parser(ac, av);
std::string section("Algorithm parameters");
unsigned int popsize = parser.createParam((unsigned int)100000, "popSize", "Population Size", 'P', section).value(); // P
unsigned int rows = parser.createParam((unsigned int)2, "lines", "Lines number", 'l', section).value(); // l
unsigned int cols = parser.createParam((unsigned int)3, "columns", "Columns number", 'c', section).value(); // c
double proba = parser.createParam((double)0.5, "proba", "Probability to estimate", 'b', section).value(); // b
if( parser.userNeedsHelp() ) {
parser.printHelp(std::cout);
exit(1);
}
make_help(parser);
std::cout << "Init distrib" << std::endl;
Eigen::MatrixXd initd = Eigen::MatrixXd::Constant(rows,cols,proba);
edoBinomialMulti<Bools> distrib( initd );
std::cout << distrib << std::endl;
edoEstimatorBinomialMulti<Bools> estimate;
edoSamplerBinomialMulti<Bools> sample;
std::cout << "Sample a pop from the init distrib" << std::endl;
eoPop<Bools> pop; pop.reserve(popsize);
for( unsigned int i=0; i < popsize; ++i ) {
pop.push_back( sample( distrib ) );
}
std::cout << "Estimate a distribution from the sampled pop" << std::endl;
distrib = estimate( pop );
std::cout << distrib << std::endl;
std::cout << "Estimated initial proba = " << distrib.mean() << std::endl;
#else
#ifdef WITH_BOOST
#pragma message "WARNING: there is no Boost::uBLAS implementation of t-binomialmulti, build WITH_EIGEN if you need it."
#endif
#endif // WITH_EIGEN
return 0;
}

40
test/edo/t-bounderno.cpp Executable file
View file

@ -0,0 +1,40 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include "Rosenbrock.h"
typedef eoReal< eoMinimizingFitness > EOT;
int main(void)
{
edoBounderNo< EOT > bounder;
return 0;
}

250
test/edo/t-cholesky.cpp Executable file
View file

@ -0,0 +1,250 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
//#include <vector>
#include <cstdlib>
#include <iostream>
#include <sstream>
#include <limits>
#include <iomanip>
#include <ctime>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/es.h>
typedef eoReal< eoMinimizingFitness > EOT;
typedef edoNormalMulti<EOT> EOD;
void setformat( std::ostream& out )
{
out << std::right;
out << std::setfill(' ');
out << std::setw( 5 + std::numeric_limits<double>::digits10);
out << std::setprecision(std::numeric_limits<double>::digits10);
out << std::setiosflags(std::ios_base::showpoint);
}
template<typename MT>
std::string format(const MT& mat )
{
std::ostringstream out;
setformat(out);
for( unsigned int i=0; i<mat.size1(); ++i) {
for( unsigned int j=0; j<mat.size2(); ++j) {
out << mat(i,j) << "\t";
} // columns
out << std::endl;
} // rows
return out.str();
}
template< typename T >
T round( T val, T prec = 1.0 )
{
return (val > 0.0) ?
floor(val * prec + 0.5) / prec :
ceil(val * prec - 0.5) / prec ;
}
template<typename MT>
bool equal( const MT& M1, const MT& M2, double prec /* = 1/std::numeric_limits<double>::digits10 ???*/ )
{
if( M1.size1() != M2.size1() || M1.size2() != M2.size2() ) {
return false;
}
for( unsigned int i=0; i<M1.size1(); ++i ) {
for( unsigned int j=0; j<M1.size2(); ++j ) {
if( round(M1(i,j),prec) != round(M2(i,j),prec) ) {
std::cout << "round(M(" << i << "," << j << "," << prec << ") == "
<< round(M1(i,j),prec) << " != " << round(M2(i,j),prec) << std::endl;
return false;
}
}
}
return true;
}
template<typename MT >
MT error( const MT& M1, const MT& M2 )
{
assert( M1.size1() == M2.size1() && M1.size1() == M2.size2() );
MT Err = ublas::zero_matrix<double>(M1.size1(),M1.size2());
for( unsigned int i=0; i<M1.size1(); ++i ) {
for( unsigned int j=0; j<M1.size2(); ++j ) {
Err(i,j) = M1(i,j) - M2(i,j);
}
}
return Err;
}
template<typename MT >
double trigsum( const MT& M )
{
double sum;
for( unsigned int i=0; i<M.size1(); ++i ) {
for( unsigned int j=i; j<M.size2(); ++j ) { // triangular browsing
sum += fabs( M(i,j) ); // absolute deviation
}
}
return sum;
}
template<typename T>
double sum( const T& c )
{
return std::accumulate(c.begin(), c.end(), 0);
}
int main(int argc, char** argv)
{
srand(time(0));
unsigned int N = 4; // size of matrix
unsigned int R = 1000; // nb of repetitions
if( argc >= 2 ) {
N = std::atoi(argv[1]);
}
if( argc >= 3 ) {
R = std::atoi(argv[2]);
}
std::cout << "Usage: t-cholesky [matrix size] [repetitions]" << std::endl;
std::cout << "matrix size = " << N << std::endl;
std::cout << "repetitions = " << R << std::endl;
typedef edoSamplerNormalMulti<EOT,EOD>::Cholesky::CovarMat CovarMat;
typedef edoSamplerNormalMulti<EOT,EOD>::Cholesky::FactorMat FactorMat;
edoSamplerNormalMulti<EOT,EOD>::Cholesky LLT( edoSamplerNormalMulti<EOT,EOD>::Cholesky::standard );
edoSamplerNormalMulti<EOT,EOD>::Cholesky LLTa( edoSamplerNormalMulti<EOT,EOD>::Cholesky::absolute );
edoSamplerNormalMulti<EOT,EOD>::Cholesky LLTz( edoSamplerNormalMulti<EOT,EOD>::Cholesky::zeroing );
edoSamplerNormalMulti<EOT,EOD>::Cholesky LDLT( edoSamplerNormalMulti<EOT,EOD>::Cholesky::robust );
std::vector<double> s0,s1,s2,s3;
for( unsigned int n=0; n<R; ++n ) {
// a variance-covariance matrix of size N*N
CovarMat V(N,N);
// random covariance matrix
for( unsigned int i=0; i<N; ++i) {
V(i,i) = std::pow(rand(),2); // variance should be >= 0
for( unsigned int j=i+1; j<N; ++j) {
V(i,j) = rand();
}
}
FactorMat L0 = LLT(V);
CovarMat V0 = ublas::prod( L0, ublas::trans(L0) );
s0.push_back( trigsum(error(V,V0)) );
FactorMat L1 = LLTa(V);
CovarMat V1 = ublas::prod( L1, ublas::trans(L1) );
s1.push_back( trigsum(error(V,V1)) );
FactorMat L2 = LLTz(V);
CovarMat V2 = ublas::prod( L2, ublas::trans(L2) );
s2.push_back( trigsum(error(V,V2)) );
FactorMat L3 = LDLT(V);
CovarMat V3 = ublas::prod( L3, ublas::trans(L3) );
s3.push_back( trigsum(error(V,V3)) );
}
std::cout << "Average error:" << std::endl;
std::cout << "\tLLT: " << sum(s0)/R << std::endl;
std::cout << "\tLLTa: " << sum(s1)/R << std::endl;
std::cout << "\tLLTz: " << sum(s2)/R << std::endl;
std::cout << "\tLDLT: " << sum(s3)/R << std::endl;
// double precision = 1e-15;
// if( argc >= 4 ) {
// precision = std::atof(argv[3]);
// }
// std::cout << "precision = " << precision << std::endl;
// std::cout << "usage: t-cholesky [N] [precision]" << std::endl;
// std::cout << "N = " << N << std::endl;
// std::cout << "precision = " << precision << std::endl;
// std::string linesep = "--------------------------------------------------------------------------------------------";
// std::cout << linesep << std::endl;
//
// setformat(std::cout);
//
// std::cout << "Covariance matrix" << std::endl << format(V) << std::endl;
// std::cout << linesep << std::endl;
//
// edoSamplerNormalMulti<EOT,EOD>::Cholesky LLT( edoSamplerNormalMulti<EOT,EOD>::Cholesky::standard );
// FactorMat L0 = LLT(V);
// CovarMat V0 = ublas::prod( L0, ublas::trans(L0) );
// CovarMat E0 = error(V,V0);
// std::cout << "LLT" << std::endl << format(E0) << std::endl;
// std::cout << trigsum(E0) << std::endl;
// std::cout << "LLT" << std::endl << format(L0) << std::endl;
// std::cout << "LLT covar" << std::endl << format(V0) << std::endl;
// assert( equal(V0,V,precision) );
// std::cout << linesep << std::endl;
//
// edoSamplerNormalMulti<EOT,EOD>::Cholesky LLTa( edoSamplerNormalMulti<EOT,EOD>::Cholesky::absolute );
// FactorMat L1 = LLTa(V);
// CovarMat V1 = ublas::prod( L1, ublas::trans(L1) );
// CovarMat E1 = error(V,V1);
// std::cout << "LLT abs" << std::endl << format(E1) << std::endl;
// std::cout << trigsum(E1) << std::endl;
// std::cout << "LLT abs" << std::endl << format(L1) << std::endl;
// std::cout << "LLT covar" << std::endl << format(V1) << std::endl;
// assert( equal(V1,V,precision) );
// std::cout << linesep << std::endl;
//
// edoSamplerNormalMulti<EOT,EOD>::Cholesky LDLT( edoSamplerNormalMulti<EOT,EOD>::Cholesky::robust );
// FactorMat L2 = LDLT(V);
// CovarMat V2 = ublas::prod( L2, ublas::trans(L2) );
// CovarMat E2 = error(V,V2);
// std::cout << "LDLT" << std::endl << format(E2) << std::endl;
// std::cout << trigsum(E2) << std::endl;
// std::cout << "LDLT" << std::endl << format(L2) << std::endl;
// std::cout << "LDLT covar" << std::endl << format(V2) << std::endl;
// assert( equal(V2,V,precision) );
// std::cout << linesep << std::endl;
}

44
test/edo/t-continue.cpp Executable file
View file

@ -0,0 +1,44 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include "Rosenbrock.h"
typedef eoReal< eoMinimizingFitness > EOT;
typedef edoUniform< EOT > Distrib;
int main(void)
{
eoState state;
edoContinue< Distrib >* continuator = new edoDummyContinue< Distrib >();
state.storeFunctor(continuator);
return 0;
}

81
test/edo/t-dispatcher-round.cpp Executable file
View file

@ -0,0 +1,81 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Pierre Savéant <pierre.saveant@thalesgroup.com>
*/
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/es.h>
typedef eoReal< eoMinimizingFitness > EOT;
int main(void)
{
EOT sol;
sol.push_back(1.1);
sol.push_back(1.1);
sol.push_back(3.9);
sol.push_back(3.9);
sol.push_back(5.4);
sol.push_back(5.6);
sol.push_back(7.011);
sol.push_back(8.09);
sol.push_back(8.21);
std::cout << "expect: INVALID 9 1 2 3 4 5 6 7 8.1 8.2" << std::endl;
edoRepairer<EOT>* rep1 = new edoRepairerFloor<EOT>();
edoRepairer<EOT>* rep2 = new edoRepairerCeil<EOT>();
edoRepairer<EOT>* rep3 = new edoRepairerRound<EOT>();
edoRepairer<EOT>* rep4 = new edoRepairerRoundDecimals<EOT>( 10 );
std::vector<unsigned int> indexes1;
indexes1.push_back(0);
indexes1.push_back(2);
std::vector<unsigned int> indexes2;
indexes2.push_back(1);
indexes2.push_back(3);
std::vector<unsigned int> indexes3;
indexes3.push_back(4);
indexes3.push_back(5);
std::vector<unsigned int> indexes4;
indexes4.push_back(6);
indexes4.push_back(7);
indexes4.push_back(8);
edoRepairerDispatcher<EOT> repare( indexes1, rep1 );
repare.add( indexes2, rep2 );
repare.add( indexes3, rep3 );
repare.add( indexes4, rep4 );
repare(sol);
std::cout << sol << std::endl;
return 0;
}

198
test/edo/t-edoEstimatorNormalMulti.cpp Executable file
View file

@ -0,0 +1,198 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include <sstream>
#include <iomanip>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
//#include <paradiseo/mo.h>
#include "Rosenbrock.h"
#include "Sphere.h"
typedef eoReal< eoMinimizingFitness > EOT;
typedef edoNormalMulti< EOT > Distrib;
typedef EOT::AtomType AtomType;
#ifdef WITH_BOOST
#include <boost/numeric/ublas/vector.hpp>
#include <boost/numeric/ublas/symmetric.hpp>
typedef ublas::vector< AtomType > Vector;
typedef ublas::symmetric_matrix< AtomType, ublas::lower > Matrix;
#else
#ifdef WITH_EIGEN
#include <Eigen/Dense>
typedef edoNormalMulti<EOT>::Vector Vector;
typedef edoNormalMulti<EOT>::Matrix Matrix;
#endif
#endif
int main(int ac, char** av)
{
// (0) parser + eo routines
eoParser parser(ac, av);
std::string section("Algorithm parameters");
unsigned int p_size = parser.createParam((unsigned int)100, "popSize", "Population Size", 'P', section).value(); // P
unsigned int s_size = parser.createParam((unsigned int)2, "dimension-size", "Dimension size", 'd', section).value(); // d
AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m
AtomType covar1_value = parser.createParam((AtomType)1.0, "covar1", "Covar value 1", '1', section).value();
AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value();
AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value();
std::ostringstream ss;
ss << p_size << "_" << std::fixed << std::setprecision(1)
<< mean_value << "_" << covar1_value << "_" << covar2_value << "_"
<< covar3_value << "_gen";
std::string gen_filename = ss.str();
if( parser.userNeedsHelp() ) {
parser.printHelp(std::cout);
exit(1);
}
make_verbose(parser);
make_help(parser);
assert(p_size > 0);
assert(s_size > 0);
eoState state;
// (1) Population init and sampler
eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5);
state.storeFunctor(gen);
eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen );
state.storeFunctor(init);
// create an empty pop and let the state handle the memory
// fill population thanks to eoInit instance
eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) );
// (2) distribution initial parameters
Vector mean( s_size );
for (unsigned int i = 0; i < s_size; ++i) {
mean( i ) = mean_value;
}
Matrix varcovar( s_size, s_size );
varcovar( 0, 0 ) = covar1_value;
varcovar( 0, 1 ) = covar2_value;
varcovar( 1, 1 ) = covar3_value;
Distrib distrib( mean, varcovar );
// (3a) distribution output preparation
edoDummyContinue< Distrib >* distrib_dummy_continue = new edoDummyContinue< Distrib >();
state.storeFunctor(distrib_dummy_continue);
edoCheckPoint< Distrib >* distrib_continue = new edoCheckPoint< Distrib >( *distrib_dummy_continue );
state.storeFunctor(distrib_continue);
edoDistribStat< Distrib >* distrib_stat = new edoStatNormalMulti< EOT >();
state.storeFunctor(distrib_stat);
distrib_continue->add( *distrib_stat );
edoFileSnapshot* distrib_file_snapshot = new edoFileSnapshot( "TestResDistrib", 1, gen_filename );
state.storeFunctor(distrib_file_snapshot);
distrib_file_snapshot->add(*distrib_stat);
distrib_continue->add(*distrib_file_snapshot);
// (3b) distribution output
(*distrib_continue)( distrib );
// Prepare bounder class to set bounds of sampling.
// This is used by edoSampler.
edoBounder< EOT >* bounder = new edoBounderRng< EOT >(
EOT(pop[0].size(), -5), EOT(pop[0].size(), 5), *gen
);
state.storeFunctor(bounder);
// Prepare sampler class with a specific distribution
edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder );
state.storeFunctor(sampler);
// (4) sampling phase
pop.clear();
for( unsigned int i = 0; i < p_size; ++i ) {
EOT candidate_solution = (*sampler)( distrib );
pop.push_back( candidate_solution );
}
// (5) population output
eoContinue< EOT >* pop_cont = new eoGenContinue< EOT >( 2 ); // never reached fitness
state.storeFunctor(pop_cont);
eoCheckPoint< EOT >* pop_continue = new eoCheckPoint< EOT >( *pop_cont );
state.storeFunctor(pop_continue);
edoPopStat< EOT >* pop_stat = new edoPopStat<EOT>;
state.storeFunctor(pop_stat);
pop_continue->add(*pop_stat);
edoFileSnapshot* pop_file_snapshot = new edoFileSnapshot( "TestResPop", 1, gen_filename );
state.storeFunctor(pop_file_snapshot);
pop_file_snapshot->add(*pop_stat);
pop_continue->add(*pop_file_snapshot);
(*pop_continue)( pop );
// (6) estimation phase
edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >();
state.storeFunctor(estimator);
distrib = (*estimator)( pop );
// (7) distribution output
(*distrib_continue)( distrib );
// (8) euclidianne distance estimation
Vector new_mean = distrib.mean();
Matrix new_varcovar = distrib.varcovar();
AtomType distance = 0;
for( unsigned int d = 0; d < s_size; ++d ) {
distance += pow( mean[ d ] - new_mean[ d ], 2 );
}
distance = sqrt( distance );
eo::log << eo::logging
<< "mean: " << mean << std::endl
<< "new mean: " << new_mean << std::endl
<< "distance: " << distance << std::endl
;
return 0;
}

243
test/edo/t-mean-distance.cpp Executable file
View file

@ -0,0 +1,243 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include <sys/stat.h>
#include <sys/types.h>
#include <sstream>
#include <iomanip>
#include <fstream>
#include <paradiseo/eo.h>
//#include <paradiseo/mo.h>
#include <paradiseo/edo.h>
#include "Rosenbrock.h"
#include "Sphere.h"
typedef eoReal< eoMinimizingFitness > EOT;
typedef edoNormalMulti< EOT > Distrib;
typedef EOT::AtomType AtomType;
#ifdef WITH_BOOST
#include <boost/numeric/ublas/vector.hpp>
#include <boost/numeric/ublas/symmetric.hpp>
typedef ublas::vector< AtomType > Vector;
typedef ublas::symmetric_matrix< AtomType, ublas::lower > Matrix;
#else
#ifdef WITH_EIGEN
#include <Eigen/Dense>
typedef edoNormalMulti<EOT>::Vector Vector;
typedef edoNormalMulti<EOT>::Matrix Matrix;
#endif
#endif
int main(int ac, char** av)
{
// (0) parser + eo routines
eoParser parser(ac, av);
std::string section("Algorithm parameters");
unsigned int r_max = parser.createParam((unsigned int)100, "run-number", "Number of run", 'r', section).value(); // r
unsigned int p_min = parser.createParam((unsigned int)10, "population-min", "Population min", 'p', section).value(); // p
unsigned int p_max = parser.createParam((unsigned int)1000, "population-max", "Population max", 'P', section).value(); // P
unsigned int p_step = parser.createParam((unsigned int)50, "population-step", "Population step", 't', section).value(); // t
unsigned int s_size = parser.createParam((unsigned int)2, "dimension-size", "Dimension size", 'd', section).value(); // d
AtomType mean_value = parser.createParam((AtomType)0, "mean", "Mean value", 'm', section).value(); // m
AtomType covar1_value = parser.createParam((AtomType)1.0, "covar1", "Covar value 1", '1', section).value(); // 1
AtomType covar2_value = parser.createParam((AtomType)0.5, "covar2", "Covar value 2", '2', section).value(); // 2
AtomType covar3_value = parser.createParam((AtomType)1.0, "covar3", "Covar value 3", '3', section).value(); // 3
std::string results_directory = parser.createParam((std::string)"means_distances_results", "results-directory", "Results directory", 'R', section).value(); // R
std::string files_description = parser.createParam((std::string)"files_description.txt", "files-description", "Files description", 'F', section).value(); // F
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
make_verbose(parser);
make_help(parser);
assert(r_max >= 1);
assert(s_size >= 2);
eo::log << eo::quiet;
::mkdir( results_directory.c_str(), 0755 );
for ( unsigned int p_size = p_min; p_size <= p_max; p_size += p_step )
{
assert(p_size >= p_min);
std::ostringstream desc_file;
desc_file << results_directory << "/" << files_description;
std::ostringstream cur_file;
cur_file << results_directory << "/pop_" << p_size << ".txt";
eo::log << eo::file( desc_file.str() ) << cur_file.str().c_str() << std::endl;
eo::log << eo::file( cur_file.str() );
eo::log << eo::logging << "run_number p_size s_size mean(0) mean(1) new-mean(0) new-mean(1) distance" << std::endl;
eo::log << eo::quiet;
for ( unsigned int r = 1; r <= r_max; ++r)
{
eoState state;
// (1) Population init and sampler
eoRndGenerator< double >* gen = new eoUniformGenerator< double >(-5, 5);
state.storeFunctor(gen);
eoInitFixedLength< EOT >* init = new eoInitFixedLength< EOT >( s_size, *gen );
state.storeFunctor(init);
// create an empty pop and let the state handle the memory
// fill population thanks to eoInit instance
eoPop< EOT >& pop = state.takeOwnership( eoPop< EOT >( p_size, *init ) );
// (2) distribution initial parameters
#ifdef WITH_BOOST
Vector mean( s_size, mean_value );
#else
#ifdef WITH_EIGEN
Vector mean( s_size );
mean = Vector::Constant( s_size, mean_value);
#endif
#endif
Matrix varcovar( s_size, s_size );
varcovar( 0, 0 ) = covar1_value;
varcovar( 0, 1 ) = covar2_value;
varcovar( 1, 1 ) = covar3_value;
Distrib distrib( mean, varcovar );
// Prepare bounder class to set bounds of sampling.
// This is used by edoSampler.
edoBounder< EOT >* bounder = new edoBounderRng< EOT >(EOT(pop[0].size(), -5),
EOT(pop[0].size(), 5),
*gen);
state.storeFunctor(bounder);
// Prepare sampler class with a specific distribution
edoSampler< Distrib >* sampler = new edoSamplerNormalMulti< EOT >( *bounder );
state.storeFunctor(sampler);
// (4) sampling phase
pop.clear();
for (unsigned int i = 0; i < p_size; ++i)
{
EOT candidate_solution = (*sampler)( distrib );
pop.push_back( candidate_solution );
}
// (6) estimation phase
edoEstimator< Distrib >* estimator = new edoEstimatorNormalMulti< EOT >();
state.storeFunctor(estimator);
distrib = (*estimator)( pop );
// (8) euclidianne distance estimation
Vector new_mean = distrib.mean();
Matrix new_varcovar = distrib.varcovar();
AtomType distance = 0;
for ( unsigned int d = 0; d < s_size; ++d )
{
distance += pow( mean[ d ] - new_mean[ d ], 2 );
}
distance = sqrt( distance );
eo::log << r << " " << p_size << " " << s_size << " "
<< mean(0) << " " << mean(1) << " "
<< new_mean(0) << " " << new_mean(1) << " "
<< distance << std::endl
;
}
}
return 0;
}

55
test/edo/t-repairer-modulo.cpp Executable file
View file

@ -0,0 +1,55 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
#define _USE_MATH_DEFINES
#include <math.h>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/es.h>
typedef eoReal< eoMinimizingFitness > EOT;
int main(void)
{
EOT sol;
sol.push_back( M_PI * 1 );
sol.push_back( M_PI * 2 );
sol.push_back( M_PI * 3 );
sol.push_back( M_PI * 4 );
sol.push_back( M_PI * 4 + M_PI / 2 );
sol.push_back( M_PI * 5 + M_PI / 2 );
// we expect {pi,0,pi,0,pi/2,pi+pi/2}
std::cout << "expect: INVALID 4 3.14159 0 3.14159 0 1.5708 4.71239" << std::endl;
edoRepairer<EOT>* repare = new edoRepairerModulo<EOT>( 2 * M_PI ); // modulo 2pi
(*repare)(sol);
std::cout << sol << std::endl;
return 0;
}

43
test/edo/t-uniform.cpp Executable file
View file

@ -0,0 +1,43 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2010 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
Caner Candan <caner.candan@thalesgroup.com>
*/
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include "Rosenbrock.h"
typedef eoReal< eoMinimizingFitness > EOT;
int main(void)
{
eoState state;
edoUniform< EOT >* distrib = new edoUniform< EOT >( EOT(3, -1), EOT(3, 1) );
state.storeFunctor(distrib);
return 0;
}

83
test/edo/t-variance.cpp Executable file
View file

@ -0,0 +1,83 @@
#include <iostream>
#include <vector>
#include <paradiseo/eo.h>
#include <paradiseo/edo.h>
#include <paradiseo/eo/es.h>
typedef eoReal<eoMinimizingFitness> Vec;
void check( Vec ex_mean, Vec ex_var, Vec es_mean, Vec es_var )
{
std::cout << "expected mean=" << ex_mean << " variance=" << ex_var << std::endl;
std::cout << "estimated mean=" << es_mean << " variance=" << es_var << std::endl;
for( unsigned int i=0; i<ex_mean.size(); ++i ) {
assert( es_mean[i] == ex_mean[i] );
assert( es_var[i] == ex_var[i] );
}
}
int main()
{
std::clog << "Variance computation on a simple vector" << std::endl;
eoPop<Vec> pop;
for( unsigned int i=1; i<7; ++i) {
Vec indiv(1,i);
pop.push_back( indiv );
std::clog << indiv << " ";
}
std::clog << std::endl;
edoEstimatorNormalMono<Vec> estimator;
edoNormalMono<Vec> distrib = estimator(pop);
Vec ex_mean(1,3.5);
Vec ex_var(1,17.5/6);
Vec es_mean = distrib.mean();
Vec es_var = distrib.variance();
check( ex_mean, ex_var, es_mean, es_var );
// Test with negative values
std::clog << "Variance computation on negative values" << std::endl;
pop.clear();
pop.push_back( Vec(1, 11.0) );
pop.push_back( Vec(1, -4.0) );
pop.push_back( Vec(1, 11.0) );
pop.push_back( Vec(1, 14.0) );
pop.push_back( Vec(1, -2.0) );
std::clog << pop << std::endl;
distrib = estimator(pop);
ex_mean = Vec(1,6.0);
ex_var = Vec(1,278.0/5);
es_mean = distrib.mean();
es_var = distrib.variance();
check( ex_mean, ex_var, es_mean, es_var );
// test single individual
std::clog << "Variance computation on a pop with a single individual" << std::endl;
pop.clear();
pop.push_back( Vec(1, 0.0) );
distrib = estimator(pop);
ex_mean = Vec(1,0.0);
ex_var = Vec(1,0.0);
es_mean = distrib.mean();
es_var = distrib.variance();
check( ex_mean, ex_var, es_mean, es_var );
}

18
test/edo/test_cov_parameters.py Executable file
View file

@ -0,0 +1,18 @@
#!/usr/bin/env python
PSIZE = 10000
MEAN = 0
CMD = "./test/t-edoEstimatorNormalMulti -P=%s -m=%.1f -1=%.1f -2=%.1f -3=%.1f && ./gplot.py -r TestResPop -p -w 5 -u -g %s -G results_for_test_cov_parameters -f %s_gen1"
from os import system
from numpy import arange
if __name__ == '__main__':
for p1 in list(arange(0.1, 1.1, 0.1)):
for p2 in list(arange(-1., 0., 0.1)) + list(arange(0., 1.1, 0.1)):
for p3 in list(arange(0.1, 1.1, 0.1)):
gen = '%d_%.1f_%.1f_%.1f_%.1f' % (PSIZE, MEAN, p1, p2, p3)
cmd = CMD % ( PSIZE, MEAN, p1, p2, p3, gen, gen )
print cmd
system( cmd )

116
test/eo/CMakeLists.txt Executable file
View file

@ -0,0 +1,116 @@
###############################################################################
##
## CMakeLists file for eo/test
##
###############################################################################
######################################################################################
### 1) Include the sources
######################################################################################
#include_directories(${EO_SRC_DIR}/src)
#include_directories(${EO_SRC_DIR}/contrib)
include_directories(${EO_SRC_DIR}/contrib/MGE)
#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
######################################################################################
### 2) Specify where CMake can find the libraries
######################################################################################
#link_directories(${EO_BIN_DIR}/lib)
######################################################################################
### 3) Define your targets and link the librairies
######################################################################################
set (TEST_LIST
t-eofitness
t-eoRandom
t-eobin
t-eoVirus
t-MGE
t-MGE1bit
t-MGE-control
t-eoStateAndParser
t-eoCheckpointing
t-eoSSGA
t-eoExternalEO
t-eoSymreg
t-eo
t-eoReplacement
t-eoSelect
t-eoGenOp
t-eoGA
t-eoReal
t-eoVector
t-eoESAll
t-eoPBIL
t-eoFitnessAssembled
t-eoFitnessAssembledEA
t-eoRoulette
t-eoSharing
t-eoCMAES
t-eoSecondsElapsedContinue
t-eoRNG
t-eoEasyPSO
t-eoInt
t-eoInitPermutation
t-eoSwapMutation
t-eoShiftMutation
t-eoTwoOptMutation
t-eoRingTopology
t-eoSyncEasyPSO
t-eoOrderXover
t-eoExtendedVelocity
t-eoLogger
#t-eoIQRStat # Temporary by-passed in order to test coverage
t-eoParallel
#t-openmp # does not work anymore since functions used in this test were removed from EO
#t-eoDualFitness
t-eoParser
)
foreach (test ${TEST_LIST})
set ("T_${test}_SOURCES" "${test}.cpp")
endforeach (test)
if(ENABLE_MINIMAL_CMAKE_TESTING)
set (MIN_TEST_LIST t-eoEasyPSO)
foreach (mintest ${MIN_TEST_LIST})
set ("T_${mintest}_SOURCES" "${mintest}.cpp")
add_executable(${mintest} ${T_${mintest}_SOURCES})
add_test(${mintest} ${mintest})
target_link_libraries(${mintest} ga es cma eoutils eo)
endforeach (mintest)
elseif(ENABLE_CMAKE_TESTING)
foreach (test ${TEST_LIST})
add_executable(${test} ${T_${test}_SOURCES})
add_test(${test} ${test})
target_link_libraries(${test} ga es cma eoutils eo)
install(TARGETS ${test} RUNTIME DESTINATION share/${PROJECT_TAG}/eo/test COMPONENT test)
endforeach (test)
set(RESOURCES
boxplot.py
boxplot_to_png.py
boxplot_to_pdf.py
t-openmp.py
)
foreach(file ${RESOURCES})
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/${file}
${CMAKE_CURRENT_BINARY_DIR}/${file}
)
endforeach(file)
endif(ENABLE_MINIMAL_CMAKE_TESTING)
######################################################################################

7
test/eo/CTestConfig.cmake Executable file
View file

@ -0,0 +1,7 @@
set(CTEST_PROJECT_NAME "ParadisEO")
set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "cdash.inria.fr")
set(CTEST_DROP_LOCATION "/CDash/submit.php?project=ParadisEO")
set(CTEST_DROP_SITE_CDASH TRUE)

36
test/eo/ChangeLog Executable file
View file

@ -0,0 +1,36 @@
2006-12-04 Jochen Kpper <jochen@fhi-berlin.mpg.de>
* Makefile.am: Add t-eoRNG
* t-eoRNG.cpp: Start test for random number generator.
2006-12-02 Jochen Kpper <jochen@fhi-berlin.mpg.de>
* t-MGE1bit.cpp: Change float to double.
* t-eoGenOp.cpp (init): Do not add std::ends to end of string, as this
results in escape-codes (^@) to be printed at runtime and is not
necessary anyway.
* test/t-eoSymreg.cpp (SymregNode::operator()): Initialize r1 and r2 to
avoid compiler warnings.
2006-07-02 Thomas Legrand <thomas.legrand@inria.fr>
* test/t-eoEasyPSO.cpp: added PSO test
* test/Makefile.am: added PSO test
2006-02-27 Thomas Legrand <thomas.legrand@inria.fr>
* test/t-eoSyncEasyPSO.cpp: added synchronous PSO test
* test/t-eoEasyPSO.cpp: customized PSO test (initialization)
* test/Makefile.am: added synchronous PSO test
* Local Variables:
* coding: iso-8859-1
* mode: flyspell
* fill-column: 80
* End:

502
test/eo/LICENSE Executable file
View file

@ -0,0 +1,502 @@
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
Licenses are intended to guarantee your freedom to share and change
free software--to make sure the software is free for all its users.
This license, the Lesser General Public License, applies to some
specially designated software packages--typically libraries--of the
Free Software Foundation and other authors who decide to use it. You
can use it too, but we suggest you first think carefully about whether
this license or the ordinary General Public License is the better
strategy to use in any particular case, based on the explanations below.
When we speak of free software, we are referring to freedom of use,
not price. Our General Public Licenses are designed to make sure that
you have the freedom to distribute copies of free software (and charge
for this service if you wish); that you receive source code or can get
it if you want it; that you can change the software and use pieces of
it in new free programs; and that you are informed that you can do
these things.
To protect your rights, we need to make restrictions that forbid
distributors to deny you these rights or to ask you to surrender these
rights. These restrictions translate to certain responsibilities for
you if you distribute copies of the library or if you modify it.
For example, if you distribute copies of the library, whether gratis
or for a fee, you must give the recipients all the rights that we gave
you. You must make sure that they, too, receive or can get the source
code. If you link other code with the library, you must provide
complete object files to the recipients, so that they can relink them
with the library after making changes to the library and recompiling
it. And you must show them these terms so they know their rights.
We protect your rights with a two-step method: (1) we copyright the
library, and (2) we offer you this license, which gives you legal
permission to copy, distribute and/or modify the library.
To protect each distributor, we want to make it very clear that
there is no warranty for the free library. Also, if the library is
modified by someone else and passed on, the recipients should know
that what they have is not the original version, so that the original
author's reputation will not be affected by problems that might be
introduced by others.
Finally, software patents pose a constant threat to the existence of
any free program. We wish to make sure that a company cannot
effectively restrict the users of a free program by obtaining a
restrictive license from a patent holder. Therefore, we insist that
any patent license obtained for a version of the library must be
consistent with the full freedom of use specified in this license.
Most GNU software, including some libraries, is covered by the
ordinary GNU General Public License. This license, the GNU Lesser
General Public License, applies to certain designated libraries, and
is quite different from the ordinary General Public License. We use
this license for certain libraries in order to permit linking those
libraries into non-free programs.
When a program is linked with a library, whether statically or using
a shared library, the combination of the two is legally speaking a
combined work, a derivative of the original library. The ordinary
General Public License therefore permits such linking only if the
entire combination fits its criteria of freedom. The Lesser General
Public License permits more lax criteria for linking other code with
the library.
We call this license the "Lesser" General Public License because it
does Less to protect the user's freedom than the ordinary General
Public License. It also provides other free software developers Less
of an advantage over competing non-free programs. These disadvantages
are the reason we use the ordinary General Public License for many
libraries. However, the Lesser license provides advantages in certain
special circumstances.
For example, on rare occasions, there may be a special need to
encourage the widest possible use of a certain library, so that it becomes
a de-facto standard. To achieve this, non-free programs must be
allowed to use the library. A more frequent case is that a free
library does the same job as widely used non-free libraries. In this
case, there is little to gain by limiting the free library to free
software only, so we use the Lesser General Public License.
In other cases, permission to use a particular library in non-free
programs enables a greater number of people to use a large body of
free software. For example, permission to use the GNU C Library in
non-free programs enables many more people to use the whole GNU
operating system, as well as its variant, the GNU/Linux operating
system.
Although the Lesser General Public License is Less protective of the
users' freedom, it does ensure that the user of a program that is
linked with the Library has the freedom and the wherewithal to run
that program using a modified version of the Library.
The precise terms and conditions for copying, distribution and
modification follow. Pay close attention to the difference between a
"work based on the library" and a "work that uses the library". The
former contains code derived from the library, whereas the latter must
be combined with the library in order to run.
GNU LESSER GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License Agreement applies to any software library or other
program which contains a notice placed by the copyright holder or
other authorized party saying it may be distributed under the terms of
this Lesser General Public License (also called "this License").
Each licensee is addressed as "you".
A "library" means a collection of software functions and/or data
prepared so as to be conveniently linked with application programs
(which use some of those functions and data) to form executables.
The "Library", below, refers to any such software library or work
which has been distributed under these terms. A "work based on the
Library" means either the Library or any derivative work under
copyright law: that is to say, a work containing the Library or a
portion of it, either verbatim or with modifications and/or translated
straightforwardly into another language. (Hereinafter, translation is
included without limitation in the term "modification".)
"Source code" for a work means the preferred form of the work for
making modifications to it. For a library, complete source code means
all the source code for all modules it contains, plus any associated
interface definition files, plus the scripts used to control compilation
and installation of the library.
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running a program using the Library is not restricted, and output from
such a program is covered only if its contents constitute a work based
on the Library (independent of the use of the Library in a tool for
writing it). Whether that is true depends on what the Library does
and what the program that uses the Library does.
1. You may copy and distribute verbatim copies of the Library's
complete source code as you receive it, in any medium, provided that
you conspicuously and appropriately publish on each copy an
appropriate copyright notice and disclaimer of warranty; keep intact
all the notices that refer to this License and to the absence of any
warranty; and distribute a copy of this License along with the
Library.
You may charge a fee for the physical act of transferring a copy,
and you may at your option offer warranty protection in exchange for a
fee.
2. You may modify your copy or copies of the Library or any portion
of it, thus forming a work based on the Library, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) The modified work must itself be a software library.
b) You must cause the files modified to carry prominent notices
stating that you changed the files and the date of any change.
c) You must cause the whole of the work to be licensed at no
charge to all third parties under the terms of this License.
d) If a facility in the modified Library refers to a function or a
table of data to be supplied by an application program that uses
the facility, other than as an argument passed when the facility
is invoked, then you must make a good faith effort to ensure that,
in the event an application does not supply such function or
table, the facility still operates, and performs whatever part of
its purpose remains meaningful.
(For example, a function in a library to compute square roots has
a purpose that is entirely well-defined independent of the
application. Therefore, Subsection 2d requires that any
application-supplied function or table used by this function must
be optional: if the application does not supply it, the square
root function must still compute square roots.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Library,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Library, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote
it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Library.
In addition, mere aggregation of another work not based on the Library
with the Library (or with a work based on the Library) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may opt to apply the terms of the ordinary GNU General Public
License instead of this License to a given copy of the Library. To do
this, you must alter all the notices that refer to this License, so
that they refer to the ordinary GNU General Public License, version 2,
instead of to this License. (If a newer version than version 2 of the
ordinary GNU General Public License has appeared, then you can specify
that version instead if you wish.) Do not make any other change in
these notices.
Once this change is made in a given copy, it is irreversible for
that copy, so the ordinary GNU General Public License applies to all
subsequent copies and derivative works made from that copy.
This option is useful when you wish to copy part of the code of
the Library into a program that is not a library.
4. You may copy and distribute the Library (or a portion or
derivative of it, under Section 2) in object code or executable form
under the terms of Sections 1 and 2 above provided that you accompany
it with the complete corresponding machine-readable source code, which
must be distributed under the terms of Sections 1 and 2 above on a
medium customarily used for software interchange.
If distribution of object code is made by offering access to copy
from a designated place, then offering equivalent access to copy the
source code from the same place satisfies the requirement to
distribute the source code, even though third parties are not
compelled to copy the source along with the object code.
5. A program that contains no derivative of any portion of the
Library, but is designed to work with the Library by being compiled or
linked with it, is called a "work that uses the Library". Such a
work, in isolation, is not a derivative work of the Library, and
therefore falls outside the scope of this License.
However, linking a "work that uses the Library" with the Library
creates an executable that is a derivative of the Library (because it
contains portions of the Library), rather than a "work that uses the
library". The executable is therefore covered by this License.
Section 6 states terms for distribution of such executables.
When a "work that uses the Library" uses material from a header file
that is part of the Library, the object code for the work may be a
derivative work of the Library even though the source code is not.
Whether this is true is especially significant if the work can be
linked without the Library, or if the work is itself a library. The
threshold for this to be true is not precisely defined by law.
If such an object file uses only numerical parameters, data
structure layouts and accessors, and small macros and small inline
functions (ten lines or less in length), then the use of the object
file is unrestricted, regardless of whether it is legally a derivative
work. (Executables containing this object code plus portions of the
Library will still fall under Section 6.)
Otherwise, if the work is a derivative of the Library, you may
distribute the object code for the work under the terms of Section 6.
Any executables containing that work also fall under Section 6,
whether or not they are linked directly with the Library itself.
6. As an exception to the Sections above, you may also combine or
link a "work that uses the Library" with the Library to produce a
work containing portions of the Library, and distribute that work
under terms of your choice, provided that the terms permit
modification of the work for the customer's own use and reverse
engineering for debugging such modifications.
You must give prominent notice with each copy of the work that the
Library is used in it and that the Library and its use are covered by
this License. You must supply a copy of this License. If the work
during execution displays copyright notices, you must include the
copyright notice for the Library among them, as well as a reference
directing the user to the copy of this License. Also, you must do one
of these things:
a) Accompany the work with the complete corresponding
machine-readable source code for the Library including whatever
changes were used in the work (which must be distributed under
Sections 1 and 2 above); and, if the work is an executable linked
with the Library, with the complete machine-readable "work that
uses the Library", as object code and/or source code, so that the
user can modify the Library and then relink to produce a modified
executable containing the modified Library. (It is understood
that the user who changes the contents of definitions files in the
Library will not necessarily be able to recompile the application
to use the modified definitions.)
b) Use a suitable shared library mechanism for linking with the
Library. A suitable mechanism is one that (1) uses at run time a
copy of the library already present on the user's computer system,
rather than copying library functions into the executable, and (2)
will operate properly with a modified version of the library, if
the user installs one, as long as the modified version is
interface-compatible with the version that the work was made with.
c) Accompany the work with a written offer, valid for at
least three years, to give the same user the materials
specified in Subsection 6a, above, for a charge no more
than the cost of performing this distribution.
d) If distribution of the work is made by offering access to copy
from a designated place, offer equivalent access to copy the above
specified materials from the same place.
e) Verify that the user has already received a copy of these
materials or that you have already sent this user a copy.
For an executable, the required form of the "work that uses the
Library" must include any data and utility programs needed for
reproducing the executable from it. However, as a special exception,
the materials to be distributed need not include anything that is
normally distributed (in either source or binary form) with the major
components (compiler, kernel, and so on) of the operating system on
which the executable runs, unless that component itself accompanies
the executable.
It may happen that this requirement contradicts the license
restrictions of other proprietary libraries that do not normally
accompany the operating system. Such a contradiction means you cannot
use both them and the Library together in an executable that you
distribute.
7. You may place library facilities that are a work based on the
Library side-by-side in a single library together with other library
facilities not covered by this License, and distribute such a combined
library, provided that the separate distribution of the work based on
the Library and of the other library facilities is otherwise
permitted, and provided that you do these two things:
a) Accompany the combined library with a copy of the same work
based on the Library, uncombined with any other library
facilities. This must be distributed under the terms of the
Sections above.
b) Give prominent notice with the combined library of the fact
that part of it is a work based on the Library, and explaining
where to find the accompanying uncombined form of the same work.
8. You may not copy, modify, sublicense, link with, or distribute
the Library except as expressly provided under this License. Any
attempt otherwise to copy, modify, sublicense, link with, or
distribute the Library is void, and will automatically terminate your
rights under this License. However, parties who have received copies,
or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.
9. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Library or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Library (or any work based on the
Library), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Library or works based on it.
10. Each time you redistribute the Library (or any work based on the
Library), the recipient automatically receives a license from the
original licensor to copy, distribute, link with or modify the Library
subject to these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties with
this License.
11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Library at all. For example, if a patent
license would not permit royalty-free redistribution of the Library by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Library.
If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply,
and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
12. If the distribution and/or use of the Library is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Library under this License may add
an explicit geographical distribution limitation excluding those countries,
so that distribution is permitted only in or among countries not thus
excluded. In such case, this License incorporates the limitation as if
written in the body of this License.
13. The Free Software Foundation may publish revised and/or new
versions of the Lesser General Public License from time to time.
Such new versions will be similar in spirit to the present version,
but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Library
specifies a version number of this License which applies to it and
"any later version", you have the option of following the terms and
conditions either of that version or of any later version published by
the Free Software Foundation. If the Library does not specify a
license version number, you may choose any version ever published by
the Free Software Foundation.
14. If you wish to incorporate parts of the Library into other free
programs whose distribution conditions are incompatible with these,
write to the author to ask for permission. For software which is
copyrighted by the Free Software Foundation, write to the Free
Software Foundation; we sometimes make exceptions for this. Our
decision will be guided by the two goals of preserving the free status
of all derivatives of our free software and of promoting the sharing
and reuse of software generally.
NO WARRANTY
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest
possible use to the public, we recommend making it free software that
everyone can redistribute and change. You can do so by permitting
redistribution under these terms (or, alternatively, under the terms of the
ordinary General Public License).
To apply these terms, attach the following notices to the library. It is
safest to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.
<one line to give the library's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the library, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!

62
test/eo/RoyalRoad.h Executable file
View file

@ -0,0 +1,62 @@
/*
RoyalRoad.h
-- Implementation of the Royal Road function for any length and block size
(c) GeNeura Team 2001, Marc Schoenauer 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
CVS Info: $Date: 2001-06-21 12:03:17 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/test/RoyalRoad.h,v 1.3 2001-06-21 12:03:17 jmerelo Exp $ $Author: jmerelo $
*/
#ifndef RoyalRoad_h
#define RoyalRoad_h
#include <paradiseo/eo.h>
template<class EOT>
class RoyalRoad: public eoEvalFunc<EOT> {
public:
typedef typename EOT::Fitness FitT;
/// Ctor: takes a length, and divides that length in equal parts
RoyalRoad( unsigned _div ): eoEvalFunc<EOT >(), div( _div ) {};
// Applies the function
virtual void operator() ( EOT & _eo ) {
FitT fitness = 0;
if (_eo.invalid()) {
for ( unsigned i = 0; i < _eo.size()/div; i ++ ) {
bool block = true;
for ( unsigned j = 0; j < div; j ++ ) {
block &= _eo[i*div+j];
}
if (block) {
fitness += div;
}
}
_eo.fitness( fitness );
}
};
private:
unsigned div;
};
#endif

16
test/eo/binary_value.h Executable file
View file

@ -0,0 +1,16 @@
#include <algorithm>
//-----------------------------------------------------------------------------
/** Just the simple function that takes binary value of a chromosome and sets
the fitnes.
@param _chrom A binary chromosome
*/
template <class Chrom> double binary_value(const Chrom& _chrom)
{
double sum = 0.0;
for (unsigned i=0; i<_chrom.size(); i++)
sum += _chrom[i];
return sum;
}

15
test/eo/boxplot.py Executable file
View file

@ -0,0 +1,15 @@
#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 2:
print 'Usage: boxplot.py [Results files, ...]'
sys.exit()
for i in range(1, len(sys.argv)):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.show()

15
test/eo/boxplot_to_pdf.py Executable file
View file

@ -0,0 +1,15 @@
#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 3:
print 'Usage: boxplot_to_pdf.py [Results files, ...] [output file in .pdf]'
sys.exit()
for i in range(1, len(sys.argv) - 1):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.savefig( sys.argv[ len(sys.argv) - 1 ], format='pdf', transparent=True )

15
test/eo/boxplot_to_png.py Executable file
View file

@ -0,0 +1,15 @@
#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 3:
print 'Usage: boxplot_to_png.py [Results files, ...] [output file in .png]'
sys.exit()
for i in range(1, len(sys.argv) - 1):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.savefig( sys.argv[ len(sys.argv) - 1 ], format='png', transparent=True, papertype='a0' )

431
test/eo/fitness_traits.cpp Executable file
View file

@ -0,0 +1,431 @@
#include <map> // for pair
#include <iostream>
#include <stdexcept>
#include <vector>
#include <algorithm>
#include <math.h> // for exp
using namespace std;
/* fitness_traits.h */
// default traits: defaults to a double that needs to be maximized
template <class T = double>
struct fitness_traits
{
// Needs mapping can be used to figure out whether you need to do fitness scaling (or not)
const static bool needs_mapping = false;
// storage_type: what to store next to the genotype
typedef T storage_type;
// performance_type: what the eoEvalFunc calculates
typedef T performance_type;
// worth_type: what the scaling function does
typedef T worth_type;
// access_performance: how to get from what is stored to a mutable performance
static performance_type& access_performance(storage_type& a) { return a; }
// access_worth: how to get from what is stored to a mutable worth
static worth_type& access_worth(storage_type& a) { return a; }
// get_performance: from storage_type to a performance figure
static performance_type get_performance(storage_type a) { return a; }
// get_worth: from storage_type to a worth figure
static worth_type get_worth(storage_type a) { return a; }
// get the fitness out of the individual
template <class EOT>
static worth_type get_fitness(const EOT& _eo) { return _eo.performance(); }
// compare the two individuals
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.performance() > _eo2.performance();
}
};
struct minimization {};
struct maximization {};
struct fitness_traits<minimization> : public fitness_traits<double>
{
// for minimization, invert the is_better
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.performance() < _eo2.performance();
}
};
// for maximization, just take the default behaviour
struct fitness_traits<maximization> : public fitness_traits<double> {};
// forward declaration
//template <class EOT> class eoPop;
//template <class Fitness, class Traits> class EO;
// unfortunately, partial template specialization is not approved by Microsoft (though ANSI says it's ok)
// Probably need some macro-magic to make this work (MicroSoft == MacroHard)
// A pair class: first == performance, second == worth, redefine all types, data and functions
template <class Performance, class Worth>
struct fitness_traits< pair<Performance, Worth> >
{
typedef pair<Performance, Worth> storage_type;
typedef Performance performance_type;
typedef Worth worth_type;
const static bool needs_mapping = true;
static performance_type& access_performance(storage_type& a) { return a.first; }
static worth_type& access_worth(storage_type& a) { return a.second; }
static performance_type get_performance(const storage_type& a) { return a.first; }
static worth_type get_worth(const storage_type& a) { return a.second; }
// This function calls _eo.worth() which in turn checks the fitness flag and calls get_worth above
// The compiler should be able to inline all these calls and come up with a very compact solution
template <class EOT>
static worth_type get_fitness(const EOT& _eo) { return _eo.worth(); }
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.worth() > _eo2.worth();
}
};
/* end fitness_traits.h */
/* EO.h
The Fitness template argument is there for backward compatibility reasons
*/
template <class Fitness, class Traits = fitness_traits<Fitness> >
class EO
{
public :
typedef Traits fitness_traits;
typedef typename Traits::storage_type storage_type;
typedef typename Traits::performance_type performance_type;
typedef typename Traits::worth_type worth_type;
EO() : valid_performance(false), valid_worth(false), rep_fitness() {}
// for backwards compatibility
void fitness(performance_type perf)
{
performance(perf);
}
void performance(performance_type perf)
{
valid_performance = true;
Traits::access_performance(rep_fitness) = perf;
}
performance_type performance(void) const
{
if(!valid_performance) throw runtime_error("no performance");
return Traits::get_performance(rep_fitness);
}
void worth(worth_type worth)
{
valid_worth = true;
Traits::access_worth(rep_fitness) = worth;
}
worth_type worth(void) const
{
if(!valid_worth) throw runtime_error("no worth");
if(!Traits::needs_mapping) throw runtime_error("no mapping");
return Traits::get_worth(rep_fitness);
}
worth_type fitness(void) const
{
return Traits::get_fitness(*this);
}
void invalidate(void)
{
valid_performance = false;
valid_worth = false;
}
void invalidate_worth(void)
{
valid_worth = false;
}
bool operator<(const EO<Fitness, Traits>& other) const
{
return !Traits::is_better(other, *this);
}
bool operator>(const EO<Fitness, Traits>& other) const
{
return Traits::is_better(other, *this);
}
private :
bool valid_performance;
bool valid_worth;
storage_type rep_fitness;
};
/* end EO.h */
/* eoPerf2Worth.h */
// get the name known
template <class EOT> class eoPop;
template <class EOT>
void exponential_scaling(eoPop<EOT>& _pop)
{
for (unsigned i = 0; i < _pop.size(); ++i)
{ // change minimimization into maximization
_pop[i].worth(exp(-_pop[i].performance()));
}
}
template <class EOT>
class eoPerf2Worth /* : public eoUF<eoPop<EOT>&, void> */
{
public :
virtual void operator()(eoPop<EOT>& _pop)
{
return exponential_scaling(_pop);
}
};
/* end eoPerf2Worth.h */
/* eoPop.h */
template <class EOT>
class eoPop : public vector<EOT>
{
public :
typedef typename EOT::fitness_traits fitness_traits;
eoPop(void) : p2w(0) {}
void sort()
{
scale(); // get the worths up to date
std::sort(begin(), end(), greater<EOT>());
}
void scale()
{
if (p2w)
{
if (!fitness_traits::needs_mapping)
{
throw runtime_error("eoPop: no scaling needed, yet a scaling function is defined");
}
(*p2w)(*this);
}
else if (fitness_traits::needs_mapping)
{
throw runtime_error("eoPop: no scaling function attached to the population, while one was certainly called for");
}
}
void setPerf2Worth(eoPerf2Worth<EOT>& _p2w)
{
p2w = &_p2w;
}
void setPerf2Worth(eoPerf2Worth<EOT>* _p2w)
{
p2w = _p2w;
}
eoPerf2Worth<EOT>* getPerf2Worth() { return p2w; }
void swap(eoPop<EOT>& other)
{
vector<EOT>::swap(other);
eoPerf2Worth<EOT>* tmp = p2w;
p2w = other.p2w;
other.p2w = tmp;
}
private :
// a pointer as it can be emtpy
eoPerf2Worth<EOT>* p2w;
};
// need this one to be able to swap the members as well...
template <class EOT>
void swap(eoPop<EOT>& _p1, eoPop<EOT>& _p2)
{
_p1.swap(_p2);
}
/* end eoPop.h */
/* main and test */
template <class EOT>
void algo(eoPop<EOT>& _pop)
{
eoPop<EOT> offspring; // how to get the scaling info into this guy??
offspring.setPerf2Worth(_pop.getPerf2Worth()); // like this!
std::copy(_pop.begin(), _pop.end(), back_inserter(offspring));
offspring.sort(); // should call scale
swap(_pop, offspring);
}
void minimization_test()
{
typedef EO<minimization> eo_type;
eo_type eo1;
eo_type eo2;
eo1.performance(1.0);
eo2.performance(2.0);
std::cout << "With minimizing fitness" << std::endl;
std::cout << eo1.fitness() << " < " << eo2.fitness() << " returns " << (eo1 < eo2) << std::endl;
std::cout << eo2.fitness() << " < " << eo1.fitness() << " returns " << (eo2 < eo1) << std::endl;
}
void the_main()
{
typedef EO<double> simple_eo;
typedef EO<pair<double, double> > scaled_eo;
simple_eo eo1;
simple_eo eo3;
/* First test some simple comparisons */
eo1.fitness(10); // could also use performance()
eo3.fitness(5);
std::cout << eo1.fitness() << std::endl;
std::cout << eo3.fitness() << std::endl;
std::cout << "eo1 < eo3 = " << (eo1 < eo3) << std::endl;
scaled_eo eo2;
scaled_eo eo4;
eo2.performance(10);
eo4.performance(8);
/* Now test if the worth gets accessed and if the flag protects it */
try
{
std::cout << eo2.fitness() << std::endl;
std::cout << "did not throw" << std::endl;
assert(false); // should throw
}
catch(std::exception& e)
{
std::cout << "Fitness threw exception, as it should" << std::endl;
std::cout << e.what() << std::endl;
}
/* Set the worth and all is well (this is normally done by some perf2worth functor */
eo2.worth(3);
eo4.worth(5);
std::cout << "with maximization " << std::endl;
std::cout << eo2.fitness() << std::endl;
std::cout << eo4.fitness() << std::endl;
std::cout << eo2.fitness() << " < " << eo4.fitness() << " returns " << (eo2 < eo4) << std::endl;
/* Test the minimization of fitness */
minimization_test();
/* Populations */
// test pop without scaling, should have no overhead save for a single empty pointer in pop
eoPop<simple_eo> pop0;
pop0.resize(1);
pop0[0].fitness(1);
algo(pop0);
std::cout << pop0[0].fitness() << std::endl;
assert(pop0[0].fitness() == 1);
/* test pop with scaling */
eoPerf2Worth<scaled_eo> perf2worth;
eoPop<scaled_eo> pop1;
pop1.resize(1);
pop1[0].fitness(1.0); // emulate evaluation
// at this point getting the fitness should throw
try
{
std::cout << pop1[0].fitness() << std::endl;
std::cout << "did not throw" << std::endl;
assert(false); // should throw
}
catch(std::exception& e)
{
std::cout << "Fitness threw exception, as it should" << std::endl;
std::cout << e.what() << std::endl;
}
// at this point trying to scale should throw
try
{
algo(pop1); // should complain that it cannot scale
assert(false); // so it would never get here
}
catch(std::exception& e)
{ // but rather ends here
std::cout << e.what() << std::endl;
}
// ok, now set the scaling
pop1.setPerf2Worth(perf2worth);
algo(pop1);
std::cout << "the fitness has been transformed from " << pop1[0].performance() << " to exp(-1) = " << pop1[0].fitness() << std::endl;
}
int main()
{
try
{
the_main();
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
}
}

16
test/eo/real_value.h Executable file
View file

@ -0,0 +1,16 @@
#include <vector>
//-----------------------------------------------------------------------------
/** Just a simple function that takes an eoEsBase<double> and sets the fitnes
to sphere
@param _ind vector<double>
*/
double real_value(const std::vector<double>& _ind)
{
double sum = 0;
for (unsigned i = 0; i < _ind.size(); i++)
sum += _ind[i] * _ind[i];
return sum/_ind.size();
}

9
test/eo/run_tests Executable file
View file

@ -0,0 +1,9 @@
#!/bin/sh
echo "Testing -h"
./t-eoCheckpointing -h
echo "Finished"
#TODO test if an error occured
echo "Ok"

104
test/eo/t-MGE-control.cpp Executable file
View file

@ -0,0 +1,104 @@
//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo/ga/eoBitOp.h>
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
eoOneBitFlip<Chrom> vm;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.2);
propSel.add(xover, 0.8);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2 );
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

109
test/eo/t-MGE.cpp Executable file
View file

@ -0,0 +1,109 @@
//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
#include <paradiseo/eo/ga/eoBitOp.h>
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
VirusMutation<float> vm;
VirusTransmission<float> vt;
VirusBitFlip<float> vf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.1);
propSel.add(vf, 0.05);
propSel.add(vt, 0.05);
propSel.add(xover, 0.8);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

112
test/eo/t-MGE1bit.cpp Executable file
View file

@ -0,0 +1,112 @@
//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
//#include "ga/eoBitOp.h"
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<double> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus1bit<double> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
VirusShiftMutation<double> vm;
VirusTransmission<double> vt;
VirusBitFlip<double> vf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.8);
propSel.add(vf, 0.05);
propSel.add(vt, 0.05);
propSel.add(xover, 0.1);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add(continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace);
// evolution
try {
ea(pop);
} catch (std::exception& e) {
std::cerr << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return EXIT_SUCCESS;
}
//-----------------------------------------------------------------------------
// Local Variables:
// mode: C++
// c-file-style: "Stroustrup"
// End:

14
test/eo/t-eo.cpp Executable file
View file

@ -0,0 +1,14 @@
#include <paradiseo/eo.h>
typedef EO<float> Chrom;
int main()
{
Chrom chrom1, chrom2;
// EO objects can be printed with stream operators
std::cout << "chrom1 = " << chrom1 << std::endl
<< "chrom2 = " << chrom2 << std::endl;
return 0;
}

220
test/eo/t-eo2dVector.cc Executable file
View file

@ -0,0 +1,220 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/*
-----------------------------------------------------------------------------
File............: t-eo2dVector.cc
Author..........: Geneura Team (this file: Victor Rivas, vrivas@ujaen.es)
Date............: 01-Oct-1999, at Fac. of Sciences, Univ. of Granada (Spain)
Description.....: Test for 2 dimensional eoVector.
================ Modif. 1 ================
Author........:
Date..........:
Description...:
-----------------------------------------------------------------------------
*/
#include <stdexcept>
#include <paradiseo/eo/eo2dVector.h> // eo2dVector
#include <paradiseo/eo/eoUniform.h> // Random generator
//-----------------------------------------------------------------------------
typedef unsigned T;
typedef double fitnessT;
typedef eo2dVector<T,fitnessT> C;
//-----------------------------------------------------------------------------
main()
{
{
C c1;
cout << "Default constructor: " << endl
<< c1 << endl;
}
{
C c1( 5,6,1 );
cout << "Default constructor with values: " << endl
<< c1 << endl;
}
{
eoUniform<T> aleat( 1,10 );
C c1( 5,6, aleat );
cout << "Random constructor: " << endl
<< c1 << endl;
}
{
C c1( 3,4,1 ), c2( c1 );
cout << "Copy constructor: " << endl
<< "Original chromosome: " << endl
<< c1 << endl
<< "Copy chromosome: " << endl
<< c2 << endl;
}
eoUniform<T> aleat( 1,10 );
C c1( 3,4,aleat );
cout << "-----------------------------------------------------" << endl
<< "Since now on all the operations are applied to " << endl
<< c1
<< "-----------------------------------------------------" << endl;
{
cout << "getGene(2,2): "
<< c1.getGene(2,2) << endl;
}
{
c1.setGene( 2,2,300 );
cout << "setGene(2,2,300): " << endl
<< c1 << endl;
}
{
unsigned u1=0, u3=333, u5=555;
vector<T> v1( 4,u1 ), v2( 4,u3 ), v3( 4,u5 );
c1.insertRow( 0,v1 );
c1.insertRow( 3,v2 );
c1.insertRow( 5,v3 );
cout << "Insert rows at positions 0, 3 and 5: " << endl
<< c1 << endl;
}
{
c1.deleteRow( 5 );
c1.deleteRow( 3 );
c1.deleteRow( 0 );
cout << "Delete rows at positions 5, 3 and 0: " << endl
<< c1 << endl;
}
{
unsigned u1=0, u3=333, u6=666;
vector<T> v1( 3,u1 ), v2( 3,u3 ), v3( 3,u6 );
c1.insertCol( 0,v1 );
c1.insertCol( 3,v2 );
c1.insertCol( 6,v3 );
cout << "Insert columns at positions 0, 3 and 6: " << endl
<< c1 << endl;
}
{
c1.deleteCol( 6 );
c1.deleteCol( 3 );
c1.deleteCol( 0 );
cout << "Delete columns at positions 6, 3 and 0: " << endl
<< c1 << endl;
}
{
cout << "Number of Rows: " << endl
<< c1.numOfRows() << endl;
}
{
cout << "Number of Columns: " << endl
<< c1.numOfCols() << endl;
}
{
cout << "Class Name: " << endl
<< c1.className() << endl;
}
cout << "-----------------------------------------------------" << endl
<< "Catching exceptions: " << endl
<< c1
<< "-----------------------------------------------------" << endl;
{
cout << "* Trying getGene(10,1): " << endl;
try {
c1.getGene( 10,1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying getGene(1,10): " << endl;
try {
c1.getGene( 1,10) ;
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying setGene( 10,1,999 ): " << endl;
try {
c1.setGene( 10,1,999 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying setGene( 1,10,999 ): " << endl;
try {
c1.setGene( 1,10,999 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 4, u1 );
cout << "* Trying insertRow( 10, v1 ): " << endl;
try {
c1.insertRow( 10,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 5, u1 );
cout << "* Trying insertRow( 1, v1 ) with v1.size()=5: " << endl;
try {
c1.insertRow( 1,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying deleteRow( 10 ): " << endl;
try {
c1.deleteRow( 10 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 3, u1 );
cout << "* Trying insertCol( 10,v1 ): " << endl;
try {
c1.insertCol( 10,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 5, u1 );
cout << "* Trying insertCol( 1,v1 ) with v1.size()=5: " << endl;
try {
c1.insertCol( 1,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying deleteCol( 10 ): " << endl;
try {
c1.deleteCol( 10 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
}
//-----------------------------------------------------------------------------

127
test/eo/t-eoCMAES.cpp Executable file
View file

@ -0,0 +1,127 @@
#include <iostream>
#include <paradiseo/eo.h>
/*
#include <paradiseo/eo/eoScalarFitness.h>
#include <paradiseo/eo/eoVector.h>
#include <paradiseo/eo/eoPop.h>
#include <paradiseo/eo/utils/eoParser.h>
#include <paradiseo/eo/utils/eoCheckPoint.h>
#include <paradiseo/eo/eoEvalFuncPtr.h>
#include <paradiseo/eo/eoGenContinue.h>
#include <paradiseo/eo/eoFitContinue.h>
#include <paradiseo/eo/utils/eoStdoutMonitor.h>
#include <paradiseo/eo/utils/eoStat.h>
#include <paradiseo/eo/utils/eoTimedMonitor.h>
#include <paradiseo/eo/eoMergeReduce.h>
#include <paradiseo/eo/eoEasyEA.h>
#include <paradiseo/eo/es/CMAState.h>
#include <paradiseo/eo/es/CMAParams.h>
#include <paradiseo/eo/es/eoCMAInit.h>
#include <paradiseo/eo/es/eoCMABreed.h>
*/
using namespace eo;
using namespace std;
typedef eoMinimizingFitness FitT;
typedef eoVector<FitT, double> EoType;
double sqr(double x) { return x*x; }
eoValueParam<int> evals(0,"Function Evals","Number of Evaluations");
double f_sphere(const vector<double>& values) {
double sum = 0.0;
for (unsigned i = 0; i < values.size(); ++i) {
sum += values[i] * values[i];
}
++evals.value();
return sum;
}
double f_rosen(const vector<double>& x) {
double sum =0.0;
for (unsigned i = 0; i < x.size()-1; ++i) {
sum += 100 * sqr(sqr(x[i])-x[i+1]) + sqr(1.-x[i]);
}
++evals.value();
return sum;
}
int main(int argc, char* argv[]) {
// make sure we have a dimensionality parameter (for testing)
char** rargv = new char*[argc+1];
rargv[0] = argv[0];
rargv[1] = (char*)"-N10";
for (int i = 2; i < argc; ++i) {
rargv[i] = argv[i-1];
}
eoParser parser(argc+1, rargv);
CMAParams params(parser);
vector<double> initial_point(params.n, 0.0);
CMAState state(params, initial_point);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
return 1;
}
eoCMAInit<FitT> init(state);
eoPop<EoType> pop(params.mu, init);
eoEvalFuncPtr<EoType, double, const vector<double>&> eval( f_rosen );
eoCMABreed<FitT> breed(state, params.lambda);
for (unsigned i = 0; i < pop.size(); ++i) {
eval(pop[i]);
}
eoCommaReplacement<EoType> comma;
eoGenContinue<EoType> gen(params.maxgen);
eoFitContinue<EoType> fit(1e-10);
eoCheckPoint<EoType> checkpoint(gen);
checkpoint.add(fit);
eoBestFitnessStat<EoType> stat;
eoStdoutMonitor mon;
mon.add(stat);
mon.add(evals);
eoTimedMonitor timed(1);// 1 seconds
timed.add(mon); // wrap it
checkpoint.add(timed);
checkpoint.add(stat);
eoEasyEA<EoType> algo(
checkpoint,
eval,
breed,
comma);
algo(pop);
pop.sort();
cout << pop[0] << endl;
cout << "Fitness achieved = " << pop[0].fitness() << endl;
cout << "Function evaluations = " << evals.value() << endl;
}

177
test/eo/t-eoCheckpointing.cpp Executable file
View file

@ -0,0 +1,177 @@
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <stdexcept> // runtime_error
#include <paradiseo/eo.h>
// general
/*
#include <paradiseo/eo/utils/eoRNG.h> // Random number generators
#include <paradiseo/eo/ga.h>
#include <paradiseo/eo/utils/eoParser.h>
#include <paradiseo/eo/utils/eoState.h>
#include <paradiseo/eo/eoGenContinue.h>
// include package checkpointing
#include <paradiseo/eo/utils/checkpointing>
*/
struct Dummy : public EO<double>
{
typedef double Type;
};
struct eoDummyPop : public eoPop<Dummy>
{
public :
eoDummyPop(int s = 2) { resize(s); }
};
int the_main(int argc, char **argv)
{ // ok, we have a command line parser and a state
typedef eoBit<float> Chrom;
eoParser parser(argc, argv);
// Define Parameters
eoValueParam<double> rate(0.01, "mutationRatePerBit", "Initial value for mutation rate per bit");
eoValueParam<double> factor(0.99, "mutationFactor", "Decrease factor for mutation rate");
eoValueParam<uint32_t> seed(time(0), "seed", "Random number seed");
eoValueParam<std::string> load_name("", "Load","Load",'L');
eoValueParam<std::string> save_name("", "Save","Save",'S');
// Register them
parser.processParam(rate, "Genetic Operators");
parser.processParam(factor, "Genetic Operators");
parser.processParam(load_name, "Persistence");
parser.processParam(save_name, "Persistence");
parser.processParam(seed, "Rng seeding");
eoState state;
state.registerObject(parser);
if (load_name.value() != "")
{ // load the parser. This is only neccessary when the user wants to
// be able to change the parameters in the state file by hand.
state.load(load_name.value()); // load the parser
}
// Create the algorithm here
typedef Dummy EoType;
eoDummyPop pop;
eoGenContinue<EoType> genTerm(5); // run for 5 generations
eoCheckPoint<EoType> checkpoint(genTerm);
// The algorithm will now quit after five generations
// Create a counter parameter
eoValueParam<unsigned> generationCounter(0, "Generation");
// Create an incrementor (wich is an eoUpdater). Note that the
// Parameter's value is passed by reference, so every time the incrementer increments,
// the data in generationCounter will change.
eoIncrementor<unsigned> increment(generationCounter.value());
// Add it to the checkpoint, this will result in the counter being incremented every generation
checkpoint.add(increment);
// The file monitor will print parameters to a comma seperated file
eoFileMonitor monitor("monitor.csv");
// the checkpoint mechanism can handle multiple monitors
checkpoint.add(monitor);
// the monitor can monitor parameters such as the generationCounter
monitor.add(generationCounter);
// Second moment stats: average and stdev
eoSecondMomentStats<EoType> stats;
// Add it to the checkpoint to get it called at the appropriate time
checkpoint.add(stats);
// Add it to the monitor to get it written to the file
monitor.add(stats);
// save state every third generation
eoCountedStateSaver stateSaver1(3, state, "generation");
// save state every 2 seconds
eoTimedStateSaver stateSaver2(2, state, "time");
// And add the two savers to the checkpoint
checkpoint.add(stateSaver1);
checkpoint.add(stateSaver2);
// Register the algorithm
state.registerObject(rng);
state.registerObject(pop);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
return 0;
}
// Either load or initialize
if (load_name.value() != "")
{
state.load(load_name.value()); // load the rest
}
else
{
// else
// initialize rng and population
rng.reseed(seed.value());
pop.resize(2);
pop[0].fitness(1);
pop[1].fitness(2);
}
while(checkpoint(pop))
{
pop[0].fitness(pop[0].fitness() + 1);
time_t now = time(0);
while (time(0) == now) {} // wait a second to test timed saver
std::cout << "gen " << generationCounter.value() << std::endl;
}
// run the algorithm
// Save when needed
if (save_name.value() != "")
{
std::string file_name = save_name.value();
save_name.value() = ""; // so that it does not appear in the parser section of the state file
state.save(file_name);
}
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
}
}

88
test/eo/t-eoDualFitness.cpp Executable file
View file

@ -0,0 +1,88 @@
#include <utility>
#include <paradiseo/eo.h>
#include <paradiseo/eo/es.h>
#include <paradiseo/eo/utils/eoStat.h>
typedef eoVector<eoDualFitness<double,eoMinimizingFitness>,double> DualVector;
template<class EOT>
class DualSphere : public eoEvalFunc<EOT>
{
public:
virtual void operator()( EOT & x )
{
if( x.invalid() ) { return; }
double sum = 0;
int sign = 1;
for( unsigned int i=0, s=x.size(); i<s; ++i ) {
sum += x[i] * x[i];
sign *= x[i]<0 ? -1 : 1;
}
x.fitness( std::make_pair( sum, sign>0 ? true : false ) );
}
};
double test( eoPop<DualVector>& pop, double target_value )
{
DualSphere<DualVector> eval;
eoPopLoopEval<DualVector> pop_eval(eval);
pop_eval(pop,pop);
eoInterquartileRangeStat<DualVector> iqr_stat( std::make_pair(0.0,false), "IQR" );
iqr_stat( pop );
std::cout << iqr_stat.longName() << "=" << iqr_stat.value() << " should be " << target_value << std::endl;
return iqr_stat.value().value();
}
int main()
{
eoPop<DualVector> pop;
// fixed test
DualVector sol1(2,-1);
DualVector sol2(2,-1);
DualVector sol3(2,1);
DualVector sol4(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
// on the sphere function everyone has the same fitness of 1
if( test(pop, 0) != 0 ) {
exit(1);
}
pop.erase(pop.begin(),pop.end());
// fixed test
sol1 = DualVector(2,0);
sol2 = DualVector(2,0);
sol3 = DualVector(2,1);
sol4 = DualVector(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
if( test(pop, 1) != 1 ) {
exit(1);
}
// test on a random normal distribution
eoNormalGenerator<double> normal(1,rng);
eoInitFixedLength<DualVector> init_N(2, normal);
pop = eoPop<DualVector>( 1000000, init_N );
double iqr = test(pop, 1.09);
if( iqr < 1.08 || iqr > 1.11 ) {
exit(1);
}
}

150
test/eo/t-eoESAll.cpp Executable file
View file

@ -0,0 +1,150 @@
// Program to test several EO-ES features
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <algorithm>
#include <string>
#include <iostream>
#include <iterator>
#include <stdexcept>
#include <ctime>
#ifdef _MSC_VER
#include <crtdbg.h>
#endif
using namespace std;
#include <paradiseo/eo.h>
// representation specific
//#include <paradiseo/eo/es/make_es.h>
#include "real_value.h" // the sphere fitness
// Now the main
///////////////
typedef eoMinimizingFitness FitT;
template <class EOT>
void runAlgorithm(EOT, eoParser& _parser, eoState& _state);
int main_function(int argc, char *argv[])
{
// Create the command-line parser
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
eoValueParam<bool>& simpleParam = parser.getORcreateParam(true, "Isotropic",
"Isotropic self-adaptive mutation",
'i', "ES mutation");
eoValueParam<bool>& stdevsParam = parser.getORcreateParam(false, "Stdev",
"One self-adaptive stDev per variable",
's', "ES mutation");
eoValueParam<bool>& corrParam = parser.getORcreateParam(false, "Correl",
"Use correlated mutations",
'c', "ES mutation");
// Run the appropriate algorithm
if (simpleParam.value() == false)
{
std::cout << "Using eoReal" << std::endl;
runAlgorithm(eoReal<FitT>(), parser, state);
}
else if (stdevsParam.value() == false)
{
std::cout << "Using eoEsSimple" << std::endl;
runAlgorithm(eoEsSimple<FitT>(), parser, state);
}
else if (corrParam.value() == false)
{
std::cout << "Using eoEsStdev" << std::endl;
runAlgorithm(eoEsStdev<FitT>(), parser, state);
}
else
{
std::cout << "Using eoEsFull" << std::endl;
runAlgorithm(eoEsFull<FitT>(), parser, state);
}
return 0;
}
// A main that catches the exceptions
int main(int argc, char **argv)
{
#ifdef _MSC_VER
// rng.reseed(42);
int flag = _CrtSetDbgFlag(_CRTDBG_LEAK_CHECK_DF);
flag |= _CRTDBG_LEAK_CHECK_DF;
_CrtSetDbgFlag(flag);
// _CrtSetBreakAlloc(100);
#endif
try
{
main_function(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << '\n';
}
}
/** The templatized main (sort of)
quite similar to the main of other genotypes (e.g. t-eoReal and t-eoGA
in test dir)
*/
template <class EOT>
void runAlgorithm(EOT, eoParser& _parser, eoState& _state)
{
typedef typename EOT::Fitness FitT;
///// FIRST, problem or representation dependent stuff
//////////////////////////////////////////////////////
// The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<EOT, double, const std::vector<double>&> mainEval( real_value );
eoEvalFuncCounter<EOT> eval(mainEval);
// the genotype - through a genotype initializer
eoRealInitBounded<EOT>& init = make_genotype(_parser, _state, EOT());
// Build the variation operator (any seq/prop construct)
eoGenOp<EOT>& op = make_op(_parser, _state, init);
//// Now the representation-independent things
//////////////////////////////////////////////
// initialize the population - and evaluate
// yes, this is representation indepedent once you have an eoInit
eoPop<EOT>& pop = make_pop(_parser, _state, init);
apply<EOT>(eval, pop);
// stopping criteria
eoContinue<EOT> & term = make_continue(_parser, _state, eval);
// output
eoCheckPoint<EOT> & checkpoint = make_checkpoint(_parser, _state, eval, term);
// algorithm (need the operator!)
eoAlgo<EOT>& ga = make_algo_scalar(_parser, _state, eval, checkpoint, op);
///// End of construction of the algorith
/////////////////////////////////////////
// to be called AFTER all parameters have been read!!!
make_help(_parser);
//// GO
///////
std::cout << "Initial Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
run_ea(ga, pop); // run the ga
std::cout << "Final Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
}

180
test/eo/t-eoESFull.cpp Executable file
View file

@ -0,0 +1,180 @@
// Program to test several EO-ES features
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <algorithm>
#include <string>
#include <iostream>
#include <iterator>
#include <stdexcept>
#include <time.h>
using namespace std;
#include <paradiseo/eo.h>
// representation specific
#include <paradiseo/eo/es.h>
#include "real_value.h" // the sphere fitness
// Now the main
///////////////
typedef eoMinimizingFitness FitT;
template <class EOT>
void runAlgorithm(EOT, eoParser& _parser, eoState& _state, eoRealVectorBounds& _bounds, eoValueParam<string> _load_name);
int main_function(int argc, char *argv[])
{
// Create the command-line parser
eoParser parser( argc, argv, "Basic EA for vector<float> with adaptive mutations");
// Define Parameters and load them
eoValueParam<uint32_t>& seed = parser.createParam(static_cast<uint32_t>(time(0)),
"seed", "Random number seed");
eoValueParam<string>& load_name = parser.createParam(string(), "Load","Load a state file",'L');
eoValueParam<string>& save_name = parser.createParam(string(), "Save","Saves a state file",'S');
eoValueParam<bool>& stdevs = parser.createParam(false, "Stdev", "Use adaptive mutation rates", 's');
eoValueParam<bool>& corr = parser.createParam(false, "Correl", "Use correlated mutations", 'c');
eoValueParam<unsigned>& chromSize = parser.createParam(unsigned(50), "ChromSize", "Number of chromosomes", 'n');
eoValueParam<double>& minimum = parser.createParam(-1.0, "Min", "Minimum for Objective Variables", 'l');
eoValueParam<double>& maximum = parser.createParam(1.0, "Max", "Maximum for Objective Variables", 'h');
eoState state;
state.registerObject(parser);
rng.reseed(seed.value());
if (!load_name.value().empty())
{ // load the parser. This is only neccessary when the user wants to
// be able to change the parameters in the state file by hand
// Note that only parameters inserted in the parser at this point
// will be loaded!.
state.load(load_name.value()); // load the parser
}
state.registerObject(rng);
eoRealVectorBounds bounds(chromSize.value(), minimum.value(), maximum.value());
// Run the appropriate algorithm
if (stdevs.value() == false && corr.value() == false)
{
runAlgorithm(eoEsSimple<FitT>() ,parser, state, bounds, load_name);
}
else if (corr.value() == true)
{
runAlgorithm(eoEsFull<FitT>(),parser, state, bounds, load_name);
}
else
{
runAlgorithm(eoEsStdev<FitT>(), parser, state, bounds, load_name);
}
// and save
if (!save_name.value().empty())
{
string file_name = save_name.value();
save_name.value() = ""; // so that it does not appear in the parser section of the state file
state.save(file_name);
}
return 0;
}
// A main that catches the exceptions
int main(int argc, char **argv)
{
#ifdef _MSC_VER
// rng.reseed(42);
int flag = _CrtSetDbgFlag(_CRTDBG_LEAK_CHECK_DF);
flag |= _CRTDBG_LEAK_CHECK_DF;
_CrtSetDbgFlag(flag);
// _CrtSetBreakAlloc(100);
#endif
try
{
main_function(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << '\n';
}
return 1;
}
template <class EOT>
void runAlgorithm(EOT, eoParser& _parser, eoState& _state, eoRealVectorBounds& _bounds, eoValueParam<string> _load_name)
{
// evaluation
eoEvalFuncPtr<EOT, double, const vector<double>&> eval( real_value );
// population parameters, unfortunately these can not be altered in the state file
eoValueParam<unsigned> mu = _parser.createParam(unsigned(7), "mu","Size of the population");
eoValueParam<double>lambda_rate = _parser.createParam(double(7.0), "lambda_rate", "Factor of children to produce");
if (lambda_rate.value() < 1.0f)
{
throw logic_error("lambda_rate must be larger than 1 in a comma strategy");
}
// Initialization
eoEsChromInit<EOT> init(_bounds);
// State takes ownership of pop because it needs to save it in caller
eoPop<EOT>& pop = _state.takeOwnership(eoPop<EOT>(mu.value(), init));
_state.registerObject(pop);
if (!_load_name.value().empty())
{ // The real loading happens here when all objects are registered
_state.load(_load_name.value()); // load all and everything
}
else
{
// evaluate initial population
apply<EOT>(eval, pop);
}
// Ok, time to set up the algorithm
// Proxy for the mutation parameters
eoEsMutationInit mutateInit(_parser);
eoEsMutate<EOT> mutate(mutateInit, _bounds);
// monitoring, statistics etc.
eoAverageStat<EOT> average;
eoStdoutMonitor monitor;
monitor.add(average);
eoGenContinue<EOT> cnt(100);
eoCheckPoint<EOT> checkpoint(cnt);
checkpoint.add(monitor);
checkpoint.add(average);
// only mutation (== with rate 1.0)
eoMonGenOp<EOT> op(mutate);
// the selection: sequential selection
eoSequentialSelect<EOT> select;
// the general breeder (lambda is a rate -> true)
eoGeneralBreeder<EOT> breed(select, op, lambda_rate.value(), true);
// the replacement - hard-coded Comma replacement
eoCommaReplacement<EOT> replace;
// now the eoEasyEA
eoEasyEA<EOT> es(checkpoint, eval, breed, replace);
es(pop);
pop.sort();
std::cout << "Final population\n" << pop << std::endl;
}

74
test/eo/t-eoEasyEA.cpp Executable file
View file

@ -0,0 +1,74 @@
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
#include "binary_value.h"
typedef eoBin<float> Chrom;
main()
{
const unsigned POP_SIZE = 8, CHROM_SIZE = 16;
unsigned i;
// a chromosome randomizer
eoBinRandom<Chrom> random;
// the populations:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( binary_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoLottery<Chrom> lottery;
// breeder
eoBinBitFlip<Chrom> bitflip;
eoBinCrossover<Chrom> xover;
eoProportionalOpSel<Chrom> propSel;
eoBreeder<Chrom> breeder( propSel );
propSel.addOp(bitflip, 0.25);
propSel.addOp(xover, 0.75);
// replacement
eoInclusion<Chrom> inclusion;
// Terminators
eoFitTerm<Chrom> term( pow(2.0, CHROM_SIZE), 1 );
// GA generation
eoEasyEA<Chrom> ea(lottery, breeder, inclusion, eval, term);
// evolution
try
{
ea(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
return 0;
}

102
test/eo/t-eoEasyPSO.cpp Executable file
View file

@ -0,0 +1,102 @@
//-----------------------------------------------------------------------------
// t-eoEasyPSO.cpp
//-----------------------------------------------------------------------------
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
//-----------------------------------------------------------------------------
typedef eoMinimizingFitness FitT;
typedef eoRealParticle < FitT > Particle;
//-----------------------------------------------------------------------------
// the objective function
double real_value (const Particle & _particle)
{
double sum = 0;
for (unsigned i = 0; i < _particle.size ()-1; i++)
sum += pow(_particle[i],2);
return (sum);
}
int main()
{
const unsigned int VEC_SIZE = 2;
const unsigned int POP_SIZE = 20;
const unsigned int NEIGHBORHOOD_SIZE= 5;
unsigned i;
// the population:
eoPop<Particle> pop;
// Evaluation
eoEvalFuncPtr<Particle, double, const Particle& > eval( real_value );
// position init
eoUniformGenerator < double >uGen (-3, 3);
eoInitFixedLength < Particle > random (VEC_SIZE, uGen);
// velocity init
eoUniformGenerator < double >sGen (-2, 2);
eoVelocityInitFixedLength < Particle > veloRandom (VEC_SIZE, sGen);
// local best init
eoFirstIsBestInit < Particle > localInit;
// perform position initialization
pop.append (POP_SIZE, random);
// topology
eoLinearTopology<Particle> topology(NEIGHBORHOOD_SIZE);
// the full initializer
eoInitializer <Particle> init(eval,veloRandom,localInit,topology,pop);
init();
// bounds
eoRealVectorBounds bnds(VEC_SIZE,-1.5,1.5);
// velocity
eoStandardVelocity <Particle> velocity (topology,1,1.6,2,bnds);
// flight
eoStandardFlight <Particle> flight;
// Terminators
eoGenContinue <Particle> genCont1 (50);
eoGenContinue <Particle> genCont2 (50);
// PS flight
eoEasyPSO<Particle> pso1(genCont1, eval, velocity, flight);
eoEasyPSO<Particle> pso2(init,genCont2, eval, velocity, flight);
// flight
try
{
pso1(pop);
std::cout << "FINAL POPULATION AFTER PSO n°1:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
pso2(pop);
std::cout << "FINAL POPULATION AFTER PSO n°2:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
return 0;
}

78
test/eo/t-eoEvalKeepBest.cpp Executable file
View file

@ -0,0 +1,78 @@
#include <iostream>
#include <paradiseo/eo/es/make_real.h>
#include <paradiseo/eo/apply.h>
#include <paradiseo/eo/eoEvalKeepBest.h>
#include "real_value.h"
using namespace std;
int main(int argc, char* argv[])
{
typedef eoReal<eoMinimizingFitness> EOT;
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
/*********************************************
* problem or representation dependent stuff *
*********************************************/
// The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<EOT, double, const std::vector<double>&>
main_eval( real_value ); // use a function defined in real_value.h
// wrap the evaluation function in a call counter
eoEvalFuncCounter<EOT> eval_counter(main_eval);
// the genotype - through a genotype initializer
eoRealInitBounded<EOT>& init = make_genotype(parser, state, EOT());
// Build the variation operator (any seq/prop construct)
eoGenOp<EOT>& op = make_op(parser, state, init);
/*********************************************
* Now the representation-independent things *
*********************************************/
// initialize the population - and evaluate
// yes, this is representation indepedent once you have an eoInit
eoPop<EOT>& pop = make_pop(parser, state, init);
// stopping criteria
eoContinue<EOT> & term = make_continue(parser, state, eval_counter);
// things that are called at each generation
eoCheckPoint<EOT> & checkpoint = make_checkpoint(parser, state, eval_counter, term);
// wrap the evaluator in another one that will keep the best individual
// evaluated so far
eoEvalKeepBest<EOT> eval_keep( eval_counter );
// algorithm
eoAlgo<EOT>& ea = make_algo_scalar(parser, state, eval_keep, checkpoint, op);
/***************************************
* Now, call functors and DO something *
***************************************/
// to be called AFTER all parameters have been read!
make_help(parser);
// evaluate intial population AFTER help and status in case it takes time
apply<EOT>(eval_keep, pop);
std::clog << "Best individual after initialization and " << eval_counter.value() << " evaluations" << std::endl;
std::cout << eval_keep.best_element() << std::endl;
ea(pop); // run the ea
std::cout << "Best individual after search and " << eval_counter.value() << " evaluations" << std::endl;
// you can also call value(), because it is an eoParam
std::cout << eval_keep.value() << std::endl;
}

76
test/eo/t-eoExtendedVelocity.cpp Executable file
View file

@ -0,0 +1,76 @@
//-----------------------------------------------------------------------------
// t-eoExtendedVelocity.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
typedef eoRealParticle < double > Particle;
//Evaluation function
double f (const Particle & _particle)
{
double sum = 0;
for (unsigned i = 0; i < _particle.size (); i++)
sum += pow(_particle[i],2);
return (-sum);
}
int main_function(int argc, char **argv)
{
const unsigned POP_SIZE = 6, VEC_SIZE = 2, NEIGHBORHOOD_SIZE=2;
// the population:
eoPop<Particle> pop;
// Evaluation
eoEvalFuncPtr<Particle, double, const Particle& > eval( f );
// position + velocity + best init
eoUniformGenerator < double >uGen (-3, 3);
eoInitFixedLength < Particle > random (VEC_SIZE, uGen);
eoUniformGenerator < double >sGen (-2, 2);
eoVelocityInitFixedLength < Particle > veloRandom (VEC_SIZE, sGen);
eoFirstIsBestInit < Particle > localInit;
pop.append (POP_SIZE, random);
// topology
eoLinearTopology<Particle> topology(NEIGHBORHOOD_SIZE);
eoInitializer <Particle> init(eval,veloRandom,localInit,topology,pop);
init();
// velocity
eoExtendedVelocity <Particle> velocity (topology,1,1,1,1);
// the test itself
for (unsigned int i = 0; i < POP_SIZE; i++)
{
std::cout << " Initial particle n°" << i << " velocity: " << std::endl;
for (unsigned int j = 0; j < VEC_SIZE; j++)
std::cout << " v" << j << "=" << pop[i].velocities[j] << std::endl;
}
for (unsigned int i = 0; i < POP_SIZE; i++)
velocity (pop[i],i);
for (unsigned int i = 0; i < POP_SIZE; i++)
{
std::cout << " Final particle n°" << i << " velocity: " << std::endl;
for (unsigned int j = 0; j < VEC_SIZE; j++)
std::cout << " v" << j << "=" << pop[i].velocities[j] << std::endl;
}
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
try
{
main_function(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << " in t-eoExtendedVelocity" << std::endl;
}
return EXIT_SUCCESS;
}

135
test/eo/t-eoExternalEO.cpp Executable file
View file

@ -0,0 +1,135 @@
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <iostream>
#include <stdexcept> // runtime_error
#include <paradiseo/eo.h>
/*
#include <paradiseo/eo/eoEvalFuncPtr.h>
#include <paradiseo/eo/other/external_eo>
#include <paradiseo/eo/utils/eoRNG.h>
*/
using namespace std;
struct UserDefStruct
{
int a;
float b;
double c;
enum Enum { just, another, test } d;
};
std::ostream& operator<<(std::ostream& os, const UserDefStruct& str)
{
return os << str.a << ' ' << str.b << ' ' << str.c << ' ' << static_cast<int>(str.d) << ' ';
}
istream& operator>>(istream& is, UserDefStruct& str)
{
is >> str.a;
is >> str.b;
is >> str.c;
int i;
is >> i;
str.d = static_cast<UserDefStruct::Enum>(i);
return is;
}
UserDefStruct RandomStruct()
{
std::cout << "RandomStruct\n";
UserDefStruct result;
result.a = rng.random(5);
result.b = rng.uniform();
result.c = rng.uniform();
result.d = UserDefStruct::another;
return result;
}
// reading and writing
bool UserDefMutate(UserDefStruct& a)
{
std::cout << "UserDefMutate\n";
a = RandomStruct(); // just for testing
if (rng.flip(0.1f))
a.d = UserDefStruct::test;
else
a.d = UserDefStruct::another;
return true;
}
bool UserDefBinCrossover(UserDefStruct& a, const UserDefStruct& b)
{
std::cout << "UserDefBinCrossover\n";
if (rng.flip(0.5))
a.a = b.a;
if (rng.flip(0.5))
a.b = b.b;
if (rng.flip(0.5))
a.c = b.c;
if (rng.flip(0.5))
a.d = b.d;
return true;
}
bool UserDefQuadCrossover(UserDefStruct& a, UserDefStruct& b)
{
std::cout << "UserDefQuadCrossover\n";
if (rng.flip(0.5))
swap(a.a, b.a);
if (rng.flip(0.5))
swap(a.b, b.b);
if (rng.flip(0.5))
swap(a.c, b.c);
if (rng.flip(0.5))
swap(a.d, b.d);
return true;
}
float UserDefEvalFunc(const UserDefStruct& a)
{
std::cout << "UserDefEvalFunc\n";
return a.b;
}
int main()
{
typedef UserDefStruct External;
typedef float FitnessType;
typedef eoExternalEO<float, External> EoType;
eoExternalInit<FitnessType, External> init(RandomStruct);
eoExternalMonOp<FitnessType, External> mutate(UserDefMutate);
eoExternalBinOp<FitnessType, External> cross1(UserDefBinCrossover);
eoExternalQuadOp<FitnessType, External> cross2(UserDefQuadCrossover);
// eoExternalEvalFunc<FitnessType, External> eval(UserDefEvalFunc);
EoType eo1;
init(eo1);
EoType eo2;
init(eo2);
std::cout << "before mutation " << eo1 << '\n';
mutate(eo1);
std::cout << "after mutation " << eo1 << '\n';
cross1(eo1, eo2);
std::cout << "after crossover " << eo1 << '\n';
cross2(eo1,eo2);
}

105
test/eo/t-eoFitnessAssembled.cpp Executable file
View file

@ -0,0 +1,105 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// t-eoFitnessAssembled.cpp
// Marc Wintermantel & Oliver Koenig
// IMES-ST@ETHZ.CH
// March 2003
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@inria.fr
mak@dhi.dk
*/
//-----------------------------------------------------------------------------
#include <iostream>
#include <stdexcept>
#include <paradiseo/eo.h>
//#include "eoScalarFitnessAssembled.h"
void test_eoScalarFitnessAssembledClass(){
// Create instances
eoAssembledMinimizingFitness A,B,C(5, 1.3, "C value");
// Add some values to them
A.push_back( 5.6, "first value" );
A.push_back( 3.2, "second value" );
A.push_back( 2.6, "third value" );
B.push_back( 1.2 );
B.push_back( 3.2 );
B.push_back( 5.2 );
B.setDescription( 1, "B descr" );
std::cout << "Created instances A,B and C, added some vals; testing << operator " << std::endl;
std::cout << "A= " << A << std::endl;
std::cout << "B= " << B << std::endl;
std::cout << "C= " << C << std::endl;
std::cout << "Printing values and descriptions: " << std::endl;
std::cout << "A: "; A.printAll( std::cout ); std::cout << std::endl;
std::cout << "B: "; B.printAll( std::cout ); std::cout << std::endl;
std::cout << "C: "; C.printAll( std::cout ); std::cout << std::endl;
A.resize(8, 100.3, "A resized");
std::cout << "Resized A: "; A.printAll( std::cout ); std::cout << std::endl;
std::cout << "Access fitness values of A and B: " << "f(A)= " << (double) A << " f(B)= " << (double) B << std::endl;
// Testing constructors and assignments
eoAssembledMinimizingFitness D(A) ,E(3.2);
std::cout << "D(A) = " << D << "\t" << "E(3.2)= " << E << std::endl;
eoAssembledMinimizingFitness F,G;
F=A;
G= 7.5;
std::cout << "F = A : " << F << "\t G = 7.5 : " << G << std::endl;
// Comparing...
std::cout << "A<B: " << (A<B) << std::endl;
std::cout << "A>B: " << (A>B) << std::endl;
std::cout << "A<=B: " << (A<=B) << std::endl;
std::cout << "A>=B: " << (A>=B) << std::endl;
}
int main(){
std::cout << "-----------------------------------" << std::endl;
std::cout << "START t-eoFitnessAssembled" << std::endl;
try{
// Test the fitness class itself
test_eoScalarFitnessAssembledClass();
}
catch(std::exception& e){
std::cout << e.what() << std::endl;
return 1;
}
std::cout << "END t-eoFitnessAssembled" << std::endl;
std::cout << "----------------------------------" << std::endl;
return 0;
}

175
test/eo/t-eoFitnessAssembledEA.cpp Executable file
View file

@ -0,0 +1,175 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// t-eoFitnessAssembledEA.cpp
// Marc Wintermantel & Oliver Koenig
// IMES-ST@ETHZ.CH
// March 2003
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@inria.fr
mak@dhi.dk
*/
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <iostream>
#include <cmath>
// General eo includes
#include <paradiseo/eo.h>
#include <paradiseo/eo/utils/eoRealVectorBounds.h> // The real bounds (not yet in general eo include)
// Representation dependent includes and typedefs
#include <paradiseo/eo/es/eoReal.h> // Definition of representation
#include <paradiseo/eo/es/eoRealInitBounded.h> // Uniformly initializes real vector in bounds
#include <paradiseo/eo/es/make_genotype_real.h> // Initialization of a genotype
#include <paradiseo/eo/eoEvalFunc.h> // Base class for fitness evaluation
#include <paradiseo/eo/es/make_op_real.h> // Variation operators using standard Real operators
#include <paradiseo/eo/eoScalarFitnessAssembled.h> // The fitness class
typedef eoReal<eoAssembledMinimizingFitness> Indi;
// Representation independent modules
#include <paradiseo/eo/do/make_pop.h> // Initialization of population
#include <paradiseo/eo/do/make_continue.h> // The stopping criterion
#include <paradiseo/eo/do/make_checkpoint_assembled.h> // Outputs (stats, population dumps, ...)
#include <paradiseo/eo/do/make_algo_scalar.h> // Evolution engine (selection and replacement)
#include <paradiseo/eo/do/make_run.h> // simple call to the algo.stays there for consistency reasons
// Define a fitness class
template <class EOT>
class eoAssembledEvalFunc : public eoEvalFunc<EOT>{
public:
// Constructor defining number and descriptions of fitness terms
eoAssembledEvalFunc() {
// Define a temporary fitness object to have access to its static traits
typename EOT::Fitness tmpfit(3, 0.0);
tmpfit.setDescription(0,"Fitness");
tmpfit.setDescription(1,"Some Value");
tmpfit.setDescription(2,"Other Value");
}
void operator()(EOT& _eo){
// Define temporary fitness object
// (automatically gets initialized with size given in constructor)
typename EOT::Fitness tmpfit;
// Eval some dummy fitness
double sum1=0.0, sum2=0.0;
for (unsigned i=0; i < _eo.size(); ++i){
sum1 += _eo[i]*_eo[i];
sum2 += fabs(_eo[i]) + fabs(_eo[i]);
}
// Store some fitness terms
tmpfit[1]= sum1;
tmpfit[2]= sum2;
// Store the fitness
tmpfit = (sum1 + sum2)/_eo.size();
// Pass it
_eo.fitness( tmpfit );
}
};
// checks for help demand, and writes the status file and make_help; in libutils
void make_help(eoParser & _parser);
// now use all of the above, + representation dependent things
int main(int argc, char* argv[]){
std::cout << "-----------------------------------" << std::endl;
std::cout << "START t-eoFitnessAssembledEA" << std::endl;
try{
// Parser & State
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
////
// A) Representation dependent stuff
////
// The fitness
eoAssembledEvalFunc<Indi> plainEval;
// turn that object into an evaluation counter
eoEvalFuncCounter<Indi> eval(plainEval);
// The genotype
eoRealInitBounded<Indi>& init = do_make_genotype(parser, state, Indi() );
// The variation operators
eoGenOp<Indi>& op = do_make_op(parser, state, init);
////
// B) Create representation independent stuff
////
// initialize the population
// yes, this is representation indepedent once you have an eoInit
eoPop<Indi>& pop = do_make_pop(parser, state, init);
// stopping criteria
eoContinue<Indi> & term = do_make_continue(parser, state, eval);
// output
eoCheckPoint<Indi> & checkpoint = do_make_checkpoint_assembled(parser, state, eval, term);
// algorithm (need the operator!)
eoAlgo<Indi>& ga = do_make_algo_scalar(parser, state, eval, checkpoint, op);
make_help(parser); // To be called after all parameters have been read !
////
// C) Run the algorithm
////
// evaluate intial population AFTER help and status in case it takes time
apply<Indi>(eval, pop);
// if you want to print it out
std::cout << "Initial Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
do_run(ga, pop); // run the ga
std::cout << "Final Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
return 1;
}
std::cout << "-----------------------------------" << std::endl;
std::cout << "END t-eoFitnessAssembledEA" << std::endl;
return 0;
}

48
test/eo/t-eoFunctor.cpp Executable file
View file

@ -0,0 +1,48 @@
#include <paradiseo/eo/eoInit.h>
#include <paradiseo/eo/eoCounter.h>
void f(eoInit<int>& func)
{
int i;
func(i);
}
class Tester : public eoInit<int>
{
public :
void operator()(int& i)
{
i=1;
}
};
#include <iostream>
#include <paradiseo/eo/eoFixedLength.h>
#include <paradiseo/eo/eoVariableLength.h>
using namespace std;
int main(void)
{
Tester test;
eoFunctorStore store;
/// make a counter and store it in 'store'
eoInit<int>& cntr = make_counter(functor_category(test), test, store);
eoUnaryFunctorCounter<eoInit<int> > cntr2(test);
f(cntr);
f(cntr2);
f(cntr2);
f(test);
typedef eoVariableLength<double, int> EoType;
EoType eo;
eo.push_back(1);
eo.push_back(2);
return 1;
}

72
test/eo/t-eoGA.cpp Executable file
View file

@ -0,0 +1,72 @@
#include <iostream>
#include <paradiseo/eo/ga/make_ga.h>
#include <paradiseo/eo/eoEvalFuncPtr.h>
#include "binary_value.h"
#include <paradiseo/eo/apply.h>
using namespace std;
int main(int argc, char* argv[])
{
try
{
typedef eoBit<double> EOT;
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
///// FIRST, problem or representation dependent stuff
//////////////////////////////////////////////////////
// The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<EOT, double> mainEval( binary_value<EOT> );
eoEvalFuncCounter<EOT> eval(mainEval);
// the genotype - through a genotype initializer
eoInit<EOT>& init = make_genotype(parser, state, EOT());
// Build the variation operator (any seq/prop construct)
eoGenOp<EOT>& op = make_op(parser, state, init);
//// Now the representation-independent things
//////////////////////////////////////////////
// initialize the population - and evaluate
// yes, this is representation indepedent once you have an eoInit
eoPop<EOT>& pop = make_pop(parser, state, init);
// stopping criteria
eoContinue<EOT> & term = make_continue(parser, state, eval);
// output
eoCheckPoint<EOT> & checkpoint = make_checkpoint(parser, state, eval, term);
// algorithm (need the operator!)
eoAlgo<EOT>& ga = make_algo_scalar(parser, state, eval, checkpoint, op);
///// End of construction of the algorith
/////////////////////////////////////////
// to be called AFTER all parameters have been read!!!
make_help(parser);
//// GO
///////
// evaluate intial population AFTER help and status in case it takes time
apply<EOT>(eval, pop);
// print it out
std::cout << "Initial Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
run_ea(ga, pop); // run the ga
std::cout << "Final Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
}
}

427
test/eo/t-eoGenOp.cpp Executable file
View file

@ -0,0 +1,427 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoGenOp.cpp
// (c) Maarten Keijzer and Marc Schoenauer, 2001
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: mkeijzer@dhi.dk
Marc.Schoenauer@polytechnique.fr
*/
//-----------------------------------------------------------------------------
/** test program for the general operator - millenium version!
* uses dummy individuals
*/
#include <sstream>
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoPopulator.h>
#include <paradiseo/eo/eoOpContainer.h>
struct Dummy : public EO<double>
{
Dummy(std::string _s="") : s(_s) {}
void printOn(std::ostream & _os) const
{
EO<double>::printOn(_os);
_os << " - " << s ;
}
std::string s;
};
typedef Dummy EOT;
unsigned int pSize; // global to be used as marker in the fitness
// DEFINITIONS of the eoOps
class monop : public eoMonOp<EOT>
{
public :
monop(char * _sig){sig=_sig;}
bool operator()(EOT& _eo)
{
_eo.s = sig + "(" + _eo.s + ")";
_eo.fitness(_eo.fitness()+pSize);
return false;
}
std::string className() const {return sig;}
private:
std::string sig;
};
class binop: public eoBinOp<EOT>
{
public :
bool operator()(EOT& _eo1, const EOT& _eo2)
{
_eo1.s = "bin(" + _eo1.s + "," + _eo2.s + ")";
double f= (_eo1.fitness()+_eo2.fitness()) * pSize;
_eo1.fitness(_eo1.fitness()+f);
return false;
}
std::string className() const {return "binop";}
};
class quadop: public eoQuadOp<EOT>
{
public :
std::string className() const {return "quadop";}
bool operator()(EOT& a, EOT& b)
{
EOT oi = a;
EOT oj = b;
a.s = "quad1(" + oi.s + "," + oj.s + ")";
b.s = "quad2(" + oj.s + "," + oi.s + ")";
double f= (a.fitness()+b.fitness()+2*pSize) * pSize;
a.fitness(a.fitness()+f);
b.fitness(b.fitness()+f);
return false;
}
};
// an eoQuadOp that does nothing
class quadClone: public eoQuadOp<EOT>
{
public :
std::string className() const {return "quadclone";}
bool operator()(EOT& , EOT& ) {return false;}
};
// User defined General Operator... adapted from Marc's example
class one2threeOp : public eoGenOp<EOT> // :-)
{
public:
unsigned max_production(void) { return 3; }
void apply(eoPopulator<EOT>& _plop)
{
EOT& eo = *_plop; // select the guy
++_plop; // advance
_plop.insert("v(" + eo.s + ", 1)");
++_plop;
_plop.insert("v(" + eo.s + ", 2)");
eo.s = "v(" + eo.s + ", 0)"; // only now change the thing
// oh right, and invalidate fitnesses
}
virtual std::string className() const {return "one2threeOp";}
};
class two2oneOp : public eoGenOp<EOT> // :-)
{
public:
unsigned max_production(void) { return 1; }
void apply(eoPopulator<EOT>& _plop)
{
EOT& eo = *_plop; // select the guy
const EOT& eo2 = _plop.select();
eo.s = "221(" + eo.s + ", " + eo2.s + ")";
// oh right, and invalidate fitnesses
}
virtual std::string className() const {return "two2oneOp";}
};
class three2threeOp : public eoGenOp<EOT> // :-)
{
public:
unsigned max_production(void) { return 3; }
void apply(eoPopulator<EOT>& _plop)
{
EOT& eo1 = *_plop; // select 1st guy
EOT& eo2 = *++_plop; // select 2nd guy
EOT& eo3 = *++_plop; // select 3rd guy
EOT a = eo1;
EOT b = eo2;
EOT c = eo3;
std::cout << "les selectionnes: a=" << a << " et b=" << b << " et c=" << c << std::endl;
eo1.s = "323-1(" + a.s + ", " + b.s + ", " + c.s + ")";
eo2.s = "323-2(" + a.s + ", " + b.s + ", " + c.s + ")";
eo3.s = "323-3(" + a.s + ", " + b.s + ", " + c.s + ")";
// oh right, and invalidate fitnesses
std::cout << "les enfants: a=" << eo1 << " et b=" << eo2 << " et c=" << eo3 << std::endl;
}
virtual std::string className() const {return "three2threeOp";}
};
// dummy intialization. Re-init if no pSize, resize first if pSize
void init(eoPop<Dummy> & _pop, unsigned _pSize)
{
if (_pSize)
{
_pop.resize(_pSize);
}
else
{
throw std::runtime_error("init pop with 0 size");
}
for (unsigned i=0; i<_pSize; i++)
{
std::ostringstream os;
os << i;
_pop[i] = Dummy(os.str());
_pop[i].fitness(i);
}
}
// ok, now for the real work
int the_main(int argc, char **argv)
{
eoParser parser(argc, argv);
eoValueParam<unsigned int> parentSizeParam(
parser.createParam(unsigned(10), "parentSize", "Parent size",'P'));
pSize = parentSizeParam.value(); // global variable
eoValueParam<uint32_t> seedParam(time(0), "seed", "Random number seed", 'S');
parser.processParam( seedParam );
eo::rng.reseed(seedParam.value());
// do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
// i.e. in case you need parameters somewhere else, postpone these
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
////////////////////////////////// define operators
monop mon((char*)"mon1");
monop clone((char*)"clone");
binop bin;
quadop quad;
quadClone quadclone;
// our own operator
one2threeOp o2t;
two2oneOp t2o;
three2threeOp t2t;
// a selector
eoDetTournamentSelect<EOT> select;
// and a recognizable selector for testing the inbedded selector mechanism
eoBestSelect<EOT> selectBest;
// proportional selection between quad and bin
// so we either do a quad or a bin
eoProportionalOp<EOT> pOp;
pOp.add(quad, 0.1);
pOp.add(bin, 0.1);
// sequential selection between pOp and mon
eoSequentialOp<EOT> sOp;
sOp.add(pOp, 0.9);
sOp.add(mon, 0.1);
// with one2three op
eoSequentialOp<EOT> sOp2;
sOp2.add(o2t, 1);
// sOp2.add(quad, 1);
// with three2three op
eoSequentialOp<EOT> sOp3;
sOp3.add(t2t, 1);
// eoSequentialOp<EOT> sOp3;
// sOp3.add(t2o, 1);
// sOp3.add(bin, 1);
// sOp3.add(quad, 1);
// try adding quads and bins to see what results you'll get
// now a sequential selection that is a simple "addition"
eoSequentialOp<EOT> sOpQuadPlusMon;
sOpQuadPlusMon.add(quad, 1);
sOpQuadPlusMon.add(mon, 1);
// this corresponds
eoProportionalOp<EOT> pOpSAGLike;
pOpSAGLike.add(sOpQuadPlusMon, 0.24);
pOpSAGLike.add(quad, 0.56);
pOpSAGLike.add(mon, 0.06);
pOpSAGLike.add(clone, 0.14);
// init
eoPop<EOT> pop;
eoPop<EOT> offspring;
init(pop, pSize);
// sort pop so seqPopulator is identical to SelectPopulator(SequentialSelect)
pop.sort();
std::cout << "Population initiale" << std::endl << pop << std::endl;
// To simulate SGA: first a prop between quadOp and quadClone
eoProportionalOp<EOT> pSGAOp;
pSGAOp.add(quad, 0.8);
pSGAOp.add(quadclone, 0.2);
// sequential selection between pSGAOp and mon
eoSequentialOp<EOT> virtualSGA;
virtualSGA.add(pSGAOp, 1.0);
virtualSGA.add(mon, 0.3);
eoSeqPopulator<EOT> popit(pop, offspring); // no selection, a copy of pop
// until we filled a new population
try
{
while (offspring.size() < pop.size())
{
virtualSGA(popit);
std::cout << "SeqPopulator boucle et incremente\n";
++popit;
}
}
catch(eoPopulator<EOT>::OutOfIndividuals&)
{
std::cout << "Warning: not enough individuals to handle\n";
}
std::swap(pop, offspring);
offspring.clear();
// ok, now print
std::cout << "Apres virtualSGA \n" << pop << std::endl;
init(pop, pSize);
std::cout << "=========================================================\n";
std::cout << "Now the eoSelectPopulator version !" << std::endl;
eoSequentialSelect<EOT> seqSelect;
// select.init(); should be sorted out: is it the setup method???
eoSelectivePopulator<EOT> it_step3(pop, offspring, seqSelect);
while (offspring.size() < 2*pop.size())
{
virtualSGA(it_step3);
std::cout << "SelectPopulator boucle et incremente\n";
++it_step3;
}
std::swap(pop, offspring);
offspring.clear();
// ok, now print
std::cout << "Apres SGA-like eoSelectivePopulator\n" << pop << std::endl;
std::cout << "=========================================================\n";
std::cout << "Now the pure addition !" << std::endl;
init(pop, pSize);
eoSelectivePopulator<EOT> it_step4(pop, offspring, seqSelect);
while (offspring.size() < 2*pop.size())
{
sOpQuadPlusMon(it_step4);
++it_step4;
}
std::swap(pop, offspring);
offspring.clear();
// ok, now print
std::cout << "Apres Quad+Mon ds un eoSelectivePopulator\n" << pop << std::endl;
// On teste 1->3
init(pop, pSize);
eoSelectivePopulator<EOT> it_step5(pop, offspring, seqSelect);
while (offspring.size() < 2*pop.size())
{
sOp2(it_step5);
++it_step5;
}
std::swap(pop, offspring);
offspring.clear();
// ok, now print
std::cout << "Apres 1->3 seul ds un eoSelectivePopulator\n" << pop << std::endl;
// On teste 3->3
init(pop, pSize);
eoSelectivePopulator<EOT> it_step6(pop, offspring, seqSelect);
while (offspring.size() < 2*pop.size())
{
sOp3(it_step6);
++it_step6;
}
std::swap(pop, offspring);
offspring.clear();
// ok, now print
std::cout << "Apres 3->3 seul ds un eoSelectivePopulator\n" << pop << std::endl;
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
}
}
/*
If you want to build an SGA, you will need a copying quad op:
class quadclone : ...
{
operator(EOT& a, EOT& b)
{
// do nothing
}
}
Then the SGA operator will look like:
quadop quad;
guadclone clone;
ProportionalGenOp pOp;
pOp.add(quad, 0.8);
pOp.add(clone, 0.2); // so 80% xover rate
SequentialGenOp sOp;
sOp.add(pOp, 1,0); // always try a xover (clone 20%)
sOp.add(mut, 0.1); // low mutation rate
will result in an algorithm with:
p_xover = 0.8
p_mut = 0.1;
p_reproduction = 0.2 * 0.9 = 0.18
this does not add up to 1 because xover and mutation can be applied to a single indi
So what do you think?
*/

67
test/eo/t-eoIQRStat.cpp Executable file
View file

@ -0,0 +1,67 @@
#include <paradiseo/eo.h>
#include <paradiseo/eo/es.h>
#include <paradiseo/eo/utils/eoStat.h>
#include "real_value.h"
typedef eoReal<eoMinimizingFitness> realVec;
double test( eoPop<realVec>& pop, double target_value )
{
eoEvalFuncPtr<realVec, double, const std::vector<double>&> eval( real_value );
eoPopLoopEval<realVec> pop_eval(eval);
pop_eval(pop,pop);
eoInterquartileRangeStat<realVec> iqr_stat(0.0, "IQR");
iqr_stat( pop );
std::cout << iqr_stat.longName() << "=" << iqr_stat.value() << " should be " << target_value << std::endl;
return iqr_stat.value();
}
int main()
{
eoPop<realVec> pop;
// fixed test
realVec sol1(2,-1);
realVec sol2(2,-1);
realVec sol3(2,1);
realVec sol4(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
// on the sphere function everyone has the same fitness of 1
if( test(pop, 0) != 0 ) {
exit(1);
}
pop.erase(pop.begin(),pop.end());
// fixed test
sol1 = realVec(2,0);
sol2 = realVec(2,0);
sol3 = realVec(2,1);
sol4 = realVec(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
if( test(pop, 1) != 1 ) {
exit(1);
}
// test on a random normal distribution
eoNormalGenerator<double> normal(1,rng);
eoInitFixedLength<realVec> init_N(2, normal);
pop = eoPop<realVec>( 1000000, init_N );
double iqr = test(pop, 1.09);
if( iqr < 1.08 || iqr > 1.11 ) {
exit(1);
}
}

68
test/eo/t-eoInitPermutation.cpp Executable file
View file

@ -0,0 +1,68 @@
//-----------------------------------------------------------------------------
// t-eoInitPermutation.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
//-----------------------------------------------------------------------------
typedef eoInt<double> Chrom;
//-----------------------------------------------------------------------------
double real_value(const Chrom & _chrom)
{
double sum = 0;
for (unsigned i = 0; i < _chrom.size(); i++)
sum += _chrom[i];
return sum/_chrom.size();
}
// Return true if the given chromosome corresponds to a permutation
// There must be an nicer way to do it (set?) ...
bool check_permutation(const Chrom & _chrom)
{
for (unsigned i = 0; i < _chrom.size(); ++i)
for (unsigned j = 0; j < _chrom.size(); ++j)
if(i!=j)
if(_chrom[i]==_chrom[j]){
std::cout << " Error: Wrong permutation !" << std::endl;
std::string s;
s.append( " Wrong permutation in t-eoInitPermutation");
throw std::runtime_error( s );
}
return true;
}
int main()
{
const unsigned POP_SIZE = 8, CHROM_SIZE = 16;
unsigned i;
// a chromosome randomizer
eoInitPermutation <Chrom> random(CHROM_SIZE);
// the population:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( real_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
std::cout << " Initial chromosome n°" << i << " : " << chrom << "..." << std::endl;
random(chrom);
eval(chrom);
std::cout << " ... becomes : " << chrom << " after initialization" << std::endl;
check_permutation(chrom);
pop.push_back(chrom);
}
return 0;
}
//-----------------------------------------------------------------------------

98
test/eo/t-eoInitVariableLength.cpp Executable file
View file

@ -0,0 +1,98 @@
#include <iostream>
#include <vector>
#include <paradiseo/eo.h>
// An adhoc atom type of our own
class Quad : public std::vector<int>
{
public:
// Just four times zero
Quad() : std::vector<int>(4,0) {}
};
// EO somewhat forces you to implement a way to read/print your atom type
// You can either inherit from eoPrintable and overload readFrom/printOn
// or, just like here, directly overload stream operators.
// read
std::istream& operator>>( std::istream& is, Quad& q )
{
for( unsigned int i=0, n=4; i<n; ++i) {
// use default int stream input
is >> q[i];
}
return is;
}
// print
std::ostream& operator<<( std::ostream& os, const Quad& q )
{
os << q[0];
for( unsigned int i=1, n=4; i<n; ++i) {
os << " " << q[i];
}
os << " ";
return os;
}
// An init for the atoms
// Note that this mask the template passed to the eoInit
class QuadInit : public eoInit<Quad>
{
public:
// this is the API: an init modify the solution
void operator()( Quad& q ) {
for( unsigned int i=0, n=4; i<n; ++i) {
// rng is the random number generator of EO
q[i] = rng.random(10);
}
}
};
// The solution/individual type.
// Just a proxy to an eoVector of atoms,
// with a fitness as double.
class QuadVec : public eoVector<double,Quad>
{};
int main()
{
unsigned int vec_size_min = 1;
unsigned int vec_size_max = 10;
unsigned int pop_size = 10;
// Fix a seed for the random generator,
// thus, the results are predictable.
// Set it to zero if you want pseudo-random numbers
// that changes at each calls.
rng.reseed( 1 );
// The operator that produce a random vector of four values.
QuadInit atom_init;
// The operator that produces a random vector of a (vector of four values).
eoInitVariableLength<QuadVec> vec_init( vec_size_min, vec_size_max, atom_init );
// You can initialize a population of N individuals by passing an initializer to it.
eoPop<QuadVec> pop( pop_size, vec_init );
// eoPop can be printed easily,
// thanks to the overloadings above.
std::cout << pop << std::endl;
// With a seed at 1, this should output:
/*
10
INVALID 6 5 9 5 9 0 1 6 0 4 8 9 0 6 9 4 9 5 5 3 6 3 0 2 8
INVALID 9 9 2 0 3 2 4 3 3 6 2 8 2 4 5 4 7 5 3 0 5 4 9 8 3 2 7 7 9 4 4 4 6 6 3 9 2
INVALID 1 1 4 1 4
INVALID 5 3 8 9 8 8 1 4 1 6 6 5 4 3 2 7 5 1 2 6 1
INVALID 3 7 8 1 4 0 9 1 0 6 4 2 1
INVALID 6 7 4 6 8 1 2 6 0 5 1 2 6 9 2 6 8 6 1 5 5 4 1 0 3
INVALID 5 2 7 7 6 1 4 0 7 5 5 9 7 2 4 7 1 6 1 9 0
INVALID 3 5 5 3 9 2 9 9 1 1 7 2 1
INVALID 6 9 9 9 0 0 7 1 7 9 7 8 5 3 7 5 6 7 3 6 7 6 3 3 5
INVALID 1 6 2 4 3
*/
}

24
test/eo/t-eoInt.cpp Executable file
View file

@ -0,0 +1,24 @@
//-----------------------------------------------------------------------------
// t-eoInt.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
//-----------------------------------------------------------------------------
typedef eoInt<double> Chrom;
//-----------------------------------------------------------------------------
int main()
{
Chrom chrom1, chrom2;
std::cout << "chrom1 = " << chrom1 << std::endl
<< "chrom2 = " << chrom2 << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

50
test/eo/t-eoLogger.cpp Executable file
View file

@ -0,0 +1,50 @@
//-----------------------------------------------------------------------------
// t-eoLogger.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
//-----------------------------------------------------------------------------
int main(int ac, char** av)
{
eoParser parser(ac, av);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
make_help(parser);
make_verbose(parser);
eo::log << eo::setlevel(eo::debug);
eo::log << eo::warnings;
eo::log << "We are writing on the default output stream" << std::endl;
eo::log << eo::file("test.txt") << "In FILE" << std::endl;
eo::log << std::cout << "on COUT" << std::endl;
eo::log << eo::setlevel("errors");
eo::log << eo::setlevel(eo::errors);
eo::log << eo::quiet << "1) in quiet mode" << std::endl;
eo::log << eo::setlevel(eo::warnings) << eo::warnings << "2) in warnings mode" << std::endl;
eo::log << eo::setlevel(eo::logging);
eo::log << eo::errors;
eo::log << "3) in errors mode";
eo::log << std::endl;
eo::log << eo::debug << 4 << ')'
<< "4) in debug mode\n";
return 0;
}
//-----------------------------------------------------------------------------

72
test/eo/t-eoOrderXover.cpp Executable file
View file

@ -0,0 +1,72 @@
//-----------------------------------------------------------------------------
// t-eoOrderXover.cpp
//-----------------------------------------------------------------------------
#include <set>
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
#include <paradiseo/eo/eoOrderXover.h>
//-----------------------------------------------------------------------------
typedef eoInt<int> Chrom;
//-----------------------------------------------------------------------------
// Return true if the given chromosome corresponds to a permutation
bool check_permutation(const Chrom& _chrom){
unsigned size= _chrom.size();
std::set<unsigned> verif;
for(unsigned i=0; i< size; i++){
if(verif.insert(_chrom[i]).second==false){
std::cout << " Error: Wrong permutation !" << std::endl;
std::string s;
s.append( " Wrong permutation in t-eoShiftMutation");
throw std::runtime_error( s );
return false;
}
}
return true;
}
int main()
{
const unsigned POP_SIZE = 3, CHROM_SIZE = 8;
unsigned i;
// a chromosome randomizer
eoInitPermutation <Chrom> random(CHROM_SIZE);
// the population:
eoPop<Chrom> pop;
// Evaluation
//eoEvalFuncPtr<Chrom> eval( real_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
random(chrom);
//eval(chrom);
pop.push_back(chrom);
}
// a shift mutation
eoOrderXover<Chrom> cross;
for (i = 0; i < POP_SIZE; ++i)
std::cout << " Initial chromosome n<>" << i << " : " << pop[i] << "..." << std::endl;
cross(pop[0],pop[1]);
cross(pop[1],pop[2]);
for (i = 0; i < POP_SIZE; ++i) {
std::cout << " Initial chromosome n<>" << i << " becomes : " << pop[i] << " after orderXover" << std::endl;
check_permutation(pop[i]);
}
return 0;
}
//-----------------------------------------------------------------------------

148
test/eo/t-eoPBIL.cpp Executable file
View file

@ -0,0 +1,148 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// t-eoPBIL.cpp
// (c) Marc Schoenauer, 2001
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: Marc.Schoenauer@inria.fr
*/
//-----------------------------------------------------------------------------
/** test program for PBIL algorithm */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <iostream>
#include <paradiseo/eo.h>
#include <paradiseo/eo/ga/make_ga.h>
#include "binary_value.h"
#include <paradiseo/eo/apply.h>
#include <paradiseo/eo/ga/eoPBILDistrib.h>
#include <paradiseo/eo/ga/eoPBILOrg.h>
#include <paradiseo/eo/ga/eoPBILAdditive.h>
#include <paradiseo/eo/eoSimpleEDA.h>
using namespace std;
typedef eoBit<double> Indi;
// instanciating the outside subroutine that creates the distribution
#include <paradiseo/eo/ga/make_PBILdistrib.h>
eoPBILDistrib<Indi> & make_PBILdistrib(eoParser& _parser, eoState&_state, Indi _eo)
{
return do_make_PBILdistrib(_parser, _state, _eo);
}
// instanciating the outside subroutine that creates the update rule
#include <paradiseo/eo/ga/make_PBILupdate.h>
eoDistribUpdater<Indi> & make_PBILupdate(eoParser& _parser, eoState&_state, Indi _eo)
{
return do_make_PBILupdate(_parser, _state, _eo);
}
int main(int argc, char* argv[])
{
try
{
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
///// FIRST, problem or representation dependent stuff
//////////////////////////////////////////////////////
// The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<Indi, double> mainEval( binary_value<Indi>);
eoEvalFuncCounter<Indi> eval(mainEval);
// Construction of the distribution
eoPBILDistrib<Indi> & distrib = make_PBILdistrib(parser, state, Indi());
// and the update rule
eoDistribUpdater<Indi> & update = make_PBILupdate(parser, state, Indi());
//// Now the representation-independent things
//////////////////////////////////////////////
// stopping criteria
eoContinue<Indi> & term = make_continue(parser, state, eval);
// output
eoCheckPoint<Indi> & checkpoint = make_checkpoint(parser, state, eval, term);
// add a graphical output for the distribution
// first, get the direname from the parser
// it has been enetered in make_checkoint
eoParam* ptParam = parser.getParamWithLongName(string("resDir"));
eoValueParam<string>* ptDirNameParam = dynamic_cast<eoValueParam<string>*>(ptParam);
if (!ptDirNameParam) // not found
throw runtime_error("Parameter resDir not found where it was supposed to be");
// now create the snapshot monitor
eoValueParam<bool>& plotDistribParam = parser.getORcreateParam(false, "plotDistrib",
"Plot Distribution", '\0',
"Output - Graphical");
if (plotDistribParam.value())
{
#ifdef HAVE_GNUPLOT
unsigned frequency=1; // frequency of plots updates
eoGnuplot1DSnapshot *distribSnapshot = new eoGnuplot1DSnapshot(ptDirNameParam->value(),
frequency, "distrib");
state.storeFunctor(distribSnapshot);
// add the distribution (it is an eoValueParam<vector<double> >)
distribSnapshot->add(distrib);
// and of course add it to the checkpoint
checkpoint.add(*distribSnapshot);
#endif
}
// the algorithm: EDA
// don't know where else to put the population size!
unsigned popSize = parser.getORcreateParam(unsigned(100), "popSize",
"Population Size", 'P', "Algorithm").value();
eoSimpleEDA<Indi> eda(update, eval, popSize, checkpoint);
///// End of construction of the algorith
/////////////////////////////////////////
// to be called AFTER all parameters have been read!!!
make_help(parser);
//// GO
///////
eda(distrib); // run the eda
std::cout << "Final Distribution\n";
distrib.printOn(std::cout);
std::cout << std::endl;
// wait - for graphical output
if (plotDistribParam.value())
{
string foo;
cin >> foo;
}
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
}
}

61
test/eo/t-eoParallel.cpp Executable file
View file

@ -0,0 +1,61 @@
//-----------------------------------------------------------------------------
// t-eoParallel.cpp
//-----------------------------------------------------------------------------
#include <omp.h>
#include <paradiseo/eo.h>
#include <paradiseo/eo/es/make_real.h>
//#include <paradiseo/eo/apply.h>
#include "real_value.h"
//-----------------------------------------------------------------------------
typedef eoReal< eoMinimizingFitness > EOT;
int main(int ac, char** av)
{
eoParser parser(ac, av);
unsigned int popSize = parser.getORcreateParam((unsigned int)100, "popSize", "Population Size", 'P', "Evolution Engine").value();
unsigned int dimSize = parser.getORcreateParam((unsigned int)10, "dimSize", "Dimension Size", 'd', "Evolution Engine").value();
uint32_t seedParam = parser.getORcreateParam((uint32_t)0, "seed", "Random number seed", 0).value();
if (seedParam == 0) { seedParam = time(0); }
make_parallel(parser);
make_help(parser);
rng.reseed( seedParam );
eoUniformGenerator< double > gen(-5, 5);
eoInitFixedLength< EOT > init( dimSize, gen );
eoEvalFuncPtr< EOT, double, const std::vector< double >& > mainEval( real_value );
eoEvalFuncCounter< EOT > eval( mainEval );
eoPop< EOT > pop( popSize, init );
//apply< EOT >( eval, pop );
eoPopLoopEval< EOT > popEval( eval );
popEval( pop, pop );
eo::log << eo::quiet << "DONE!" << std::endl;
#ifdef ENABLE_OPENMP
#pragma omp parallel
{
if ( 0 == omp_get_thread_num() ) //Warning: omp_get_thread_num doestn't work with pragma and required openMP
{
eo::log << "num of threads: " << omp_get_num_threads() << std::endl; //Warning: omp_get_num_threads doestn't work with pragma and required openMP
}
}
return 0;
#endif
}
//-----------------------------------------------------------------------------

31
test/eo/t-eoParser.cpp Executable file
View file

@ -0,0 +1,31 @@
#include <iostream>
#include <paradiseo/eo.h>
int main(int ac, char** av)
{
eoParser parser(ac, av);
unsigned int alpha1 = parser.createParam(10, "alpha1", "Alpha parameter").value();
unsigned int alpha2 = parser.createParam(10, "alpha2", "Alpha parameter").value();
unsigned int alpha3 = parser.createParam(10, "alpha3", "Alpha parameter").value();
unsigned int alpha4 = parser.createParam(10, "alpha4", "Alpha parameter").value();
unsigned int alpha5 = parser.createParam(10, "alpha5", "Alpha parameter").value();
unsigned int alpha6 = parser.createParam(10, "alpha6", "Alpha parameter").value();
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
make_help(parser);
std::cout << "alpha1: " << alpha1 << std::endl;
std::cout << "alpha2: " << alpha2 << std::endl;
std::cout << "alpha3: " << alpha3 << std::endl;
std::cout << "alpha4: " << alpha4 << std::endl;
std::cout << "alpha5: " << alpha5 << std::endl;
std::cout << "alpha6: " << alpha6 << std::endl;
return 0;
}

53
test/eo/t-eoRNG.cpp Executable file
View file

@ -0,0 +1,53 @@
//-----------------------------------------------------------------------------
// t-rng.cpp
//-----------------------------------------------------------------------------
// This file really needs to be implementes usign some stringent tests, for now
// we simply check that the impementation of some methods does generally work...
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <iostream>
#include <paradiseo/eo.h>
#include <paradiseo/eo/utils/eoRNG.h>
using namespace std;
int main()
{
const size_t num(10000);
double mean(100.);
double sigma(5.);
double sum(0.);
for(size_t i=0; i<num; ++i)
sum += abs(rng.normal(sigma));
sum /= double(num);
if(sum > sigma / 0.68) {
cerr << "Normal distribution seems out of bounds; "
<< "rerun to make sure it wasn't a statistical outlier" << endl;
return -1;
}
sum = 0.;
for(size_t i=0; i<num; ++i)
sum += abs(rng.normal(mean, sigma) - mean);
sum /= double(num);
if(sum > sigma / 0.68) {
cerr << "Normal distribution seems out of bounds; "
<< "rerun to make sure it wasn't a statistical outlier" << endl;
return -1;
}
return 0;
}
// Local Variables:
// coding: iso-8859-1
// mode: C++
// c-file-offsets: ((c . 0))
// c-file-style: "Stroustrup"
// fill-column: 80
// End:

66
test/eo/t-eoRandom.cpp Executable file
View file

@ -0,0 +1,66 @@
/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
t-eoRandom.cpp
Test program for random generator
(c) GeNeura Team, 1999
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
/**
CVS Info: $Date: 2003-02-27 19:20:24 $ $Author: okoenig $ $Revision: 1.13 $
*/
//-----------------------------------------------------------------------------
#include <iostream> // cout
#include <fstream> // ostrstream, istrstream
#include <paradiseo/eo/utils/eoRndGenerators.h> // eoBin
//#include <paradiseo/eo/eoNormal.h>
//#include <paradiseo/eo/eoNegExp.h>
//-----------------------------------------------------------------------------
int main() {
eoUniformGenerator<float> u1(-2.5,3.5);
eoUniformGenerator<double> u2(0.003, 0.05 );
eoUniformGenerator<unsigned long> u3( 10000U, 10000000U);
try
{ // throws an error
eoUniformGenerator<unsigned long> utest( 10000000U, 10000U);
throw; // if this succeeds something is wrong, make sure that that is noticed
}
catch (std::logic_error& e)
{
std::cout << e.what() << std::endl;
}
std::ofstream os("t-eoRandom.out");
for ( unsigned i = 0; i < 100; i ++)
{
os << u1() << "\t" << u2() << "\t" << u3() << std::endl;
}
return 0; // to avoid VC++ complaints
}
//-----------------------------------------------------------------------------

72
test/eo/t-eoReal.cpp Executable file
View file

@ -0,0 +1,72 @@
#include <iostream>
#include <paradiseo/eo/es/make_real.h>
#include "real_value.h"
#include <paradiseo/eo/apply.h>
using namespace std;
int main(int argc, char* argv[])
{
try
{
typedef eoReal<eoMinimizingFitness> EOT;
eoParser parser(argc, argv); // for user-parameter reading
eoState state; // keeps all things allocated
///// FIRST, problem or representation dependent stuff
//////////////////////////////////////////////////////
// The evaluation fn - encapsulated into an eval counter for output
eoEvalFuncPtr<EOT, double, const std::vector<double>&>
mainEval( real_value );
eoEvalFuncCounter<EOT> eval(mainEval);
// the genotype - through a genotype initializer
eoRealInitBounded<EOT>& init = make_genotype(parser, state, EOT());
// Build the variation operator (any seq/prop construct)
eoGenOp<EOT>& op = make_op(parser, state, init);
//// Now the representation-independent things
//////////////////////////////////////////////
// initialize the population - and evaluate
// yes, this is representation indepedent once you have an eoInit
eoPop<EOT>& pop = make_pop(parser, state, init);
// stopping criteria
eoContinue<EOT> & term = make_continue(parser, state, eval);
// output
eoCheckPoint<EOT> & checkpoint = make_checkpoint(parser, state, eval, term);
// algorithm (need the operator!)
eoAlgo<EOT>& ea = make_algo_scalar(parser, state, eval, checkpoint, op);
///// End of construction of the algorith
/////////////////////////////////////////
// to be called AFTER all parameters have been read!!!
make_help(parser);
//// GO
///////
// evaluate intial population AFTER help and status in case it takes time
apply<EOT>(eval, pop);
// print it out
std::cout << "Initial Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
run_ea(ea, pop); // run the ea
std::cout << "Final Population\n";
pop.sortedPrintOn(std::cout);
std::cout << std::endl;
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
}
}

223
test/eo/t-eoReplacement.cpp Executable file
View file

@ -0,0 +1,223 @@
//-----------------------------------------------------------------------------
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <stdexcept> // runtime_error
//-----------------------------------------------------------------------------
// tt.cpp:
//
//-----------------------------------------------------------------------------
// general
#include <paradiseo/eo.h>
//-----------------------------------------------------------------------------
struct Dummy : public EO<double>
{
typedef double Type;
void printOn(std::ostream & _os) const
{
_os << " - ";
EO<double>::printOn(_os);
}
};
struct eoDummyPop : public eoPop<Dummy>
{
public :
eoDummyPop(int s=0) { resize(s); }
};
//-----------------------------------------------------------------------------
int the_main(int argc, char **argv)
{
eoParser parser(argc, argv);
eoValueParam<unsigned int> parentSizeParam(10, "parentSize", "Parent size",'P');
parser.processParam( parentSizeParam );
unsigned int pSize = parentSizeParam.value();
eoValueParam<unsigned int> offsrpringSizeParam(10, "offsrpringSize", "Offsrpring size",'O');
parser.processParam( offsrpringSizeParam );
unsigned int oSize = offsrpringSizeParam.value();
eoValueParam<unsigned int> tournamentSizeParam(2, "tournamentSize", "Deterministic tournament size",'T');
parser.processParam( tournamentSizeParam );
unsigned int tSize = tournamentSizeParam.value();
eoValueParam<double> tournamentRateParam(0.75, "tournamentRate", "Stochastic tournament rate",'R');
parser.processParam( tournamentRateParam );
double tRate = tournamentRateParam.value();
eoValueParam<double> sParentsElitismRateParam(0.1, "sParentsElitismRateParam", "Strong elitism rate for parents",'E');
parser.processParam( sParentsElitismRateParam );
double sParentsElitismRate = sParentsElitismRateParam.value();
eoValueParam<double> sParentsEugenismRateParam(0, "sParentsEugenismRateParam", "Strong Eugenism rate",'e');
parser.processParam( sParentsEugenismRateParam );
double sParentsEugenismRate = sParentsEugenismRateParam.value();
eoValueParam<double> sOffspringElitismRateParam(0, "sOffspringElitismRateParam", "Strong elitism rate for parents",'E');
parser.processParam( sOffspringElitismRateParam );
double sOffspringElitismRate = sOffspringElitismRateParam.value();
eoValueParam<double> sOffspringEugenismRateParam(0, "sOffspringEugenismRateParam", "Strong Eugenism rate",'e');
parser.processParam( sOffspringEugenismRateParam );
double sOffspringEugenismRate = sOffspringEugenismRateParam.value();
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
unsigned i;
std::cout << "Testing the replacements\nParents SIze = " << pSize
<< " and offspring size = " << oSize << std::endl;
rng.reseed(42);
eoDummyPop orgParents(pSize);
eoDummyPop orgOffspring(oSize);
// initialize so we can recognize them later!
for (i=0; i<pSize; i++)
orgParents[i].fitness(2*i+1);
for (i=0; i<oSize; i++)
orgOffspring[i].fitness(2*i);
std::cout << "Initial parents (odd)\n" << orgParents << "\n And initial offsprings (even)\n" << orgOffspring << std::endl;
// now the ones we're going to play with
eoDummyPop parents(0);
eoDummyPop offspring(0);
// the replacement procedures under test
eoGenerationalReplacement<Dummy> genReplace;
eoPlusReplacement<Dummy> plusReplace;
eoEPReplacement<Dummy> epReplace(tSize);
eoCommaReplacement<Dummy> commaReplace;
eoWeakElitistReplacement<Dummy> weakElitistReplace(commaReplace);
// the SSGA replacements
eoSSGAWorseReplacement<Dummy> ssgaWorseReplace;
eoSSGADetTournamentReplacement<Dummy> ssgaDTReplace(tSize);
eoSSGAStochTournamentReplacement<Dummy> ssgaDSReplace(tRate);
// here we go
// Generational
parents = orgParents;
offspring = orgOffspring;
std::cout << "eoGenerationalReplacement\n";
std::cout << "=========================\n";
genReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (orogonally even\n" << offspring << std::endl;
// Plus
parents = orgParents;
offspring = orgOffspring;
std::cout << "eoPlusReplacement\n";
std::cout << "=================\n";
plusReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
// EP (proche d'un PLUS
parents = orgParents;
offspring = orgOffspring;
std::cout << "eoEPReplacement\n";
std::cout << "===============\n";
epReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
// Comma
parents = orgParents;
offspring = orgOffspring;
if (parents.size() > offspring.size() )
std::cout << "Skipping Comma Replacement, more parents than offspring\n";
else
{
std::cout << "eoCommaReplacement\n";
std::cout << "==================\n";
commaReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
// Comma with weak elitism
parents = orgParents;
offspring = orgOffspring;
std::cout << "The same, with WEAK elitism\n";
std::cout << "===========================\n";
weakElitistReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
}
// preparing SSGA replace worse
parents = orgParents;
offspring = orgOffspring;
if (parents.size() < offspring.size() )
std::cout << "Skipping all SSGA Replacements, more offspring than parents\n";
else
{
std::cout << "SSGA replace worse\n";
std::cout << "==================\n";
ssgaWorseReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
// SSGA deterministic tournament
parents = orgParents;
offspring = orgOffspring;
std::cout << "SSGA deterministic tournament\n";
std::cout << "=============================\n";
ssgaDTReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
// SSGA stochastic tournament
parents = orgParents;
offspring = orgOffspring;
std::cout << "SSGA stochastic tournament\n";
std::cout << "==========================\n";
ssgaDTReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
}
// the general replacement
eoDeterministicSaDReplacement<Dummy> sAdReplace(sParentsElitismRate, sParentsEugenismRate, sOffspringElitismRate, sOffspringEugenismRate);// 10% parents survive
parents = orgParents;
offspring = orgOffspring;
std::cout << "General - strong elitism\n";
std::cout << "========================\n";
sAdReplace(parents, offspring);
std::cout << "Parents (originally odd)\n" << parents << "\n And offsprings (originally even)\n" << offspring << std::endl;
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
}
}

67
test/eo/t-eoRingTopology.cpp Executable file
View file

@ -0,0 +1,67 @@
//-----------------------------------------------------------------------------
// t-eoRingTopology.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
typedef eoRealParticle < double >Indi;
//Evaluation function
double f (const Indi & _indi)
{
double sum = 0;
for (unsigned i = 0; i < _indi.size (); i++)
sum += pow(_indi[i],2);
return (-sum);
}
int main_function(int argc, char **argv)
{
//Parameters
const unsigned int VEC_SIZE = 2;
const unsigned int POP_SIZE = 10;
const unsigned int NEIGHBORHOOD_SIZE= 3;
rng.reseed (33);
eoEvalFuncPtr<Indi, double, const Indi& > plainEval(f);
eoEvalFuncCounter < Indi > eval (plainEval);
eoUniformGenerator < double >uGen (0., 5.);
eoInitFixedLength < Indi > random (VEC_SIZE, uGen);
eoUniformGenerator < double >sGen (-1., 1.);
eoVelocityInitFixedLength < Indi > veloRandom (VEC_SIZE, sGen);
eoFirstIsBestInit < Indi > localInit;
eoPop < Indi > pop;
pop.append (POP_SIZE, random);
apply(eval, pop);
apply < Indi > (veloRandom, pop);
apply < Indi > (localInit, pop);
eoRingTopology<Indi> topology(NEIGHBORHOOD_SIZE);
topology.setup(pop);
std::cout<<"\n\n\nPopulation :\n\n"<<pop;
std::cout<<"\n\nNeighborhood :\n\n";
topology.printOn();
int k = NEIGHBORHOOD_SIZE/2;
for(unsigned i=0;i<pop.size();i++)
{
std::cout<<"\nBetween : ";
for(unsigned j=0;j<NEIGHBORHOOD_SIZE;j++)
std::cout<<"\n"<<pop[((pop.size()+i-k+j)%pop.size())];
std::cout<<"\nThe best is : \n"<<topology.best(i)<<"\n";
}
std::cout<<"\n\n";
return 1;
}
int main(int argc, char **argv)
{
try
{
main_function(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << " in t-eoRingTopology" << std::endl;
}
}

66
test/eo/t-eoRoulette.cpp Executable file
View file

@ -0,0 +1,66 @@
#include <paradiseo/eo/eoPop.h>
#include <paradiseo/eo/EO.h>
#include <paradiseo/eo/eoProportionalSelect.h>
#include <paradiseo/eo/eoStochasticUniversalSelect.h>
class TestEO : public EO<double> { public: unsigned index; };
using namespace std;
template <class Select>
int test_select()
{
vector<double> probs(4);
probs[0] = 0.1;
probs[1] = 0.4;
probs[2] = 0.2;
probs[3] = 0.3;
vector<double> counts(4,0.0);
// setup population
eoPop<TestEO> pop;
for (unsigned i = 0; i < probs.size(); ++i)
{
pop.push_back( TestEO());
pop.back().fitness( probs[i] * 2.1232 ); // some number to check scaling
pop.back().index = i;
}
Select select;
unsigned ndraws = 10000;
for (unsigned i = 0; i < ndraws; ++i)
{
const TestEO& eo = select(pop);
counts[eo.index]++;
}
cout << "Threshold = " << 1./sqrt(double(ndraws)) << endl;
for (unsigned i = 0; i < 4; ++i)
{
cout << counts[i]/ndraws << ' ';
double c = counts[i]/ndraws;
if (fabs(c - probs[i]) > 1./sqrt((double)ndraws)) {
cout << "ERROR" << endl;
return 1;
}
}
cout << endl;
return 0;
}
int main()
{
rng.reseed(44);
if (test_select<eoProportionalSelect<TestEO> >()) return 1;
return test_select<eoStochasticUniversalSelect<TestEO> >();
}

117
test/eo/t-eoSSGA.cpp Executable file
View file

@ -0,0 +1,117 @@
#include <paradiseo/eo.h>
// tests a Steady State GA
// Needed to define this breeder, maybe make it a breeder
template <class EOT>
class eoBreedOne : public eoBreed<EOT>
{
public :
eoBreedOne(eoSelectOne<EOT>& _select, eoGenOp<EOT>& _op) : select(_select), op(_op) {}
void operator()(const eoPop<EOT>& _src, eoPop<EOT>& _dest)
{
_dest.clear();
eoSelectivePopulator<EOT> pop(_src, _dest, select);
op(pop);
}
private :
eoSelectOne<EOT>& select;
eoGenOp<EOT>& op;
};
typedef eoMinimizingFitness FitnessType;
typedef eoVector<FitnessType, unsigned> EoType;
template <class EOT>
class eoMyEval : public eoEvalFunc<EOT>
{
public :
void operator()(EOT& _eo)
{
_eo.fitness(*std::max_element(_eo.begin(), _eo.end()));
}
};
template <class EOT>
class Xover : public eoBinOp<EOT>
{
bool operator()(EOT& _eo, const EOT& _eo2)
{
unsigned point = rng.random(_eo.size());
std::copy(_eo2.begin() + point, _eo2.end(), _eo.begin() + point);
return true;
}
};
template <class EOT>
class Mutate : public eoMonOp<EOT>
{
bool operator()(EOT& _eo)
{
unsigned point = rng.random(_eo.size());
_eo[point] = rng.random(1024);
return true;
}
};
int main()
{
int pop_size = 10;
eoGenContinue<EoType> cnt(10);
eoCheckPoint<EoType> cp(cnt);
Xover<EoType> xover;
Mutate<EoType> mutate;
eoProportionalOp<EoType> opsel;
opsel.add(xover, 0.8);
opsel.add(mutate, 0.2);
eoDetTournamentSelect<EoType> selector(3);
eoBreedOne<EoType> breed(selector, opsel);
// Replace a single one
eoSSGAWorseReplacement<EoType> replace;
// eoRandomSelect<EoType> selector;
// eoGeneralBreeder<EoType> breed(selector, opsel);
// eoPlusReplacement<EoType> replace;
eoMyEval<EoType> eval;
eoEasyEA<EoType> algo(cp, eval, breed, replace);
eoUniformGenerator<unsigned> unif(0,1024);
eoInitFixedLength<EoType> init(20, unif);
eoPop<EoType> pop(pop_size, init);
// evaluate
apply<EoType>(eval, pop);
eoBestFitnessStat<EoType> best("Best_Fitness");
eoAverageStat<EoType> avg("Avg_Fitness");
eoStdoutMonitor mon;
cp.add(best);
cp.add(avg);
// cp.add(mon);
mon.add(best);
mon.add(avg);
// and run
algo(pop);
}

30
test/eo/t-eoSecondsElapsedContinue.cpp Executable file
View file

@ -0,0 +1,30 @@
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <time.h>
#include <paradiseo/eo/eoSecondsElapsedContinue.h>
#include <paradiseo/eo/eoPop.h>
#include <paradiseo/eo/EO.h>
class Dummy : public EO<double> {};
int main() {
eoPop<Dummy> pop;
eoSecondsElapsedContinue<Dummy> cnt(1);
time_t start_time = time(0);
while (cnt(pop)) {}
time_t end_time = time(0);
int diff = end_time = start_time;
if (diff < 1) return 1;
return 0;
}

222
test/eo/t-eoSelect.cpp Executable file
View file

@ -0,0 +1,222 @@
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <cstring>
#include <stdexcept>
#include <paradiseo/eo.h>
//-----------------------------------------------------------------------------
struct Dummy : public EO<double>
{
typedef double Type;
void printOn(std::ostream & _os) const
{
_os << " - ";
EO<double>::printOn(_os);
}
};
bool operator==(const Dummy & _d1, const Dummy & _d2)
{
return _d1.fitness() == _d2.fitness();
}
struct eoDummyPop : public eoPop<Dummy>
{
public :
eoDummyPop(int s=0) { resize(s); }
};
// helper - DOES NOT WORK if different individuals have same fitness!!!
template <class EOT>
unsigned isInPop(EOT & _indi, eoPop<EOT> & _pop)
{
for (unsigned i=0; i<_pop.size(); i++)
if (_pop[i] == _indi)
return i;
return _pop.size();
}
unsigned int pSize; // global variable, bouh!
std::string fitnessType; // yes, a global variable :-)
eoDummyPop parentsOrg;
template <class EOT>
void testSelectMany(eoSelect<EOT> & _select, std::string _name)
{
unsigned i;
std::cout << "\n\n" << fitnessType + _name << std::endl;
std::cout << "===============\n";
eoDummyPop parents(parentsOrg);
eoDummyPop offspring(0);
// do the selection
_select(parents, offspring);
// compute stats
std::vector<unsigned> nb(parents.size(), 0);
for (i=0; i<offspring.size(); i++)
{
unsigned trouve = isInPop<Dummy>(offspring[i], parents);
if (trouve == parents.size()) // pas trouve
throw std::runtime_error("Pas trouve ds parents");
nb[trouve]++;
}
// dump to file so you can plot using gnuplot - dir name is hardcoded!
std::string fName = "ResSelect/" + fitnessType + _name + ".select";
std::ofstream os(fName.c_str());
for (i=0; i<parents.size(); i++)
{
std::cout << i << " -> " << ( (double)nb[i])/offspring.size() << std::endl;
os << i << " " << ( (double)nb[i])/offspring.size() << std::endl;
}
}
template <class EOT>
void testSelectOne(eoSelectOne<EOT> & _select, eoHowMany & _offspringRate,
eoHowMany & _fertileRate, std::string _name)
{
eoTruncatedSelectOne<EOT> truncSelect(_select, _fertileRate);
eoSelectMany<EOT> percSelect(truncSelect, _offspringRate);
testSelectMany<EOT>(percSelect, _name);
}
//-----------------------------------------------------------------------------
int the_main(int argc, char **argv)
{
eoParser parser(argc, argv);
eoValueParam<unsigned> parentSizeParam = parser.createParam(unsigned(10), "parentSize", "Parent size",'P');
pSize = parentSizeParam.value(); // global variable
// eoValueParam<double> offsrpringRateParam = parser.createParam<double>(1.0, "offsrpringRate", "Offsrpring rate",'O');
// double oRate = offsrpringRateParam.value();
eoValueParam<eoHowMany> offsrpringRateParam = parser.createParam(eoHowMany(1.0), "offsrpringRate", "Offsrpring rate (% or absolute)",'O');
eoHowMany oRate = offsrpringRateParam.value();
eoValueParam<eoHowMany> fertileRateParam = parser.createParam(eoHowMany(1.0), "fertileRate", "Fertility rate (% or absolute)",'F');
eoHowMany fRate = fertileRateParam.value();
eoValueParam<unsigned> tournamentSizeParam = parser.createParam(unsigned(2), "tournamentSize", "Deterministic tournament size",'T');
unsigned int tSize = tournamentSizeParam.value();
eoValueParam<double> tournamentRateParam = parser.createParam(1.0, "tournamentRate", "Stochastic tournament rate",'t');
double tRate = tournamentRateParam.value();
eoValueParam<double> rankingPressureParam = parser.createParam(2.0, "rankingPressure", "Selective pressure for the ranking selection",'p');
double rankingPressure = rankingPressureParam.value();
eoValueParam<double> rankingExponentParam = parser.createParam(1.0, "rankingExponent", "Exponent for the ranking selection",'e');
double rankingExponent = rankingExponentParam.value();
eoValueParam<std::string> fitTypeParam = parser.createParam(std::string("linear"), "fitType", "Type of fitness (linear, exp, log, super",'f');
fitnessType = fitTypeParam.value();
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(0);
}
// hard-coded directory name ...
system("mkdir ResSelect");
std::cout << "Testing the Selections\nParents size = " << pSize
<< ", offspring rate = " << oRate;
std::cout << " and putting rsulting files in dir ResSelect" << std::endl;
// initialize parent population
parentsOrg.resize(pSize);
if (fitnessType == std::string("linear"))
for (unsigned i=0; i<pSize; i++)
parentsOrg[i].fitness(i);
else if (fitnessType == std::string("exp"))
for (unsigned i=0; i<pSize; i++)
parentsOrg[i].fitness(exp((double)i));
else if (fitnessType == std::string("log"))
for (unsigned i=0; i<pSize; i++)
parentsOrg[i].fitness(log(i+1.));
else if (fitnessType == std::string("super"))
{
for (unsigned i=0; i<pSize-1; i++)
parentsOrg[i].fitness(i);
parentsOrg[pSize-1].fitness(10*pSize);
}
else
throw std::runtime_error("Invalid fitness Type"+fitnessType);
std::cout << "Initial parents (odd)\n" << parentsOrg << std::endl;
// random seed
eoValueParam<uint32_t>& seedParam = parser.createParam(uint32_t(0), "seed",
"Random number seed", 'S');
if (seedParam.value() == 0)
seedParam.value() = time(0);
rng.reseed(seedParam.value());
char fileName[1024];
// the selection procedures under test
// eoDetSelect<Dummy> detSelect(oRate);
// testSelectMany(detSelect, "detSelect");
// Roulette
eoProportionalSelect<Dummy> propSelect;
testSelectOne<Dummy>(propSelect, oRate, fRate, "PropSelect");
// Linear ranking using the perf2Worth construct
eoRankingSelect<Dummy> newRankingSelect(rankingPressure);
sprintf(fileName,"LinRank_%g",rankingPressure);
testSelectOne<Dummy>(newRankingSelect, oRate, fRate, fileName);
// Exponential ranking using the perf2Worth construct
std::cout << "rankingExponent " << rankingExponent << std::endl;
eoRankingSelect<Dummy> expRankingSelect(rankingPressure,rankingExponent);
sprintf(fileName,"ExpRank_%g_%g",rankingPressure, rankingExponent);
testSelectOne<Dummy>(expRankingSelect, oRate, fRate, fileName);
// Det tournament
eoDetTournamentSelect<Dummy> detTourSelect(tSize);
sprintf(fileName,"DetTour_%d",tSize);
testSelectOne<Dummy>(detTourSelect, oRate, fRate, fileName);
// Stoch tournament
eoStochTournamentSelect<Dummy> stochTourSelect(tRate);
sprintf(fileName,"StochTour_%g",tRate);
testSelectOne<Dummy>(stochTourSelect, oRate, fRate, fileName);
// Fitness scaling
eoFitnessScalingSelect<Dummy> newFitScaleSelect(rankingPressure);
sprintf(fileName,"LinFitScale_%g",rankingPressure);
testSelectOne<Dummy>(newFitScaleSelect, oRate, fRate, fileName);
// Sequential selections
eoSequentialSelect<Dummy> seqSel(false);
strcpy(fileName,"Sequential");
testSelectOne<Dummy>(seqSel, oRate, fRate, fileName);
eoEliteSequentialSelect<Dummy> eliteSeqSel;
strcpy(fileName,"EliteSequential");
testSelectOne<Dummy>(eliteSeqSel, oRate, fRate, fileName);
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
return 1;
}
}

240
test/eo/t-eoSharing.cpp Executable file
View file

@ -0,0 +1,240 @@
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <iostream>
#include <sstream>
#include <stdexcept>
#include <vector>
// general
#include <paradiseo/eo.h>
#include <paradiseo/eo/utils/eoDistance.h>
//-----------------------------------------------------------------------------
struct Dummy : public EO<double>
{
typedef double Type;
void printOn(std::ostream & _os) const
{
EO<double>::printOn(_os);
std::cout << " " << xdist ;
}
double xdist;
};
class
eoDummyDistance : public eoDistance<Dummy>
{
double operator()(const Dummy & _v1, const Dummy & _v2)
{
double r= _v1.xdist - _v2.xdist;
return sqrt(r*r);
}
};
bool operator==(const Dummy & _d1, const Dummy & _d2)
{
return _d1.fitness() == _d2.fitness();
}
struct eoDummyPop : public eoPop<Dummy>
{
public :
eoDummyPop(int s=0) { resize(s); }
};
// helper - DOES NOT WORK if different individuals have same fitness!!!
template <class EOT>
unsigned isInPop(EOT & _indi, eoPop<EOT> & _pop)
{
for (unsigned i=0; i<_pop.size(); i++)
if (_pop[i] == _indi)
return i;
return _pop.size();
}
unsigned int pSize; // global variable, bouh!
std::string fitnessType; // yes, a global variable :-)
eoDummyPop parentsOrg;
template <class EOT>
void testSelectMany(eoSelect<EOT> & _select, std::string _name)
{
unsigned i;
std::cout << "\n\n" << fitnessType + _name << std::endl;
std::cout << "===============\n";
eoDummyPop parents(parentsOrg);
eoDummyPop offspring(0);
// do the selection
_select(parents, offspring);
// cout << "Pop offspring \n" << offspring << endl;
// compute stats
std::vector<unsigned> nb(parents.size(), 0);
for (i=0; i<offspring.size(); i++)
{
unsigned trouve = isInPop<Dummy>(offspring[i], parents);
if (trouve == parents.size()) // pas trouve
throw std::runtime_error("Pas trouve ds parents");
nb[trouve]++;
}
// dump to file so you can plot using gnuplot - dir name is hardcoded!
std::string fName = "ResSelect/" + fitnessType + _name + ".select";
std::ofstream os(fName.c_str());
for (i=0; i<parents.size(); i++)
{
std::cout << i << " -> " << ( (double)nb[i])/offspring.size() << std::endl;
os << i << " " << ( (double)nb[i])/offspring.size() << std::endl;
}
}
template <class EOT>
void testSelectOne(eoSelectOne<EOT> & _select, eoHowMany & _offspringRate,
eoHowMany & _fertileRate, std::string _name)
{
eoTruncatedSelectOne<EOT> truncSelect(_select, _fertileRate);
eoSelectMany<EOT> percSelect(truncSelect, _offspringRate);
testSelectMany<EOT>(percSelect, _name);
}
//-----------------------------------------------------------------------------
int the_main(int argc, char **argv)
{
eoParser parser(argc, argv);
// random seed
eoValueParam<uint32_t>& seedParam = parser.createParam(uint32_t(0), "seed", "Random number seed", 'S');
if (seedParam.value() == 0)
seedParam.value() = time(0);
rng.reseed(seedParam.value());
// pSize global variable !
eoValueParam<unsigned> pSizeParam = parser.createParam(unsigned(10), "parentSize", "Parent size",'P');
pSize = pSizeParam.value();
eoHowMany oRate = parser.createParam(eoHowMany(1.0), "offsrpringRate", "Offsrpring rate (% or absolute)",'O').value();
eoHowMany fRate = parser.createParam(eoHowMany(1.0), "fertileRate", "Fertility rate (% or absolute)",'F').value();
double nicheSize = parser.createParam(0.1, "nicheSize", "Paramter Sigma for Sharing",'\0').value();
eoParamParamType & peakParam = parser.createParam(eoParamParamType("2(1,2)"), "peaks", "Description of the peaks: N(nb1,nb2,...,nbN)", 'p').value();
// the number of peaks: first item of the paramparam
unsigned peakNumber = atoi(peakParam.first.c_str());
if (peakNumber < 2)
{
std::cerr << "WARNING, nb of peaks must be larger than 2, using 2" << std::endl;
peakNumber = 2;
}
std::vector<unsigned> nbIndiPerPeak(peakNumber);
unsigned i, sum=0;
// the second item is a vector<string> containing all values
if (!peakParam.second.size()) // no other parameter : equal peaks
{
std::cerr << "WARNING, no nb of indis per peaks, using equal nbs" << std::endl;
for (i=0; i<peakNumber; i++)
nbIndiPerPeak[i] = pSize/peakNumber;
}
else // parameters passed by user
if (peakParam.second.size() != peakNumber)
{
std::cerr << "ERROR, not enough nb of indis per peaks" << std::endl;
exit(1);
}
else // now we have in peakParam.second all numbers
{
for (i=0; i<peakNumber; i++)
sum += ( nbIndiPerPeak[i] = atoi(peakParam.second[i].c_str()) );
// now normalize
for (i=0; i<peakNumber; i++)
nbIndiPerPeak[i] = nbIndiPerPeak[i] * pSize / sum;
}
// compute exact total
sum = 0;
for (i=0; i<peakNumber; i++)
sum += nbIndiPerPeak[i];
if (sum != pSize)
{
pSize = pSizeParam.value() = sum;
std::cerr << "WARNING, adjusting pSize to " << pSize << std::endl;
}
make_help(parser);
// hard-coded directory name ...
std::cout << "Testing the Sharing\n";
std::cout << " There will be " << peakNumber << " peaks";
std::cout << " with respective pops ";
for (i=0; i<peakNumber; i++)
std::cout << nbIndiPerPeak[i] << ", ";
std::cout << "\n Peaks are at distance 1 from one-another (dim 1),\n";
std::cout << " fitness of each peak is nb of peak, and\n";
std::cout << " fitness of individuals = uniform[fitness of peak +- 0.01]\n\n";
std::cout << "The resulting file (in dir ResSelect), contains \n";
std::cout << " the empirical proba. for each indi to be selected." << std::endl;
system("mkdir ResSelect");
// initialize parent population
parentsOrg.resize(pSize);
// all peaks of equal size in fitness, with different nn of individuals
unsigned index=0;
for (unsigned nbP=0; nbP<peakNumber; nbP++)
for (i=0; i<nbIndiPerPeak[nbP]; i++)
{
parentsOrg[index].fitness(nbP+1 + 0.02*eo::rng.uniform() - 0.01);
parentsOrg[index].xdist = nbP+1 + 0.02*eo::rng.uniform() - 0.01;
index++;
}
std::cout << "Initial population\n" << parentsOrg << std::endl;
char fileName[1024];
// the selection procedures under test
// eoDetSelect<Dummy> detSelect(oRate);
// testSelectMany(detSelect, "detSelect");
// Sharing using the perf2Worth construct
// need a distance for that
eoDummyDistance dist;
eoSharingSelect<Dummy> newSharingSelect(nicheSize, dist);
sprintf(fileName,"Niche_%g",nicheSize);
testSelectOne<Dummy>(newSharingSelect, oRate, fRate, fileName);
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
return 1;
}
}

79
test/eo/t-eoShiftMutation.cpp Executable file
View file

@ -0,0 +1,79 @@
//-----------------------------------------------------------------------------
// t-eoShiftMutation.cpp
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
#include <paradiseo/eo/eoShiftMutation.h>
#include <set>
//-----------------------------------------------------------------------------
typedef eoInt<double> Chrom;
//-----------------------------------------------------------------------------
double real_value(const Chrom & _chrom)
{
double sum = 0;
for (unsigned i = 0; i < _chrom.size(); i++)
sum += _chrom[i];
return sum/_chrom.size();
}
// Return true if the given chromosome corresponds to a permutation
bool check_permutation(const Chrom& _chrom){
unsigned size= _chrom.size();
std::set<unsigned> verif;
for(unsigned i=0; i< size; i++){
if(verif.insert(_chrom[i]).second==false){
std::cout << " Error: Wrong permutation !" << std::endl;
std::string s;
s.append( " Wrong permutation in t-eoShiftMutation");
throw std::runtime_error( s );
return false;
}
}
return true;
}
int main()
{
const unsigned POP_SIZE = 3, CHROM_SIZE = 8;
unsigned i;
// a chromosome randomizer
eoInitPermutation <Chrom> random(CHROM_SIZE);
// the population:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( real_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
// a shift mutation
eoShiftMutation <Chrom> shift;
for (i = 0; i < POP_SIZE; ++i)
{
std::cout << " Initial chromosome n°" << i << " : " << pop[i] << "..." << std::endl;
shift(pop[i]);
std::cout << " ... becomes : " << pop[i] << " after shift mutation" << std::endl;
check_permutation(pop[i]);
}
return 0;
}
//-----------------------------------------------------------------------------

139
test/eo/t-eoStateAndParser.cpp Executable file
View file

@ -0,0 +1,139 @@
//-----------------------------------------------------------------------------
// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <stdexcept> // runtime_error
//-----------------------------------------------------------------------------
// tt.cpp:
//
//-----------------------------------------------------------------------------
// general
#include <paradiseo/eo/utils/eoRNG.h> // Random number generators
#include <paradiseo/eo/ga.h>
#include <paradiseo/eo/utils/eoParser.h>
#include <paradiseo/eo/utils/eoState.h>
//-----------------------------------------------------------------------------
// include package checkpointing
#include <paradiseo/eo/utils/checkpointing>
// and provisions for Bounds reading
#include <paradiseo/eo/utils/eoRealVectorBounds.h>
struct Dummy : public EO<double>
{
typedef double Type;
};
//-----------------------------------------------------------------------------
int the_main(int argc, char **argv)
{ // ok, we have a command line parser and a state
typedef eoBit<float> Chrom;
eoParser parser(argc, argv);
// Define Parameters
eoValueParam<unsigned int> dimParam((unsigned int)(5), "dimension", "dimension");
eoValueParam<double> rate(0.01, "mutationRatePerBit", "Initial value for mutation rate per bit");
eoValueParam<double> factor(0.99, "mutationFactor", "Decrease factor for mutation rate");
eoValueParam<uint32_t> seed(time(0), "seed", "Random number seed");
// test if user entered or if default value used
if (parser.isItThere(seed))
std::cout << "YES\n";
else
std::cout << "NO\n";
eoValueParam<std::string> load_name("", "Load","Load",'L');
eoValueParam<std::string> save_name("", "Save","Save",'S');
// Register them
parser.processParam(dimParam, "Genetic Operators");
parser.processParam(rate, "Genetic Operators");
parser.processParam(factor, "Genetic Operators");
parser.processParam(load_name, "Persistence");
parser.processParam(save_name, "Persistence");
parser.processParam(seed, "Rng seeding");
// a bound param (need dim)
eoValueParam<eoRealVectorBounds> boundParam(eoRealVectorBounds(dimParam.value(),eoDummyRealNoBounds), "bounds","bounds",'b');
parser.processParam(boundParam, "Genetic Operators");
std::cout << "Bounds: " << boundParam.value() << std::endl;
eoState state;
state.registerObject(parser);
if (load_name.value() != "")
{ // load the parser. This is only neccessary when the user wants to
// be able to change the parameters in the state file by hand.
state.load(load_name.value()); // load the parser
}
// Create the algorithm here
// Register the algorithm
state.registerObject(rng);
//state.registerObject(pop);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
return 0;
}
// Either load or initialize
if (load_name.value() != "")
{
state.load(load_name.value()); // load the rest
}
else
{
// else
// initialize rng and population
rng.reseed(seed.value());
}
// run the algorithm
// Save when needed
if (save_name.value() != "")
{
std::string file_name = save_name.value();
save_name.value() = ""; // so that it does not appear in the parser section of the state file
state.save(file_name);
}
for (int i = 0; i < 100; ++i)
rng.rand();
std::cout << "a random number is " << rng.random(1024) << std::endl;;
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
}
}

81
test/eo/t-eoSwapMutation.cpp Executable file
View file

@ -0,0 +1,81 @@
//-----------------------------------------------------------------------------
// t-eoSwapMutation.cpp
//-----------------------------------------------------------------------------
#include <set>
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
#include <paradiseo/eo/eoSwapMutation.h>
//-----------------------------------------------------------------------------
typedef eoInt<double> Chrom;
//-----------------------------------------------------------------------------
double real_value(const Chrom & _chrom)
{
double sum = 0;
for (unsigned i = 0; i < _chrom.size(); i++)
sum += _chrom[i];
return sum/_chrom.size();
}
//-----------------------------------------------------------------------------
// Return true if the given chromosome corresponds to a permutation
bool check_permutation(const Chrom& _chrom){
unsigned size= _chrom.size();
std::set<unsigned> verif;
for(unsigned i=0; i< size; i++){
if(verif.insert(_chrom[i]).second==false){
std::cout << " Error: Wrong permutation !" << std::endl;
std::string s;
s.append( " Wrong permutation in t-eoShiftMutation");
throw std::runtime_error( s );
return false;
}
}
return true;
}
int main()
{
const unsigned POP_SIZE = 8, CHROM_SIZE = 16;
unsigned i;
// a chromosome randomizer
eoInitPermutation <Chrom> random(CHROM_SIZE);
// the population:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( real_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
// a swap mutation
eoSwapMutation <Chrom> swap;
for (i = 0; i < POP_SIZE; ++i)
{
std::cout << " Initial chromosome n°" << i << " : " << pop[i] << "..." << std::endl;
swap(pop[i]);
std::cout << " ... becomes : " << pop[i] << " after swap mutation" << std::endl;
check_permutation(pop[i]);
}
return 0;
}
//-----------------------------------------------------------------------------

299
test/eo/t-eoSymreg.cpp Executable file
View file

@ -0,0 +1,299 @@
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <paradiseo/eo/gp/eoParseTree.h>
#include <paradiseo/eo.h>
using namespace gp_parse_tree;
using namespace std;
//-----------------------------------------------------------------------------
class SymregNode
{
public :
enum Operator {X = 'x', Plus = '+', Min = '-', Mult = '*', PDiv = '/'};
SymregNode() { init(); }
SymregNode(Operator _op) { op = _op; }
virtual ~SymregNode() {}
// arity function, need this function!
int arity() const { return op == X? 0 : 2; }
void randomize() {}
// evaluation function, single case, using first argument to give value of variable
template <class Children>
void operator()(double& result, Children args, double var) const
{
double r1(0.), r2(0.);
if (arity() == 2)
{
args[0].apply(r1, var);
args[1].apply(r2, var);
}
switch (op)
{
case Plus : result = r1 + r2; break;
case Min : result = r1 - r2; break;
case Mult : result = r1 * r2; break;
case PDiv : {
if (r2 == 0.0)
// protection a la Koza, realistic implementations
// should maybe throw an exception
result = 1.0;
else
result = r1 / r2;
break;
}
case X : result = var; break;
}
}
/// 'Pretty' print to ostream function
template <class Children>
void operator()(string& result, Children args) const
{
static const string lb = "(";
static const string rb = ")";
char opStr[4] = " ";
opStr[1] = op;
if (arity() == 0)
{
result = "x";
return;
}
// else
string r1;
args[0].apply(r1);
result = lb + r1;
result += opStr;
args[1].apply(r1);
result += r1 + rb;
}
Operator getOp() const { return op; }
protected :
void init() { op = X; }
private :
Operator op; // the type of node
};
/// initializor
static SymregNode init_sequence[5] = {SymregNode::X, SymregNode::Plus, SymregNode::Min, SymregNode::Mult, SymregNode::PDiv}; // needed for intialization
// MSVC does not recognize the lt_arity<Node> in eoParseTreeDepthInit
// without this specialization ...
// 2 months later, it seems it does not accept this definition ...
// but dies accept the lt_arity<Node> in eoParseTreeDepthInit
// !!!
// #ifdef _MSC_VER
// template <>
// bool lt_arity(const SymregNode &node1, const SymregNode &node2)
// {
// return (node1.arity() < node2.arity());
// }
// #endif
//-----------------------------------------------------------
// saving, loading
std::ostream& operator<<(std::ostream& os, const SymregNode& eot)
{
os << static_cast<char>(eot.getOp());
return os;
}
std::istream& operator>>(std::istream& is, SymregNode& eot)
{
char type;
type = (char) is.get();
eot = SymregNode(static_cast<SymregNode::Operator>(type));
return is;
}
//-----------------------------------------------------------------------------
/** Implementation of a function evaluation object. */
double targetFunction(double x)
{
return x * x * x * x - x * x * x + x * x * x - x * x + x - 10;
}
// parameters controlling the sampling of points
const double xbegin = -10.0f;
const double xend = 10.0f;
const double xstep = 1.3f;
template <class FType, class Node> struct RMS: public eoEvalFunc< eoParseTree<FType, Node> >
{
public :
typedef eoParseTree<FType, Node> EoType;
typedef eoParseTree<FType, Node> argument_type;
typedef double fitness_type;
RMS() : eoEvalFunc<EoType>()
{
int n = int( (xend - xbegin) / xstep);
inputs.resize(n);
target.resize(n);
int i = 0;
for (double x = xbegin; x < xend && i < n; ++i, x+=xstep)
{
target[i] = targetFunction(x);
inputs[i] = x;
}
}
~RMS() {}
void operator()( EoType & _eo )
{
vector<double> outputs;
outputs.resize(inputs.size());
double fitness = 0.0;
for (unsigned i = 0; i < inputs.size(); ++i)
{
_eo.apply(outputs[i], inputs[i]);
fitness += (outputs[i] - target[i]) * (outputs[i] - target[i]);
}
fitness /= (double) target.size();
fitness = sqrt(fitness);
if (fitness > 1e+20)
fitness = 1e+20;
_eo.fitness(fitness);
}
private :
vector<double> inputs;
vector<double> target;
};
template <class EOT, class FitnessType>
void print_best(eoPop<EOT>& pop)
{
std::cout << std::endl;
FitnessType best = pop[0].fitness();
int index = 0;
for (unsigned i = 1; i < pop.size(); ++i)
{
if (best < pop[i].fitness())
{
best = pop[i].fitness();
index = i;
}
}
std::cout << "\t";
string str;
pop[index].apply(str);
std::cout << str.c_str();
std::cout << std::endl << "RMS Error = " << pop[index].fitness() << std::endl;
}
int main()
{
typedef eoMinimizingFitness FitnessType;
typedef SymregNode GpNode;
typedef eoParseTree<FitnessType, GpNode> EoType;
typedef eoPop<EoType> Pop;
const int MaxSize = 100;
const int nGenerations = 10; // only a test, so few generations
// Initializor sequence, contains the allowable nodes
vector<GpNode> init(init_sequence, init_sequence + 5);
// Depth Initializor, defaults to grow method.
eoGpDepthInitializer<FitnessType, GpNode> initializer(10, init);
// Root Mean Squared Error Measure
RMS<FitnessType, GpNode> eval;
Pop pop(50, initializer);
apply<EoType>(eval, pop);
eoSubtreeXOver<FitnessType, GpNode> xover(MaxSize);
eoBranchMutation<FitnessType, GpNode> mutation(initializer, MaxSize);
// The operators are encapsulated into an eoTRansform object,
// that performs sequentially crossover and mutation
eoSGATransform<EoType> transform(xover, 0.75, mutation, 0.25);
// The robust tournament selection
eoDetTournamentSelect<EoType> selectOne(2); // tSize in [2,POPSIZE]
// is now encapsulated in a eoSelectMany: 2 at a time -> SteadyState
eoSelectMany<EoType> select(selectOne,2, eo_is_an_integer);
// and the Steady-State replacement
eoSSGAWorseReplacement<EoType> replace;
// Terminators
eoGenContinue<EoType> term(nGenerations);
eoCheckPoint<EoType> checkPoint(term);
eoAverageStat<EoType> avg;
eoBestFitnessStat<EoType> best;
eoStdoutMonitor monitor;
checkPoint.add(monitor);
checkPoint.add(avg);
checkPoint.add(best);
monitor.add(avg);
monitor.add(best);
// GP generation
eoEasyEA<EoType> gp(checkPoint, eval, select, transform, replace);
std::cout << "Initialization done" << std::endl;
print_best<EoType, FitnessType>(pop);
try
{
gp(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
print_best<EoType, FitnessType>(pop);
}
// Local Variables:
// coding: iso-8859-1
// mode: C++
// c-file-offsets: ((c . 0))
// c-file-style: "Stroustrup"
// fill-column: 80
// End:

104
test/eo/t-eoSyncEasyPSO.cpp Executable file
View file

@ -0,0 +1,104 @@
//-----------------------------------------------------------------------------
// t-eoEasySyncPSO.cpp
//-----------------------------------------------------------------------------
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
//-----------------------------------------------------------------------------
typedef eoMinimizingFitness FitT;
typedef eoRealParticle < FitT > Particle;
//-----------------------------------------------------------------------------
// the objective function
double real_value (const Particle & _particle)
{
double sum = 0;
for (unsigned i = 0; i < _particle.size ()-1; i++)
sum += pow(_particle[i],2);
return (sum);
}
int main()
{
const unsigned int VEC_SIZE = 2;
const unsigned int POP_SIZE = 20;
const unsigned int NEIGHBORHOOD_SIZE= 5;
unsigned i;
// the population:
eoPop<Particle> pop;
// Evaluation
eoEvalFuncPtr<Particle, double, const Particle& > eval( real_value );
// position init
eoUniformGenerator < double >uGen (-3, 3);
eoInitFixedLength < Particle > random (VEC_SIZE, uGen);
// velocity init
eoUniformGenerator < double >sGen (-2, 2);
eoVelocityInitFixedLength < Particle > veloRandom (VEC_SIZE, sGen);
// local best init
eoFirstIsBestInit < Particle > localInit;
// perform position initialization
pop.append (POP_SIZE, random);
// topology
eoLinearTopology<Particle> topology(NEIGHBORHOOD_SIZE);
// the full initializer
eoInitializer <Particle> init(eval,veloRandom,localInit,topology,pop);
init();
// bounds
eoRealVectorBounds bnds(VEC_SIZE,-1.5,1.5);
// velocity
eoStandardVelocity <Particle> velocity (topology,1,1.6,2,bnds);
// flight
eoStandardFlight <Particle> flight;
// Terminators
eoGenContinue <Particle> genCont1 (50);
eoGenContinue <Particle> genCont2 (50);
// PS flight
eoSyncEasyPSO<Particle> pso1(genCont1, eval, velocity, flight);
eoSyncEasyPSO<Particle> pso2(init,genCont2, eval, velocity, flight);
// flight
try
{
pso1(pop);
std::cout << "FINAL POPULATION AFTER SYNC PSO n°1:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
pso2(pop);
std::cout << "FINAL POPULATION AFTER SYNC PSO n°2:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
return 0;
}
//-----------------------------------------------------------------------------

80
test/eo/t-eoTwoOptMutation.cpp Executable file
View file

@ -0,0 +1,80 @@
//-----------------------------------------------------------------------------
// t-eoTwoOptMutation.cpp
//-----------------------------------------------------------------------------
#include <set>
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoInt.h>
#include <paradiseo/eo/eoTwoOptMutation.h>
//-----------------------------------------------------------------------------
typedef eoInt<double> Chrom;
//-----------------------------------------------------------------------------
double real_value(const Chrom & _chrom)
{
double sum = 0;
for (unsigned i = 0; i < _chrom.size(); i++)
sum += _chrom[i];
return sum/_chrom.size();
}
//-----------------------------------------------------------------------------
// Return true if the given chromosome corresponds to a permutation
bool check_permutation(const Chrom& _chrom){
unsigned size= _chrom.size();
std::set<unsigned> verif;
for(unsigned i=0; i< size; i++){
if(verif.insert(_chrom[i]).second==false){
std::cout << " Error: Wrong permutation !" << std::endl;
std::string s;
s.append( " Wrong permutation in t-eoShiftMutation");
throw std::runtime_error( s );
return false;
}
}
return true;
}
int main()
{
const unsigned POP_SIZE = 3, CHROM_SIZE = 8;
unsigned i;
// a chromosome randomizer
eoInitPermutation <Chrom> random(CHROM_SIZE);
// the population:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( real_value );
for (i = 0; i < POP_SIZE; ++i)
{
Chrom chrom(CHROM_SIZE);
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
// a twoOpt mutation
eoTwoOptMutation <Chrom> twoOpt;
for (i = 0; i < POP_SIZE; ++i)
{
std::cout << " Initial chromosome n°" << i << " : " << pop[i] << "..." << std::endl;
twoOpt(pop[i]);
std::cout << " ... becomes : " << pop[i] << " after twoOpt mutation" << std::endl;
check_permutation(pop[i]);
}
return 0;
}
//-----------------------------------------------------------------------------

22
test/eo/t-eoUniform.cpp Executable file
View file

@ -0,0 +1,22 @@
//-----------------------------------------------------------------------------
// t-eouniform
//-----------------------------------------------------------------------------
#include <iostream> // std::cout
#include <strstream> // ostrstream, istrstream
#include <paradiseo/eo/eoUniform.h> // eoBin
//-----------------------------------------------------------------------------
main() {
eoUniform<float> u1(-2.5,3.5);
eoUniform<double> u2(0.003, 0 );
eoUniform<unsigned long> u3( 10000U, 10000000U);
std::cout << "u1\t\tu2\t\tu3" << std::endl;
for ( unsigned i = 0; i < 100; i ++) {
std::cout << u1() << "\t" << u2() << "\t" << u3() << std::endl;
}
}
//-----------------------------------------------------------------------------

74
test/eo/t-eoVector.cpp Executable file
View file

@ -0,0 +1,74 @@
/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
t-eoVector.cpp
This program tests vector-like chromosomes
(c) GeNeura Team, 1999, 2000
Modified by Maarten Keijzer 2001
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <cassert>
#include <iostream>
#include <paradiseo/eo/utils/eoRndGenerators.h>
#include <paradiseo/eo/eoVector.h> // eoVector
#include <paradiseo/eo/eoInit.h>
#include <paradiseo/eo/eoScalarFitness.h>
//-----------------------------------------------------------------------------
typedef eoVector<eoMaximizingFitness, int> Chrom1;
typedef eoVector<eoMinimizingFitness, int> Chrom2;
//-----------------------------------------------------------------------------
int main()
{
const unsigned SIZE = 4;
// check if the appropriate ctor gets called
Chrom1 chrom(SIZE, 5);
for (unsigned i = 0; i < chrom.size(); ++i)
{
assert(chrom[i] == 5);
}
eoUniformGenerator<Chrom1::AtomType> uniform(-1,1);
eoInitFixedLength<Chrom1> init(SIZE, uniform);
init(chrom);
std::cout << chrom << std::endl;
Chrom2 chrom2(chrom);
std::cout << chrom2 << std::endl;
// eoInitVariableLength<Chrom1> initvar(
return 0;
}
//-----------------------------------------------------------------------------

76
test/eo/t-eoVirus.cpp Executable file
View file

@ -0,0 +1,76 @@
/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
t-eoVirus.cpp
This program tests the the binary cromosomes and several genetic operators
(c) GeNeura Team, 1999
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#include <iostream> // std::cout
#include <paradiseo/eo.h> // general EO
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
#include <paradiseo/eo/utils/eoRndGenerators.h>
#include "binary_value.h"
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned SIZE = 8;
eoBooleanGenerator gen;
eo::rng.reseed( time( 0 ) );
Chrom chrom(SIZE), chrom2(SIZE);
chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
std::cout << chrom << std::endl;
std::cout << chrom2 << std::endl;
// Virus Mutation
VirusBitFlip<float> vf;
unsigned i;
for ( i = 0; i < 10; i++ ) {
vf( chrom );
std::cout << chrom << std::endl;
}
// Chrom Mutation
std::cout << "Chrom mutation--------" << std::endl;
VirusMutation<float> vm;
for ( i = 0; i < 10; i++ ) {
vm( chrom );
std::cout << chrom << std::endl;
}
// Chrom Transmision
std::cout << "Chrom transmission--------" << std::endl;
VirusTransmission<float> vt;
vt( chrom2, chrom );
std::cout << chrom2 << std::endl;
return 0;
}

219
test/eo/t-eobin.cpp Executable file
View file

@ -0,0 +1,219 @@
/* -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
t-eobin.cpp
This program tests the the binary cromosomes and several genetic operators
(c) GeNeura Team, 1999
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <iostream> // std::cout
#include <sstream>
#include <paradiseo/eo.h> // general EO
#include <paradiseo/eo/ga.h> // bitstring representation & operators
#include <paradiseo/eo/utils/eoRndGenerators.h>
#include "binary_value.h"
//-----------------------------------------------------------------------------
typedef eoBit<double> Chrom;
//-----------------------------------------------------------------------------
void main_function()
{
const unsigned SIZE = 8;
unsigned i, j;
eoBooleanGenerator gen;
Chrom chrom(SIZE), chrom2;
chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
std::cout << "chrom: " << chrom << std::endl;
chrom[0] = chrom[SIZE - 1] = true; chrom.fitness(binary_value(chrom));
std::cout << "chrom: " << chrom << std::endl;
chrom[0] = chrom[SIZE - 1] = false; chrom.fitness(binary_value(chrom));
std::cout << "chrom: " << chrom << std::endl;
chrom[0] = chrom[SIZE - 1] = true; chrom.fitness(binary_value(chrom));
std::cout << "chrom.className() = " << chrom.className() << std::endl;
std::cout << "chrom: " << chrom << std::endl
<< "chrom2: " << chrom2 << std::endl;
std::ostringstream os;
os << chrom;
std::istringstream is(os.str());
is >> chrom2; chrom.fitness(binary_value(chrom2));
std::cout << "\nTesting reading, writing\n";
std::cout << "chrom: " << chrom << "\nchrom2: " << chrom2 << '\n';
std::fill(chrom.begin(), chrom.end(), false);
std::cout << "--------------------------------------------------"
<< std::endl << "eoMonOp's aplied to .......... " << chrom << std::endl;
eoInitFixedLength<Chrom>
random(chrom.size(), gen);
random(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBinRandom ............ " << chrom << std::endl;
eoOneBitFlip<Chrom> bitflip;
bitflip(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBitFlip .............. " << chrom << std::endl;
eoBitMutation<Chrom> mutation(0.5);
mutation(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBinMutation(0.5) ..... " << chrom << std::endl;
eoBitInversion<Chrom> inversion;
inversion(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBinInversion ......... " << chrom << std::endl;
eoBitNext<Chrom> next;
next(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBinNext .............. " << chrom << std::endl;
eoBitPrev<Chrom> prev;
prev(chrom); chrom.fitness(binary_value(chrom));
std::cout << "after eoBinPrev .............. " << chrom << std::endl;
std::fill(chrom.begin(), chrom.end(), false); chrom.fitness(binary_value(chrom));
std::fill(chrom2.begin(), chrom2.end(), true); chrom2.fitness(binary_value(chrom2));
std::cout << "--------------------------------------------------"
<< std::endl << "eoBinOp's aplied to ... "
<< chrom << " " << chrom2 << std::endl;
eo1PtBitXover<Chrom> xover;
std::fill(chrom.begin(), chrom.end(), false);
std::fill(chrom2.begin(), chrom2.end(), true);
xover(chrom, chrom2);
chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
std::cout << "eoBinCrossover ........ " << chrom << " " << chrom2 << std::endl;
for (i = 1; i < SIZE; i++)
{
eoNPtsBitXover<Chrom> nxover(i);
std::fill(chrom.begin(), chrom.end(), false);
std::fill(chrom2.begin(), chrom2.end(), true);
nxover(chrom, chrom2);
chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
std::cout << "eoBinNxOver(" << i << ") ........ "
<< chrom << " " << chrom2 << std::endl;
}
for (i = 1; i < SIZE / 2; i++)
for (j = 1; j < SIZE / 2; j++)
{
eoBitGxOver<Chrom> gxover(i, j);
std::fill(chrom.begin(), chrom.end(), false);
std::fill(chrom2.begin(), chrom2.end(), true);
gxover(chrom, chrom2);
chrom.fitness(binary_value(chrom)); chrom2.fitness(binary_value(chrom2));
std::cout << "eoBinGxOver(" << i << ", " << j << ") ..... "
<< chrom << " " << chrom2 << std::endl;
}
// test SGA algorithm
eoGenContinue<Chrom> continuator1(50);
eoFitContinue<Chrom> continuator2(65535.f);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
monitor.add(stats);
checkpoint.add(stats);
eoProportionalSelect<Chrom> select;
eoEvalFuncPtr<Chrom> eval(binary_value);
eoSGA<Chrom> sga(select, xover, 0.8f, bitflip, 0.1f, eval, checkpoint);
eoInitFixedLength<Chrom> init(16, gen);
eoPop<Chrom> pop(100, init);
apply<Chrom>(eval, pop);
sga(pop);
pop.sort();
std::cout << "Population " << pop << std::endl;
std::cout << "\nBest: " << pop[0].fitness() << '\n';
/*
Commented this out, waiting for a definite decision what to do with the mOp's
// Check multiOps
eoMultiMonOp<Chrom> mOp( &next );
mOp.adOp( &bitflip );
std::cout << "before multiMonOp............ " << chrom << std::endl;
mOp( chrom );
std::cout << "after multiMonOp .............. " << chrom << std::endl;
eoBinGxOver<Chrom> gxover(2, 4);
eoMultiBinOp<Chrom> mbOp( &gxover );
mOp.adOp( &bitflip );
std::cout << "before multiBinOp............ " << chrom << " " << chrom2 << std::endl;
mbOp( chrom, chrom2 );
std::cout << "after multiBinOp .............. " << chrom << " " << chrom2 <<std::endl;
*/
}
//-----------------------------------------------------------------------------
// For MSVC memory lead detection
#ifdef _MSC_VER
#include <crtdbg.h>
#endif
int main()
{
#ifdef _MSC_VER
// rng.reseed(42);
int flag = _CrtSetDbgFlag(_CRTDBG_LEAK_CHECK_DF);
flag |= _CRTDBG_LEAK_CHECK_DF;
_CrtSetDbgFlag(flag);
// _CrtSetBreakAlloc(100);
#endif
try
{
main_function();
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << '\n';
}
}

89
test/eo/t-eofitness.cpp Executable file
View file

@ -0,0 +1,89 @@
//-----------------------------------------------------------------------------
// t-eofitness.cpp
// (c) GeNeura Team 1998
//-----------------------------------------------------------------------------
#include <time.h> // time
#include <stdlib.h> // srand, rand
#include <iostream> // std::cout
#include <paradiseo/eo/eoScalarFitness.h>
using namespace std;
//-----------------------------------------------------------------------------
template <class Fitness>
int test_fitness(Fitness a, Fitness b)
{
// srand(time(0));
// Fitness a = aval; //static_cast<double>(rand()) / RAND_MAX;
// Fitness b = bval; //static_cast<double>(rand()) / RAND_MAX;
std::cout.precision(2);
unsigned repeat = 2;
while (repeat--)
{
std::cout << "------------------------------------------------------" << std::endl;
std::cout << "testing < ";
if (a < b)
std::cout << a << " < " << b << " is true" << std::endl;
else
std::cout << a << " < " << b << " is false" <<std::endl;
std::cout << "testing > ";
if (a > b)
std::cout << a << " > " << b << " is true" << std::endl;
else
std::cout << a << " > " << b << " is false" <<std::endl;
std::cout << "testing == ";
if (a == b)
std::cout << a << " == " << b << " is true" << std::endl;
else
std::cout << a << " == " << b << " is false" <<std::endl;
std::cout << "testing != ";
if (a != b)
std::cout << a << " != " << b << " is true" << std::endl;
else
std::cout << a << " != " << b << " is false" <<std::endl;
a = b;
}
return 1;
}
int main()
{
std::cout << "Testing minimizing fitness with 1 and 2" << std::endl;
std::cout << "------------------------------------------------------" << std::endl;
eoMinimizingFitness a = 1;
eoMinimizingFitness b = 2;
test_fitness(a, b);
std::cout << "Testing minimizing fitness with 2 and 1" << std::endl;
std::cout << "------------------------------------------------------" << std::endl;
test_fitness(b, a);
std::cout << "Testing maximizing fitness with 1 and 2" << std::endl;
std::cout << "------------------------------------------------------" << std::endl;
eoMaximizingFitness a1 = 1;
eoMaximizingFitness b1 = 2;
test_fitness(a1,b1);
std::cout << "Testing maximizing fitness with 2 and 1" << std::endl;
std::cout << "------------------------------------------------------" << std::endl;
test_fitness(b1,a1);
}
//-----------------------------------------------------------------------------

224
test/eo/t-openmp.cpp Executable file
View file

@ -0,0 +1,224 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/*
(c) Thales group, 2010
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Caner Candan <caner.candan@thalesgroup.com>
*/
//-----------------------------------------------------------------------------
// t-openmp.cpp
//-----------------------------------------------------------------------------
#include <fstream>
#include <sstream>
#include <climits>
#include <paradiseo/eo.h>
#include <paradiseo/eo/es/make_real.h>
#include <paradiseo/eo/apply.h>
#include <omp.h>
#include <unistd.h>
#include "real_value.h"
//-----------------------------------------------------------------------------
typedef eoReal< eoMinimizingFitness > EOT;
//-----------------------------------------------------------------------------
inline uint32_t get_rdtsc() { __asm__ ("xor %eax, %eax; cpuid; rdtsc"); }
double variable_time_function(const std::vector<double>&)
{
eoRng myrng( get_rdtsc() );
::usleep( myrng.random( 10 ) );
return 0.0;
}
double measure_apply( size_t p,
void (*fct)(eoUF<EOT&, void>&, std::vector<EOT>&),
eoInitFixedLength< EOT >& init,
eoEvalFuncCounter< EOT >& eval )
{
eoPop< EOT > pop( p, init );
double t1 = omp_get_wtime();
fct( eval, pop );
double t2 = omp_get_wtime();
return t2 - t1;
}
void measure( size_t p,
eoInitFixedLength< EOT >& init,
eoEvalFuncCounter< EOT >& eval,
std::ofstream& speedupFile,
std::ofstream& efficiencyFile,
std::ofstream& dynamicityFile,
size_t nbtask )
{
// sequential scope
double Ts = measure_apply( p, apply< EOT >, init, eval );
// parallel scope
double Tp = measure_apply( p, omp_apply< EOT >, init, eval );
// parallel scope dynamic
double Tpd = measure_apply( p, omp_dynamic_apply< EOT >, init, eval );
double speedup = Ts / Tp;
if ( speedup > nbtask ) { return; }
double efficiency = speedup / nbtask;
speedupFile << speedup << ' ';
efficiencyFile << efficiency << ' ';
eo::log << eo::debug;
eo::log << "Ts = " << Ts << std::endl;
eo::log << "Tp = " << Tp << std::endl;
eo::log << "S_p = " << speedup << std::endl;
eo::log << "E_p = " << efficiency << std::endl;
double dynamicity = Tp / Tpd;
if ( dynamicity > nbtask ) { return; }
eo::log << "Tpd = " << Tpd << std::endl;
eo::log << "D_p = " << dynamicity << std::endl;
dynamicityFile << dynamicity << ' ';
}
int main(int ac, char** av)
{
eoParser parser(ac, av);
unsigned int popMin = parser.getORcreateParam((unsigned int)1, "popMin", "Population Min", 'p', "Evolution Engine").value();
unsigned int popStep = parser.getORcreateParam((unsigned int)1, "popStep", "Population Step", 0, "Evolution Engine").value();
unsigned int popMax = parser.getORcreateParam((unsigned int)100, "popMax", "Population Max", 'P', "Evolution Engine").value();
unsigned int dimMin = parser.getORcreateParam((unsigned int)1, "dimMin", "Dimension Min", 'd', "Evolution Engine").value();
unsigned int dimStep = parser.getORcreateParam((unsigned int)1, "dimStep", "Dimension Step", 0, "Evolution Engine").value();
unsigned int dimMax = parser.getORcreateParam((unsigned int)100, "dimMax", "Dimension Max", 'D', "Evolution Engine").value();
unsigned int nRun = parser.getORcreateParam((unsigned int)100, "nRun", "Number of runs", 'r', "Evolution Engine").value();
std::string fileNamesPrefix = parser.getORcreateParam(std::string(""), "fileNamesPrefix", "Prefix of all results files name", 'H', "Results").value();
std::string speedupFileName = parser.getORcreateParam(std::string("speedup"), "speedupFileName", "Speedup file name", 0, "Results").value();
std::string efficiencyFileName = parser.getORcreateParam(std::string("efficiency"), "efficiencyFileName", "Efficiency file name", 0, "Results").value();
std::string dynamicityFileName = parser.getORcreateParam(std::string("dynamicity"), "dynamicityFileName", "Dynamicity file name", 0, "Results").value();
uint32_t seedParam = parser.getORcreateParam((uint32_t)0, "seed", "Random number seed", 0).value();
if (seedParam == 0) { seedParam = time(0); }
unsigned int measureConstTime = parser.getORcreateParam((unsigned int)1, "measureConstTime", "Toggle measure of constant time", 'C', "Results").value();
unsigned int measureVarTime = parser.getORcreateParam((unsigned int)1, "measureVarTime", "Toggle measure of variable time", 'V', "Results").value();
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
exit(1);
}
make_help(parser);
make_verbose(parser);
rng.reseed( seedParam );
eoEvalFuncPtr< EOT, double, const std::vector< double >& > mainEval( real_value );
eoEvalFuncCounter< EOT > eval( mainEval );
eoEvalFuncPtr< EOT, double, const std::vector< double >& > mainEval_variable( variable_time_function );
eoEvalFuncCounter< EOT > eval_variable( mainEval_variable );
eoUniformGenerator< double > gen(-5, 5);
std::ostringstream params;
params << "_p" << popMin << "_pS" << popStep << "_P" << popMax
<< "_d" << dimMin << "_dS" << dimStep << "_D" << dimMax
<< "_r" << nRun << "_s" << seedParam;
std::ofstream speedupFile( std::string( fileNamesPrefix + speedupFileName + params.str() ).c_str() );
std::ofstream efficiencyFile( std::string( fileNamesPrefix + efficiencyFileName + params.str() ).c_str() );
std::ofstream dynamicityFile( std::string( fileNamesPrefix + dynamicityFileName + params.str() ).c_str() );
std::ofstream speedupFile_variable( std::string( fileNamesPrefix + "variable_" + speedupFileName + params.str() ).c_str() );
std::ofstream efficiencyFile_variable( std::string( fileNamesPrefix + "variable_" + efficiencyFileName + params.str() ).c_str() );
std::ofstream dynamicityFile_variable( std::string( fileNamesPrefix + "variable_" + dynamicityFileName + params.str() ).c_str() );
size_t nbtask = 1;
#pragma omp parallel
{
nbtask = omp_get_num_threads();
}
eo::log << eo::logging << "Nb task: " << nbtask << std::endl;
for ( size_t p = popMin; p <= popMax; p += popStep )
{
for ( size_t d = dimMin; d <= dimMax; d += dimStep )
{
eo::log << eo::logging << p << 'x' << d << std::endl;
for ( size_t r = 0; r < nRun; ++r )
{
eoInitFixedLength< EOT > init( d, gen );
// for constant time measure
if ( measureConstTime == 1 )
{
measure( p, init, eval, speedupFile, efficiencyFile, dynamicityFile, nbtask );
}
// for variable time measure
if ( measureVarTime == 1 )
{
measure( p, init, eval_variable, speedupFile_variable, efficiencyFile_variable, dynamicityFile_variable, nbtask );
}
} // end of runs
if ( measureConstTime == 1 )
{
speedupFile << std::endl;
efficiencyFile << std::endl;
dynamicityFile << std::endl;
}
if ( measureVarTime == 1 )
{
speedupFile_variable << std::endl;
efficiencyFile_variable << std::endl;
dynamicityFile_variable << std::endl;
}
} // end of dimension
} // end of population
return 0;
}
//-----------------------------------------------------------------------------

161
test/eo/t-openmp.py Executable file
View file

@ -0,0 +1,161 @@
#!/usr/bin/env python
#
# (c) Thales group, 2010
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation;
# version 2 of the License.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# Contact: http://eodev.sourceforge.net
#
# Authors:
# Caner Candan <caner.candan@thalesgroup.com>
#
import optparse, logging, sys, os
from datetime import datetime
LEVELS = {'debug': logging.DEBUG,
'info': logging.INFO,
'warning': logging.WARNING,
'error': logging.ERROR,
'critical': logging.CRITICAL}
LOG_DEFAULT_FILENAME='notitle.log'
RESULT_FILE_FORMAT='%s%s_p%d_pS%d_P%d_d%d_dS%d_D%d_r%d_s%d'
def parser(parser=optparse.OptionParser()):
# general parameters
parser.add_option('-v', '--verbose', choices=LEVELS.keys(), default='info', help='set a verbose level')
parser.add_option('-f', '--file', help='give an input project filename', default='')
parser.add_option('-o', '--output', help='give an output filename for logging', default=LOG_DEFAULT_FILENAME)
# general parameters ends
parser.add_option('-r', '--nRun', type='int', default=100, help='how many times you would compute each iteration ?')
parser.add_option('-s', '--seed', type='int', default=1, help='give here a seed value')
parser.add_option('-n', '--nProc', type='int', default=1, help='give a number of processus, this value is multiplied by the measures bounds')
parser.add_option('-F', '--fixedBound', type='int', default=1000, help='give the fixed bound value common for all measures')
topic = str(datetime.today())
for char in [' ', ':', '-', '.']: topic = topic.replace(char, '_')
parser.add_option('-t', '--topic', default='openmp_measures_' + topic + '/', help='give here a topic name used to create the folder')
parser.add_option('-E', '--onlyexecute', action='store_true', default=False, help='used this option if you only want to execute measures without generating images')
parser.add_option('-X', '--onlyprint', action='store_true', default=False, help='used this option if you only want to generate images without executing measures, dont forget to set the good path in using --topic with a "/" at the end')
parser.add_option('-C', '--onlyConstTime', action='store_true', default=False, help='only measures constant time problem')
parser.add_option('-V', '--onlyVarTime', action='store_true', default=False, help='only measures variable time problem')
parser.add_option('-m', '--measure', action='append', type='int', help='select all measure you want to produce, by default all are produced')
options, args = parser.parse_args()
logger(options.verbose, options.output)
return options
def logger(level_name, filename=LOG_DEFAULT_FILENAME):
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
filename=filename, filemode='a'
)
console = logging.StreamHandler()
console.setLevel(LEVELS.get(level_name, logging.NOTSET))
console.setFormatter(logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s'))
logging.getLogger('').addHandler(console)
options = parser()
if not options.onlyexecute:
import pylab
def get_boxplot_data( filename ):
try:
f = open( filename )
return [ [ float(value) for value in line.split() ] for line in f.readlines() ]
except:
raise ValueError('got an issue during the reading of file %s' % filename)
def do_measure( name, p, ps, P, d, ds, D, r=options.nRun, s=options.seed, v='logging' ):
OPENMP_EXEC_FORMAT='./test/t-openmp -p=%d --popStep=%d -P=%d -d=%d --dimStep=%d -D=%d -r=%d --seed=%d -v=%s -H=%s -C=%d -V=%d'
pwd = options.topic + name + '_'
cmd = OPENMP_EXEC_FORMAT % (p, ps, P, d, ds, D, r, s, v, pwd,
0 if options.onlyVarTime else 1,
0 if options.onlyConstTime else 1)
logging.info( cmd )
if not options.onlyprint:
os.system( cmd )
if not options.onlyexecute:
def generate( filenames ):
for cur in filenames:
filename = RESULT_FILE_FORMAT % (pwd, cur, p, ps, P, d, ds, D, r, s)
pylab.boxplot( get_boxplot_data( filename ) )
nonzero = lambda x: x if x > 0 else 1
iters = ( nonzero( P - p ) / ps ) * ( nonzero( D - d ) / ds )
pylab.xlabel('%d iterations from %d,%d to %d,%d' % ( iters, p, d, P, D) )
pylab.ylabel('%s - %s' % (cur, name))
pylab.savefig( filename + '.pdf', format='pdf' )
pylab.savefig( filename + '.png', format='png' )
pylab.cla()
pylab.clf()
if not options.onlyVarTime:
generate( ['speedup', 'efficiency', 'dynamicity'] )
if not options.onlyConstTime:
generate( ['variable_speedup', 'variable_efficiency', 'variable_dynamicity'] )
def main():
if not options.onlyprint:
logging.info('creates first the new topic repository %s', options.topic)
os.mkdir( options.topic )
logging.info('do all tests with r = %d and a common seed value = %d' % (options.nRun, options.seed))
logging.info('EA in time O(1) and O(n) - speedup measure Sp, Ep and Dp for P & D')
n = options.nProc
F = options.fixedBound
if options.measure is None or 1 in options.measure:
logging.info('(1) measure for all combinaisons of P n D')
do_measure( '1', 1*n, 10*n, 101*n, 1*n, 10*n, 101*n )
if options.measure is None or 2 in options.measure:
logging.info('(2) measure for P \in [%d, %d[ with D fixed to %d' % (1*n, 101*n, F))
do_measure( '2', 1*n, 1*n, 101*n, F, 1, F )
if options.measure is None or 3 in options.measure:
logging.info('(3) measure for P \in [%d, %d[ with ps = %d and D fixed to %d' % (1*n, 1001*n, 10*n, F))
do_measure( '3', 1*n, 10*n, 1001*n, F, 1, F )
if options.measure is None or 4 in options.measure:
logging.info('(4) measure for D \in [%d, %d[ with P fixed to %d' % (1*n, 101*n, F))
do_measure( '4', F, 1, F, 1*n, 1*n, 101*n )
if options.measure is None or 5 in options.measure:
logging.info('(5) measure for D \in [%d, %d[ with ds = %d and P fixed to %d' % (1*n, 1001*n, 10*n, F))
do_measure( '5', F, 1, F, 1*n, 10*n, 1001*n )
# when executed, just run main():
if __name__ == '__main__':
logging.debug('### plotting started ###')
main()
logging.debug('### plotting ended ###')

88
test/eo/t-selectOne.cpp Executable file
View file

@ -0,0 +1,88 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// t-selectOne.cpp
// This program test the breeder object
// (c) GeNeura Team, 1998
/*
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
*/
//-----------------------------------------------------------------------------
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo/ga/eoBin.h> // eoBin, eoPop, eoBreeder
#include <paradiseo/eo/eoPop.h>
#include <paradiseo/eo/ga/eoBitOp.h>
#include <paradiseo/eo/eoUniformSelect.h>
#include <paradiseo/eo/eoStochTournament.h>
#include <paradiseo/eo/eoDetTournament.h>
//-----------------------------------------------------------------------------
typedef eoBin<float> Chrom;
#include "binary_value.h"
//-----------------------------------------------------------------------------
main()
{
const unsigned POP_SIZE = 8, CHROM_SIZE = 4;
unsigned i;
eoBinRandom<Chrom> random;
eoPop<Chrom> pop;
// Create the population
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom(CHROM_SIZE);
random(chrom);
BinaryValue()(chrom);
pop.push_back(chrom);
}
// print population
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << pop[i] << " " << pop[i].fitness() << std::endl;
// Declare 1-selectors
eoUniformSelect<Chrom> uSelect;
Chrom aChrom;
aChrom = uSelect( pop );
std::cout << "Uniform Select " << aChrom << " " << aChrom.fitness() << std::endl;
eoStochTournament<Chrom> sSelect(0.7);
aChrom = sSelect( pop );
std::cout << "Stochastic Tournament " << aChrom << " " << aChrom.fitness() << std::endl;
eoDetTournament<Chrom> dSelect(3);
aChrom = dSelect( pop );
std::cout << "Deterministic Tournament " << aChrom << " " << aChrom.fitness() << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

53
test/eompi/CMakeLists.txt Executable file
View file

@ -0,0 +1,53 @@
###############################################################################
##
## CMakeLists file for eo/test/mpi
##
###############################################################################
######################################################################################
### 1) Include the sources
######################################################################################
#include_directories(${EOMPI_SRC_DIR}/src)
#include_directories(${EOSERIAL_SRC_DIR}/src)
#include_directories(${EO_SRC_DIR}/src)
#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
######################################################################################
### 2) Specify where CMake can find the libraries
######################################################################################
link_directories(${EO_BIN_DIR}/lib)
link_directories(${EOMPI_BIN_DIR}/lib)
link_directories(${EOSERIAL_BIN_DIR}/lib)
######################################################################################
### 3) Define your targets and link the librairies
######################################################################################
set (TEST_LIST
t-mpi-parallelApply
t-mpi-wrapper
t-mpi-multipleRoles
#t-mpi-eval
#t-mpi-multistart
t-mpi-distrib-exp
)
foreach (test ${TEST_LIST})
set ("T_${test}_SOURCES" "${test}.cpp")
endforeach (test)
set(CMAKE_CXX_COMPILER "mpicxx")
add_definitions(-DWITH_MPI)
if(ENABLE_CMAKE_TESTING)
foreach (test ${TEST_LIST})
add_executable(${test} ${T_${test}_SOURCES})
add_test(${test} ${test})
target_link_libraries(${test} eoutils eompi eoserial eo)
install(TARGETS ${test} RUNTIME DESTINATION share/eo/test COMPONENT test)
endforeach (test)
endif()
######################################################################################

25
test/eompi/DISTRIB_XP_README.md Executable file
View file

@ -0,0 +1,25 @@
README
------
To launch a set of experiments with t-mpi-distrib-exp:
0) Compile it:
mpic++ -o distrib-exp t-mpi-distrib-exp.cpp -I../../src/ -I../../src/mpi/ -DWITH_MPI -L ../../../build/eo/lib/ -leoutils -leo -leompi -leoserial
1) Generate the experiments, thanks to the script gen-xp.py
This script will guide you and ask you for all experiments. The prefix is used in the results filenames.
You may want to modify the name of the experiments file (default value: "experiments.json") or
the pattern of the results files. However, you have to ensure that the pattern is an one-to-one
function of the parameters, otherwise some results could be lost.
2) Launch the t-mpi-distrib-exp program with mpirun:
For 4 cores (= 1 master + 3 workers)
mpirun -np 4 ./t-mpi-distrib-exp --use-experiment-file=1 --experiment-file=/home/eodev/eo/test/mpi/experiments.json
For 16 cores (= 1 master + 15 workers)
mpirun -np 5 ./t-mpi-distrib-exp --use-experiment-file=1 --experiment-file=/home/eodev/eo/test/mpi/experiments.json
3) The program will generate the results of the experiments, as txt files. There is one result file for each run of each
experiment.

6
test/eompi/experiments.json Executable file
View file

@ -0,0 +1,6 @@
{
"experiments":[
{"size":"10", "packet_size":"1", "seed":"1337", "distribution":{"name":"normal", "mean":"500", "stddev":"100"}, "worker_print_waiting_time":"1", "filename":"exp1.result.txt"},
{"size":"10", "packet_size":"1", "seed":"1337", "distribution":{"name":"normal", "mean":"100", "stddev":"20"}, "worker_print_waiting_time":"1", "filename":"exp2.result.txt"}
]
}

152
test/eompi/gen-xp.py Executable file
View file

@ -0,0 +1,152 @@
# -*- coding:utf-8 -*-
"""
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Authors:
Benjamin Bouvier <benjamin.bouvier@gmail.com>
"""
import json
# Where will be saved the experiments?
EXPERIMENTS_FILENAME = "experiments.json"
# What will be the pattern for experiments filenames?
FILENAME_PATTERN = "%(prefix)s_%(distrib_name)s_%(size)s_%(packet_size)s_%(run)s.txt"
def input_number_at_least( min ):
n = min - 1
while n < min:
try:
n = int(raw_input("Enter a number greater or equal to %s: "% min))
except Exception:
print "Please enter an integer."
return n
def input_number_between( min, max ):
n = min - 1
while n < min or n > max:
try:
n = int(raw_input("Enter a number between %s and %s: " % (min,max)))
except Exception:
print "Please enter a number."
return n
def choose_continue():
print """Do you want to continue?
0. No
1. Yes"""
return bool( input_number_between(0,1) )
def choose_distribution_uniform():
distribution = {}
distribution["name"] = "uniform"
print "Enter the minimum value (in milliseconds): "
min = input_number_at_least( 0 )
distribution["min"] = str(min)
print "Enter the maximum value (in milliseconds): "
distribution["max"] = str(input_number_at_least( min ))
return distribution
def choose_distribution_normal():
distribution = {}
distribution["name"] = "normal"
print "Enter the mean (in milliseconds): "
distribution["mean"] = str(input_number_at_least( 0 ))
print "Enter the standard deviation (in milliseconds): "
distribution["stddev"] = str(input_number_at_least( 0 ))
return distribution
def choose_distribution_power():
distribution = {}
distribution["name"] = "exponential"
print "Enter the mean (in milliseconds): "
distribution["mean"] = str(input_number_at_least( 0 ))
return distribution
def choose_distribution():
print """Choose your distribution:
0. Uniform
1. Normal
2. Exponential"""
choice = input_number_between( 0, 2 )
choose_distrib_functions = [ choose_distribution_uniform, choose_distribution_normal, choose_distribution_power ]
return choose_distrib_functions[ choice ]()
def choose_packet_size():
print "Enter the size of a packet (group of elements):"
return str(input_number_at_least( 0 ))
def choose_size():
print "Enter the total size (size of population):"
return str(input_number_at_least( 0 ))
def choose_worker_print():
print """Should the workers print the time they sleep on stdout?
0. No
1. Yes"""
return str(input_number_between( 0, 1 ))
def choose_nb_runs():
print """How many runs should be launched for this configuration? Seeds will be automatically affected to the number
of run+1 (for instance, the first run has a seed of 1, the second has a seed of 2, etc.)."""
return input_number_at_least( 1 )
def choose_prefix():
print """What is the name of the experiment? It will be used as the prefix of file names."""
return raw_input("Enter the prefix name: ")
def main():
prefix = choose_prefix()
exps = []
while True:
exp = {}
exp["distribution"] = choose_distribution()
exp["size"] = choose_size()
exp["packet_size"] = choose_packet_size()
exp["worker_print_waiting_time"] = choose_worker_print()
runs = choose_nb_runs()
for i in range( runs ):
exp["seed"] = str(i+1)
filename_map = exp.copy()
filename_map["run"] = exp["seed"]
filename_map["distrib_name"] = exp["distribution"]["name"]
filename_map["prefix"] = prefix
filename = FILENAME_PATTERN % filename_map
exp["filename"] = filename
copy = exp.copy()
exps.append( copy )
if not choose_continue():
break
# Write the experiments in a file
f = file( EXPERIMENTS_FILENAME , 'wb')
f.write("""{"experiments":[""")
i = 0
for exp in exps:
if i > 0:
f.write(",\n")
i += 1
f.write( json.dumps(exp) )
f.write("]}")
f.close()
if __name__ == "__main__":
main()

51
test/eompi/t-mpi-common.h Executable file
View file

@ -0,0 +1,51 @@
# ifndef __T_MPI_COMMON_H__
# define __T_MPI_COMMON_H__
#include <paradiseo/eoserial.h>
/**
* @file t-mpi-common.h
*
* This file shows an example of serialization of a primitive type, so as to be used in a parallel algorithm.
* It is fully compatible with the basic type, by implementing conversion operator and constructor based on type.
* It can contain any simple type which can be written in a std::ostream.
*/
template< class T >
struct SerializableBase : public eoserial::Persistent
{
public:
operator T&()
{
return _value;
}
SerializableBase() : _value()
{
// empty
}
SerializableBase( T base ) : _value( base )
{
// empty
}
void unpack( const eoserial::Object* obj )
{
eoserial::unpack( *obj, "value", _value );
}
eoserial::Object* pack(void) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add("value", eoserial::make( _value ) );
return obj;
}
private:
T _value;
};
# endif // __T_MPI_COMMON_H__

556
test/eompi/t-mpi-distrib-exp.cpp Executable file
View file

@ -0,0 +1,556 @@
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
* Authors:
* Benjamin Bouvier <benjamin.bouvier@gmail.com>
*/
/**
* @file t-mpi-distrib-exp.cpp
* @brief File for parallel experimentations.
*
* When using parallel evaluation, the individuals to evaluate are sent by packets (group),
* so as to avoid that communication time be more important than worker's execution time.
* However, the ideal size of packet depends on the problem and the time needed to carry out
* the atomic operation on each individual. This experiment tries to find a relation between
* the total number of elements to process (size), the execution time and the size of packet.
* This could lead to an heuristic allowing to optimize the size of packet according to the
* processing times.
*/
# include <unistd.h> // usleep
# include <iostream>
# include <iomanip>
# include <string>
# include <sstream>
# include <vector>
# include <paradiseo/eo.h>
# include <paradiseo/eompi.h>
# include "t-mpi-common.h"
using namespace eo::mpi;
// Serializable int
typedef SerializableBase<int> type;
/*
* The task is the following: the worker receives a number of milliseconds to wait, which
* simulates the process of one individual. This way, the sequences of processing times are
* generated only by the master and are more easily reproductible.
*/
struct Wait : public eoUF< type &, void >
{
Wait( bool print ) : _print( print )
{
// empty
}
void operator()( type & milliseconds )
{
if( _print )
std::cout << "Sleeping for " << milliseconds << "ms..." << std::endl;
// usleep takes an input in microseconds
usleep( milliseconds * 1000 );
}
private:
bool _print;
};
/**
* @brief Represents a distribution of processing times.
*/
class Distribution : public std::vector< type >, public eoserial::Persistent
{
public:
/**
* @brief Really fills the vector with the distribution values.
*/
void fill( unsigned size )
{
for( unsigned i = 0; i < size; ++i )
{
int next = next_element();
if( next < 0 ) next = 0;
push_back( next );
}
}
/**
* @brief Returns the next element of the distribution to put in the
* vector.
*
* @returns Number of milliseconds to wait. Can be negative ; in this case,
* the number will be truncated to 0ms.
*/
virtual int next_element() = 0;
/**
* @brief Creates params and retrieves values from parser
*
* Parser's params should take milliseconds as inputs.
*/
virtual void make_parser( eoParser & parser ) = 0;
/**
* @brief Returns true if this distribution has been activated by the
* command line.
*
* Used by the main program so as to check if at least one distribution has been
* activated.
*/
bool isActive() { return _active; }
/**
* @brief Prints the name and the parameters of the distribution
*/
virtual std::string toString() const = 0;
protected:
bool _active;
};
/**
* @brief Uniform distribution.
*
* This is an uniform distribution, defined by a minimum value and a maximum value.
* In the uniform distribution, every number from min to max has the same probability
* to appear.
*
* The 3 parameters activable from a parser are the following:
* - uniform=1 : if we want to use the uniform distribution
* - uniform-min=x : use x milliseconds as the minimum value of waiting time.
* - uniform-max=y : use y milliseconds as the maximum value of waiting time.
* Ensure that x < y, or the results are unpredictable.
*/
class UniformDistribution : public Distribution
{
public:
UniformDistribution()
{
// empty
}
void make_parser( eoParser & parser )
{
_active = parser.createParam( false, "uniform", "Uniform distribution", '\0', "Uniform").value();
_min = parser.createParam( 0.0, "uniform-min", "Minimum for uniform distribution, in ms.", '\0', "Uniform").value();
_max = parser.createParam( 1.0, "uniform-max", "Maximum for uniform distribution, in ms.", '\0', "Uniform").value();
}
int next_element()
{
return std::floor( eo::rng.uniform( _min, _max ) );
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "name", eoserial::make( "uniform" ) );
obj->add( "min", eoserial::make( _min ) );
obj->add( "max", eoserial::make( _max ) );
return obj;
}
void unpack( const eoserial::Object* obj )
{
eoserial::unpack( *obj, "min", _min );
eoserial::unpack( *obj, "max", _max );
}
std::string toString() const
{
std::stringstream ss;
ss << "uniform" << '\n'
<< "min: " << _min << '\n'
<< "max: " << _max << '\n';
return ss.str();
}
protected:
double _min;
double _max;
} uniformDistribution;
/**
* @brief Normal (gaussian) distribution of times.
*
* A normal distribution is defined by a mean and a standard deviation.
* The 3 parameters activable from the parser are the following:
* - normal=1: activates the gaussian distribution.
* - normal-mean=50: use 50ms as the mean of the distribution.
* - normal-stddev=10: use 10ms as the standard deviation of the distribution.
*/
class NormalDistribution : public Distribution
{
public:
NormalDistribution()
{
// empty
}
void make_parser( eoParser & parser )
{
_active = parser.createParam( false, "normal", "Normal distribution", '\0', "Normal").value();
_mean = parser.createParam( 0.0, "normal-mean", "Mean for the normal distribution (0 by default), in ms.", '\0', "Normal").value();
_stddev = parser.createParam( 1.0, "normal-stddev", "Standard deviation for the normal distribution (1ms by default), 0 isn't acceptable.", '\0', "Normal").value();
}
int next_element()
{
return std::floor( eo::rng.normal( _mean, _stddev ) );
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "name", eoserial::make( "normal" ) );
obj->add( "mean", eoserial::make( _mean ) );
obj->add( "stddev", eoserial::make( _stddev ) );
return obj;
}
void unpack( const eoserial::Object* obj )
{
eoserial::unpack( *obj, "mean", _mean );
eoserial::unpack( *obj, "stddev", _stddev );
}
std::string toString() const
{
std::stringstream ss;
ss << "normal" << '\n'
<< "mean: " << _mean << '\n'
<< "stddev: " << _stddev << '\n';
return ss.str();
}
protected:
double _mean;
double _stddev;
} normalDistribution;
/**
* @brief Exponential distribution.
*
* This distribution belongs to the category of the decreasing power laws and are affected by long trails
* phenomenons.
* An exponential distribution is only defined by its mean.
*
* The 2 parameters activable from the parser are the following:
* - exponential=1: to activate the exponential distribution.
* - exponential-mean=50: indicates that the mean must be 50ms.
*/
class ExponentialDistribution : public Distribution
{
public:
ExponentialDistribution()
{
// empty
}
void make_parser( eoParser & parser )
{
_active = parser.createParam( false, "exponential", "Exponential distribution", '\0', "Exponential").value();
_mean = parser.createParam( 0.0, "exponential-mean", "Mean for the exponential distribution (0 by default), in ms.", '\0', "Exponential").value();
}
int next_element()
{
return std::floor( eo::rng.negexp( _mean ) );
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "name", eoserial::make( "exponential" ) );
obj->add( "mean", eoserial::make( _mean ) );
return obj;
}
void unpack( const eoserial::Object* obj )
{
eoserial::unpack( *obj, "mean", _mean );
}
std::string toString() const
{
std::stringstream ss;
ss << "exponential" << '\n'
<< "mean: " << _mean << '\n';
return ss.str();
}
protected:
double _mean;
} exponentialDistribution;
/**
* @brief Serializable experiment.
*
* Allows an experiment to be saved and loaded via a file, using eoserial.
*
* Construct the experiment with the good parameters from the command line or load experiments from a file. Then call run() to launch the parallel job.
*
* If a filename is given to the constructor (or during the loading), the results of the experiments (time series) will
* be redirected to the file with the given file name. Otherwise (filename == ""), the output will just be shown on the
* standard output.
*/
class Experiment : public eoserial::Persistent
{
public:
Experiment() : _distribution(0), _worker_print_waiting_time( false ), _fileName("")
{
// empty
}
Experiment( Distribution* distrib, unsigned size, unsigned packet_size, bool print_waiting_time, unsigned seed, const std::string& fileName = "" ) :
_distribution( distrib ),
_size( size ),
_packet_size( packet_size ),
_worker_print_waiting_time( print_waiting_time ),
_seed( seed ),
_fileName( fileName )
{
// empty
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "size", eoserial::make( _size ) );
obj->add( "packet_size", eoserial::make( _packet_size ) );
obj->add( "worker_print_waiting_time", eoserial::make( _worker_print_waiting_time ) );
obj->add( "seed", eoserial::make( _seed ) );
if( _distribution )
{
obj->add( "distribution", _distribution );
}
obj->add( "filename", eoserial::make( _fileName ) );
return obj;
}
void unpack( const eoserial::Object* obj )
{
eoserial::unpack( *obj, "size", _size );
eoserial::unpack( *obj, "packet_size", _packet_size );
eoserial::unpack( *obj, "worker_print_waiting_time", _worker_print_waiting_time );
eoserial::unpack( *obj, "seed", _seed );
eoserial::unpack( *obj, "filename", _fileName );
eoserial::Object* distribObject = static_cast<eoserial::Object*>( obj->find("distribution")->second );
std::string distribName = *static_cast<eoserial::String*>( distribObject->find("name")->second );
// TODO find a better design...
if( distribName == "normal" ) {
_distribution = & normalDistribution;
} else if( distribName == "uniform" ) {
_distribution = & uniformDistribution;
} else if( distribName == "exponential" ) {
_distribution = & exponentialDistribution;
} else {
throw std::runtime_error("When unpacking experience, no distribution found.");
}
eoserial::unpackObject( *obj, "distribution", *_distribution );
}
void run()
{
mpi::communicator& comm = eo::mpi::Node::comm();
// reinits every objects
eo::rng.reseed( _seed );
eo::rng.clearCache(); // trick for repeatable sequences of normal numbers, cf eo::rng
_distribution->clear();
_distribution->fill( _size );
eo::mpi::timerStat.start("run");
Wait wait( _worker_print_waiting_time );
ParallelApplyStore< type > store( wait, DEFAULT_MASTER, _packet_size );
store.data( *_distribution );
DynamicAssignmentAlgorithm scheduling;
ParallelApply< type > job( scheduling, DEFAULT_MASTER, store );
job.run();
eo::mpi::timerStat.stop("run");
if( job.isMaster() )
{
EmptyJob( scheduling, DEFAULT_MASTER ); // to terminate parallel apply
// Receive statistics
typedef std::map< std::string, eoTimerStat::Stat > typeStats;
std::ostream* pout;
std::ofstream file;
bool fileSaveActivated = false;
if( _fileName == "" ) {
pout = & std::cout;
} else {
pout = & file;
file.open( _fileName.c_str() );
fileSaveActivated = true;
}
std::ostream& out = *pout;
// Reminder of the parameters
out << "size: " << _size << '\n'
<< "packet_size: " << _packet_size << '\n'
<< "distribution: " << _distribution->toString()
<< "seed: " << _seed << '\n' << std::endl;
// Results
out << std::fixed << std::setprecision( 5 );
for( int i = 1, s = comm.size(); i < s; ++i )
{
eoTimerStat timerStat;
comm.recv( i, eo::mpi::Channel::Commands, timerStat );
typeStats stats = timerStat.stats();
for( typeStats::iterator it = stats.begin(),
end = stats.end();
it != end;
++it )
{
out << i << " " << it->first << std::endl;
for( int j = 0, t = it->second.wtime.size(); j < t; ++j )
{
out << it->second.wtime[j] << " ";
}
out << std::endl;
}
out << std::endl;
}
if( fileSaveActivated ) {
file.close();
}
} else
{
// Send statistics
comm.send( DEFAULT_MASTER, eo::mpi::Channel::Commands, eo::mpi::timerStat );
}
timerStat.clear();
}
private:
Distribution* _distribution;
unsigned _size;
unsigned _packet_size;
bool _worker_print_waiting_time;
unsigned _seed;
std::string _fileName;
};
int main( int argc, char** argv )
{
Node::init( argc, argv );
eoParser parser( argc, argv );
// forces the statistics to be retrieved
eo::mpi::timerStat.forceDoMeasure();
// General parameters for the experimentation
unsigned size = parser.createParam( 10U, "size", "Number of elements to distribute.", 's', "Distribution").value();
unsigned packet_size = parser.createParam( 1U, "packet-size", "Number of elements to distribute at each time for a single worker.", 'p', "Parallelization").value();
bool worker_print_waiting_time = parser.createParam( false, "print-waiting-time", "Do the workers need to print the time they wait?", '\0', "Parallelization").value();
unsigned seed = parser.createParam( 0U, "seed", "Seed of random generator", '\0', "General").value();
std::string fileName = parser.createParam( std::string(""), "filename", "File name to which redirect the results (for a single experiment)", '\0', "General").value();
bool useExperimentFile = parser.createParam( false, "use-experiment-file", "Put to true if you want to launch experiments from a file formatted in JSON (see experiment-file).", '\0', "General").value();
std::string experimentFile = parser.createParam( std::string("experiments.json"), "experiment-file", "File name of experiments to provide, in format JSON.", '\0', "General").value();
if( !useExperimentFile )
{
std::vector<Distribution*> distribs;
distribs.push_back( &uniformDistribution );
distribs.push_back( &normalDistribution );
distribs.push_back( &exponentialDistribution );
// for each available distribution, check if activated.
// If no distribution is activated, show an error message
// If two distributions or more are activated, show an error message
// Otherwise, use the activated distribution as distrib
bool isChosenDistrib = false;
Distribution* pdistrib = 0;
for( int i = 0, s = distribs.size(); i < s; ++i )
{
distribs[i]->make_parser( parser );
if( distribs[i]->isActive() )
{
if( isChosenDistrib )
{
throw std::runtime_error("Only one distribution can be chosen during a launch!");
} else
{
isChosenDistrib = true;
pdistrib = distribs[i];
}
}
}
make_parallel( parser );
make_help( parser );
if( !isChosenDistrib )
{
throw std::runtime_error("No distribution chosen. One distribution should be chosen.");
}
Experiment e( pdistrib, size, packet_size, worker_print_waiting_time, seed, fileName );
e.run();
}
else // use experiments file
{
// read content of file
std::ifstream file( experimentFile.c_str() );
std::string fileContent;
while( file )
{
char temp[4096];
file.getline( temp, 4096, '\n' );
fileContent += temp;
fileContent += '\n';
}
file.close();
// transform content into array of experiments
eoserial::Object* wrapper = eoserial::Parser::parse( fileContent );
eoserial::Array& experiments = *static_cast< eoserial::Array* >( wrapper->find("experiments")->second );
for( unsigned i = 0, s = experiments.size(); i < s; ++i )
{
std::cout << "Launching experiment " << (i+1) << "..." << std::endl;
eoserial::Object* expObj = static_cast< eoserial::Object* >( experiments[i] );
Experiment exp;
exp.unpack( expObj );
exp.run();
}
delete wrapper;
}
return 0;
}

206
test/eompi/t-mpi-eval.cpp Executable file
View file

@ -0,0 +1,206 @@
/*
(c) Thales group, 2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Benjamin Bouvier <benjamin.bouvier@gmail.com>
*/
/*
* This file shows an example of parallel evaluation of a population, when using an eoEasyEA algorithm.
* Moreover, we add a basic wrapper on the parallel evaluation, so as to show how to retrieve the best solutions.
*/
//-----------------------------------------------------------------------------
#include <paradiseo/eo.h>
#include <paradiseo/eo/eoPopEvalFunc.h>
#include <paradiseo/eo/es/make_real.h>
#include "../eo/real_value.h"
#include <paradiseo/eompi.h>
#include <vector>
using namespace std;
//-----------------------------------------------------------------------------
class eoRealSerializable : public eoReal< eoMinimizingFitness >, public eoserial::Persistent
{
public:
eoRealSerializable(unsigned size = 0, double value = 0.0):
eoReal<eoMinimizingFitness>(size, value) {}
eoserial::Object* pack() const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "array",
eoserial::makeArray< vector<double>, eoserial::MakeAlgorithm >
( *this )
);
bool invalidFitness = invalid();
obj->add("invalid", eoserial::make( invalidFitness ) );
if( !invalidFitness )
{
double fitnessVal = fitness();
obj->add("fitness", eoserial::make( fitnessVal ) );
}
return obj;
}
void unpack( const eoserial::Object* obj )
{
this->clear();
eoserial::unpackArray< vector<double>, eoserial::Array::UnpackAlgorithm >
( *obj, "array", *this );
bool invalidFitness;
eoserial::unpack( *obj, "invalid", invalidFitness );
if( invalidFitness ) {
invalidate();
} else {
double fitnessVal;
eoserial::unpack<double>( *obj, "fitness", fitnessVal );
fitness( fitnessVal );
}
}
};
typedef eoRealSerializable EOT;
/*
* Wrapper for HandleResponse: shows the best answer, as it is found.
*
* Finding the best solution is an associative operation (as it is based on a "min" function, which is associative too)
* and that's why we can perform it here. Indeed, the min element of 5 elements is the min element of the 3 first
* elements and the min element of the 2 last elements:
* min(1, 2, 3, 4, 5) = min( min(1, 2, 3), min(4, 5) )
*
* This is a reduction. See MapReduce example to have another examples of reduction.
*/
struct CatBestAnswers : public eo::mpi::HandleResponseParallelApply<EOT>
{
CatBestAnswers()
{
best.fitness( 1000000000. );
}
/*
our structure inherits the member _wrapped from HandleResponseFunction,
which is a HandleResponseFunction pointer;
it inherits also the member _d (like Data), which is a pointer to the
ParallelApplyData used in the HandleResponseParallelApply&lt;EOT&gt;. Details
of this data are contained in the file eoParallelApply. We need just to know that
it contains a member assignedTasks which maps a worker rank and the sent slice
to be processed by the worker, and a reference to the processed table via the
call of the data() function.
*/
// if EOT were a template, we would have to do: (thank you C++ :)
// using eo::mpi::HandleResponseParallelApply<EOT>::_wrapped;
// using eo::mpi::HandleResponseParallelApply<EOT>::d;
void operator()(int wrkRank)
{
eo::mpi::ParallelApplyData<EOT> * d = _data;
// Retrieve informations about the slice processed by the worker
int index = d->assignedTasks[wrkRank].index;
int size = d->assignedTasks[wrkRank].size;
// call to the wrapped function HERE
(*_wrapped)( wrkRank );
// Compare fitnesses of evaluated individuals with the best saved
for(int i = index; i < index+size; ++i)
{
if( best.fitness() < d->table()[ i ].fitness() )
{
eo::log << eo::quiet << "Better solution found:" << d->table()[i].fitness() << std::endl;
best = d->table()[ i ];
}
}
}
protected:
EOT best;
};
int main(int ac, char** av)
{
eo::mpi::Node::init( ac, av );
// eo::log << eo::setlevel( eo::debug );
eo::log << eo::setlevel( eo::quiet );
eoParser parser(ac, av);
unsigned int popSize = parser.getORcreateParam((unsigned int)100, "popSize", "Population Size", 'P', "Evolution Engine").value();
unsigned int dimSize = parser.getORcreateParam((unsigned int)10, "dimSize", "Dimension Size", 'd', "Evolution Engine").value();
uint32_t seedParam = parser.getORcreateParam((uint32_t)0, "seed", "Random number seed", 0).value();
if (seedParam == 0) { seedParam = time(0); }
make_parallel(parser);
make_help(parser);
rng.reseed( seedParam );
eoUniformGenerator< double > gen(-5, 5);
eoInitFixedLength< EOT > init( dimSize, gen );
eoEvalFuncPtr< EOT, double, const std::vector< double >& > mainEval( real_value );
eoEvalFuncCounter< EOT > eval( mainEval );
// until this point, everything (but eo::mpi::Node::init) is exactly as in an sequential version.
// We then instanciate the parallel algorithm. The store is directly used by the eoParallelPopLoopEval, which
// internally uses parallel apply.
int rank = eo::mpi::Node::comm().rank();
eo::mpi::DynamicAssignmentAlgorithm assign;
if( rank == eo::mpi::DEFAULT_MASTER )
{
eoPop< EOT > pop( popSize, init );
eo::log << "Size of population : " << popSize << std::endl;
eo::mpi::ParallelApplyStore< EOT > store( eval, eo::mpi::DEFAULT_MASTER );
store.wrapHandleResponse( new CatBestAnswers );
eoParallelPopLoopEval< EOT > popEval( assign, eo::mpi::DEFAULT_MASTER, &store );
//eoParallelPopLoopEval< EOT > popEval( assign, eo::mpi::DEFAULT_MASTER, eval, 5 );
eo::log << eo::quiet << "Before first evaluation." << std::endl;
popEval( pop, pop );
eo::log << eo::quiet << "After first evaluation." << std::endl;
pop = eoPop< EOT >( popSize, init );
popEval( pop, pop );
eo::log << eo::quiet << "After second evaluation." << std::endl;
eo::log << eo::quiet << "DONE!" << std::endl;
} else
{
eoPop< EOT > pop; // the population doesn't have to be initialized, as it is not used by workers.
eoParallelPopLoopEval< EOT > popEval( assign, eo::mpi::DEFAULT_MASTER, eval );
popEval( pop, pop );
}
return 0;
}
//-----------------------------------------------------------------------------

196
test/eompi/t-mpi-multipleRoles.cpp Executable file
View file

@ -0,0 +1,196 @@
/*
(c) Thales group, 2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Benjamin Bouvier <benjamin.bouvier@gmail.com>
*/
/*
* This file shows an example of how to make a hierarchy between nodes, when using a parallel apply. In this basic
* test, the master delegates the charge of finding workers to 2 "sub" masters, which then send part of the table to
* their workers.
*
* It's convenient to establish a role map, so as to clearly identify every role:
* - The node 0 is the general master, that delegates the job. It sends the table to the 2 submasters, and waits for the
* results.
* - Nodes 1 and 2 are the worker of the first job: the delegates. They receive the elements of the table and
* retransmit them to the subworkers. They play the roles of worker in the delegating job, and master in the plus one
* job.
* - Following nodes (3 to 6) are workers of the plus one job. They do the real job. Nodes 3 and 5 are attached to
* submaster 1, 4 and 6 to submaster 2.
*
* This test requires exactly 7 hosts. If the size is bigger, an exception will be thrown at the beginning.
**/
# include <paradiseo/eompi.h>
# include <paradiseo/eompi/eoParallelApply.h>
# include <paradiseo/eompi/eoTerminateJob.h>
# include "t-mpi-common.h"
# include <iostream>
# include <vector>
using namespace std;
using namespace eo::mpi;
/*
* This class allows the user to easily serialize a vector of elements which implement eoserial::Persistent too.
*
* T is the type of the contained element, which must implement eoserial::Persistent too.
*
* Here, it contains SerializableBase<int>, which is a serializable integer that can be used as an integer.
*/
template< class T >
struct SerializableVector : public std::vector<T>, public eoserial::Persistent
{
public:
void unpack( const eoserial::Object* obj )
{
this->clear();
eoserial::Array* vector = static_cast<eoserial::Array*>( obj->find("vector")->second );
vector->deserialize< std::vector<T>, eoserial::Array::UnpackObjectAlgorithm >( *this );
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add("vector", eoserial::makeArray< std::vector<T>, eoserial::SerializablePushAlgorithm >( *this ) );
return obj;
}
};
// The real job to execute, for the subworkers: add one to each element of a table.
struct SubWork: public eoUF< SerializableBase<int>&, void >
{
void operator() ( SerializableBase<int> & x )
{
cout << "Subwork phase." << endl;
++x;
}
};
// Function called by both subworkers and delegates.
// v is the vector to process, rank is the MPI rank of the sub master
void subtask( vector< SerializableBase<int> >& v, int rank )
{
// Attach workers according to nodes.
// Submaster with rank 1 will have ranks 3 and 5 as subworkers.
// Submaster with rank 2 will have ranks 4 and 6 as subworkers.
vector<int> workers;
workers.push_back( rank + 2 );
workers.push_back( rank + 4 );
DynamicAssignmentAlgorithm algo( workers );
SubWork sw;
// Launch the job!
ParallelApplyStore< SerializableBase<int> > store( sw, rank );
store.data( v );
ParallelApply< SerializableBase<int> > job( algo, rank, store );
job.run();
EmptyJob stop( algo, rank );
}
// Functor applied by submasters. Wait for the subworkers responses and then add some random processing (here, multiply
// each result by two).
// Note that this work receives a vector of integers as an entry, while subworkers task's operator receives a simple
// integer.
struct Work: public eoUF< SerializableVector< SerializableBase<int> >&, void >
{
void operator() ( SerializableVector< SerializableBase<int> >& v )
{
cout << "Work phase..." << endl;
subtask( v, Node::comm().rank() );
for( unsigned i = 0; i < v.size(); ++i )
{
v[i] *= 2;
}
}
};
int main(int argc, char** argv)
{
// eo::log << eo::setlevel( eo::debug );
Node::init( argc, argv );
if( Node::comm().size() != 7 ) {
throw std::runtime_error("World size should be 7.");
}
SerializableVector< SerializableBase<int> > v;
v.push_back(1);
v.push_back(3);
v.push_back(3);
v.push_back(7);
v.push_back(42);
// As submasters' operator receives a vector<int> as an input, and ParallelApply takes a vector of
// operator's input as an input, we have to deal with a vector of vector of integers for the master task.
vector< SerializableVector< SerializableBase<int> > > metaV;
// Here, we send twice the same vector. We could also have splitted the first vector into two vectors, one
// containing the beginning and another one containing the end.
metaV.push_back( v );
metaV.push_back( v );
// Assigning roles is done by comparing MPI ranks.
switch( Node::comm().rank() )
{
// Nodes from 0 to 2 are implicated into the delegating task.
case 0:
case 1:
case 2:
{
Work w;
DynamicAssignmentAlgorithm algo( 1, 2 );
ParallelApplyStore< SerializableVector< SerializableBase<int> > > store( w, 0 );
store.data( metaV );
ParallelApply< SerializableVector< SerializableBase<int> > > job( algo, 0, store );
job.run();
if( job.isMaster() )
{
EmptyJob stop( algo, 0 );
v = metaV[0];
cout << "Results : " << endl;
for(unsigned i = 0; i < v.size(); ++i)
{
cout << v[i] << ' ';
}
cout << endl;
}
}
break;
// Other nodes are implicated into the subwork task.
default:
{
// all the other nodes are sub workers
int rank = Node::comm().rank();
if ( rank == 3 or rank == 5 )
{
subtask( v, 1 );
} else {
subtask( v, 2 );
}
}
break;
}
return 0;
}

169
test/eompi/t-mpi-multistart.cpp Executable file
View file

@ -0,0 +1,169 @@
# include <paradiseo/eompi/eoMultiStart.h>
using namespace eo::mpi;
#include <stdexcept>
#include <iostream>
#include <sstream>
#include <paradiseo/eo.h>
#include <paradiseo/eo/es.h>
/*
* This file is based on the tutorial lesson 1. We'll consider that you know all the EO
* related parts of the algorithm and we'll focus our attention on parallelization.
*
* This file shows an example of multistart applied to a eoSGA (simple genetic
* algorithm). As individuals need to be serialized, we implement a class inheriting
* from eoReal (which is the base individual), so as to manipulate individuals as they
* were eoReal AND serialize them.
*
* The main function shows how to launch a multistart job, with default functors. If you
* don't know which functors to use, these ones should fit the most of your purposes.
*/
using namespace std;
/*
* eoReal is a vector of double: we just have to serializes the value and the fitness.
*/
class SerializableEOReal: public eoReal<double>, public eoserial::Persistent
{
public:
SerializableEOReal(unsigned size = 0, double value = 0.0) :
eoReal<double>(size, value)
{
// empty
}
void unpack( const eoserial::Object* obj )
{
this->clear();
eoserial::unpackArray
< std::vector<double>, eoserial::Array::UnpackAlgorithm >
( *obj, "vector", *this );
bool invalidFitness;
eoserial::unpack( *obj, "invalid_fitness", invalidFitness );
if( invalidFitness )
{
this->invalidate();
} else
{
double f;
eoserial::unpack( *obj, "fitness", f );
this->fitness( f );
}
}
eoserial::Object* pack( void ) const
{
eoserial::Object* obj = new eoserial::Object;
obj->add( "vector", eoserial::makeArray< std::vector<double>, eoserial::MakeAlgorithm >( *this ) );
bool invalidFitness = this->invalid();
obj->add( "invalid_fitness", eoserial::make( invalidFitness ) );
if( !invalidFitness )
{
obj->add( "fitness", eoserial::make( this->fitness() ) );
}
return obj;
}
};
// REPRESENTATION
//-----------------------------------------------------------------------------
// define your individuals
typedef SerializableEOReal Indi;
// EVAL
//-----------------------------------------------------------------------------
// a simple fitness function that computes the euclidian norm of a real vector
// @param _indi A real-valued individual
double real_value(const Indi & _indi)
{
double sum = 0;
for (unsigned i = 0; i < _indi.size(); i++)
sum += _indi[i]*_indi[i];
return (-sum); // maximizing only
}
/************************** PARALLELIZATION JOB *******************************/
int main(int argc, char **argv)
{
Node::init( argc, argv );
// PARAMETRES
// all parameters are hard-coded!
const unsigned int SEED = 133742; // seed for random number generator
const unsigned int VEC_SIZE = 8; // Number of object variables in genotypes
const unsigned int POP_SIZE = 100; // Size of population
const unsigned int T_SIZE = 3; // size for tournament selection
const unsigned int MAX_GEN = 100; // Maximum number of generation before STOP
const float CROSS_RATE = 0.8; // Crossover rate
const double EPSILON = 0.01; // range for real uniform mutation
const float MUT_RATE = 0.5; // mutation rate
eoEvalFuncPtr<Indi> eval( real_value );
eoPop<Indi> pop;
eoUniformGenerator< double > generator;
eoInitFixedLength< Indi > init( VEC_SIZE, generator );
pop = eoPop<Indi>( POP_SIZE, init );
eoDetTournamentSelect<Indi> select(T_SIZE);
eoSegmentCrossover<Indi> xover;
eoUniformMutation<Indi> mutation(EPSILON);
eoGenContinue<Indi> continuator(MAX_GEN);
/* Does work too with a steady fit continuator. */
// eoSteadyFitContinue< Indi > continuator( 10, 50 );
eoSGA<Indi> gga(select, xover, CROSS_RATE, mutation, MUT_RATE,
eval, continuator);
/* How to assign tasks, which are starts? */
DynamicAssignmentAlgorithm assignmentAlgo;
/* Before a worker starts its algorithm, how does it reinits the population?
* There are a few default usable functors, defined in eoMultiStart.h.
*
* This one (ReuseSamePopEA) doesn't modify the population after a start, so
* the same population is reevaluated on each multistart: the solution tend
* to get better and better.
*/
ReuseSamePopEA< Indi > resetAlgo( continuator, pop, eval );
/**
* How to send seeds to the workers, at the beginning of the parallel job?
* This functors indicates that seeds should be random values.
*/
GetRandomSeeds< Indi > getSeeds( SEED );
// Builds the store
MultiStartStore< Indi > store(
gga,
DEFAULT_MASTER,
resetAlgo,
getSeeds);
// Creates the multistart job and runs it.
// The last argument indicates that we want to launch 5 runs.
MultiStart< Indi > msjob( assignmentAlgo, DEFAULT_MASTER, store, 5 );
msjob.run();
if( msjob.isMaster() )
{
msjob.best_individuals().sort();
std::cout << "Global best individual has fitness " << msjob.best_individuals().best_element().fitness() << std::endl;
}
MultiStart< Indi > msjob10( assignmentAlgo, DEFAULT_MASTER, store, 10 );
msjob10.run();
if( msjob10.isMaster() )
{
msjob10.best_individuals().sort();
std::cout << "Global best individual has fitness " << msjob10.best_individuals().best_element().fitness() << std::endl;
}
return 0;
}

220
test/eompi/t-mpi-parallelApply.cpp Executable file
View file

@ -0,0 +1,220 @@
/*
(c) Thales group, 2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Benjamin Bouvier <benjamin.bouvier@gmail.com>
*/
/*
* This file shows an example of use of parallel apply, in the following context: each element of a table is
* incremented... in a parallel fashion. While this operation is very easy to perform even on a single host, it's just
* an example for parallel apply use.
*
* The table of integers has to be serialized before it's sent. The wrapper object SerializableBase allows to serialize
* any type and manipulate it like this type: SerializableBase<int> can be exactly be used as an integer.
*
* Besides, this is also a test for assignment (scheduling) algorithms, in different cases. The test succeeds if and
* only if the program terminates without any segfault ; otherwise, there could be a deadlock which prevents the end or
* a segfault at any time.
*
* One important thing is to instanciate an EmptyJob after having launched a ParallelApplyJob, so as the workers to be
* aware that the job is done (as it's a MultiJob).
*
* This test needs at least 3 processes to be launched. Under this size, it will directly throw an exception, at the
* beginning;
*/
# include <paradiseo/eompi.h>
# include <paradiseo/eompi/eoParallelApply.h>
# include <paradiseo/eompi/eoTerminateJob.h>
# include "t-mpi-common.h"
# include <iostream>
# include <cstdlib>
# include <vector>
using namespace std;
using namespace eo::mpi;
/*
* The function to be called on each element of the table: just increment the value.
*/
struct plusOne : public eoUF< SerializableBase<int>&, void >
{
void operator() ( SerializableBase<int> & x )
{
++x; // implicit conversion of SerializableBase<int> in the integer it contains
}
};
/*
* Internal structure representating a test.
*/
struct Test
{
AssignmentAlgorithm * assign; // used assignment algorithm for this test.
string description; // textual description of the test
int requiredNodesNumber; // number of required nodes. NB : chosen nodes ranks must be sequential
};
int main(int argc, char** argv)
{
// eo::log << eo::setlevel( eo::debug ); // if you like tty full of rainbows, decomment this line and comment the following one.
eo::log << eo::setlevel( eo::quiet );
bool launchOnlyOne = false ; // Set this to true if you wanna launch only the first test.
Node::init( argc, argv );
// Initializes a vector with random values.
srand( time(0) );
vector< SerializableBase<int> > v;
for( int i = 0; i < 1000; ++i )
{
v.push_back( rand() );
}
// We need to be sure the values are correctly incremented between each test. So as to check this, we save the
// original vector into a variable originalV, and put an offset variable to 0. After each test, the offset is
// incremented and we can compare the returned value of each element to the value of each element in originalV +
// offset. If the two values are different, there has been a problem.
int offset = 0;
vector< SerializableBase<int> > originalV = v;
// Instanciates the functor to apply on each element
plusOne plusOneInstance;
vector< Test > tests;
const int ALL = Node::comm().size();
if( ALL < 3 ) {
throw std::runtime_error("Needs at least 3 processes to be launched!");
}
// Tests are auto described thanks to member "description"
Test tIntervalStatic;
tIntervalStatic.assign = new StaticAssignmentAlgorithm( 1, REST_OF_THE_WORLD, v.size() );
tIntervalStatic.description = "Correct static assignment with interval."; // workers have ranks from 1 to size - 1
tIntervalStatic.requiredNodesNumber = ALL;
tests.push_back( tIntervalStatic );
if( !launchOnlyOne )
{
Test tWorldStatic;
tWorldStatic.assign = new StaticAssignmentAlgorithm( v.size() );
tWorldStatic.description = "Correct static assignment with whole world as workers.";
tWorldStatic.requiredNodesNumber = ALL;
tests.push_back( tWorldStatic );
Test tStaticOverload;
tStaticOverload.assign = new StaticAssignmentAlgorithm( v.size()+100 );
tStaticOverload.description = "Static assignment with too many runs.";
tStaticOverload.requiredNodesNumber = ALL;
tests.push_back( tStaticOverload );
Test tUniqueStatic;
tUniqueStatic.assign = new StaticAssignmentAlgorithm( 1, v.size() );
tUniqueStatic.description = "Correct static assignment with unique worker.";
tUniqueStatic.requiredNodesNumber = 2;
tests.push_back( tUniqueStatic );
Test tVectorStatic;
vector<int> workers;
workers.push_back( 1 );
workers.push_back( 2 );
tVectorStatic.assign = new StaticAssignmentAlgorithm( workers, v.size() );
tVectorStatic.description = "Correct static assignment with precise workers specified.";
tVectorStatic.requiredNodesNumber = 3;
tests.push_back( tVectorStatic );
Test tIntervalDynamic;
tIntervalDynamic.assign = new DynamicAssignmentAlgorithm( 1, REST_OF_THE_WORLD );
tIntervalDynamic.description = "Dynamic assignment with interval.";
tIntervalDynamic.requiredNodesNumber = ALL;
tests.push_back( tIntervalDynamic );
Test tUniqueDynamic;
tUniqueDynamic.assign = new DynamicAssignmentAlgorithm( 1 );
tUniqueDynamic.description = "Dynamic assignment with unique worker.";
tUniqueDynamic.requiredNodesNumber = 2;
tests.push_back( tUniqueDynamic );
Test tVectorDynamic;
tVectorDynamic.assign = new DynamicAssignmentAlgorithm( workers );
tVectorDynamic.description = "Dynamic assignment with precise workers specified.";
tVectorDynamic.requiredNodesNumber = tVectorStatic.requiredNodesNumber;
tests.push_back( tVectorDynamic );
Test tWorldDynamic;
tWorldDynamic.assign = new DynamicAssignmentAlgorithm;
tWorldDynamic.description = "Dynamic assignment with whole world as workers.";
tWorldDynamic.requiredNodesNumber = ALL;
tests.push_back( tWorldDynamic );
}
for( unsigned int i = 0; i < tests.size(); ++i )
{
// Instanciates a store with the functor, the master rank and size of packet (see ParallelApplyStore doc).
ParallelApplyStore< SerializableBase<int> > store( plusOneInstance, eo::mpi::DEFAULT_MASTER, 3 );
// Updates the contained data
store.data( v );
// Creates the job with the assignment algorithm, the master rank and the store
ParallelApply< SerializableBase<int> > job( *(tests[i].assign), eo::mpi::DEFAULT_MASTER, store );
// Only master writes information
if( job.isMaster() )
{
cout << "Test : " << tests[i].description << endl;
}
// Workers whose rank is inferior to required nodes number have to run the test, the other haven't anything to
// do.
if( Node::comm().rank() < tests[i].requiredNodesNumber )
{
job.run();
}
// After the job run, the master checks the result with offset and originalV
if( job.isMaster() )
{
// This job has to be instanciated, not launched, so as to tell the workers they're done with the parallel
// job.
EmptyJob stop( *(tests[i].assign), eo::mpi::DEFAULT_MASTER );
++offset;
for(unsigned i = 0; i < v.size(); ++i)
{
cout << v[i] << ' ';
if( originalV[i] + offset != v[i] )
{
cout << " <-- ERROR at this point." << endl;
exit( EXIT_FAILURE );
}
}
cout << endl;
}
// MPI synchronization (all the processes wait to be here).
Node::comm().barrier();
delete tests[i].assign;
}
return 0;
}

133
test/eompi/t-mpi-wrapper.cpp Executable file
View file

@ -0,0 +1,133 @@
/*
(c) Thales group, 2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation;
version 2 of the License.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: http://eodev.sourceforge.net
Authors:
Benjamin Bouvier <benjamin.bouvier@gmail.com>
*/
/*
* This file shows an example of how to wrap a handler of a job store. Here, the wrapped handler is the "IsFinished"
* one. The only function that has been added is that the wrapper prints a message on standard output, indicating what
* the wrapped function returns as a result.
*
* This test is performed on a parallel apply job, the same as in parallelApply. The main difference is when
* instanciating the store.
*/
# include <paradiseo/eompi.h>
# include <paradiseo/eompi/eoParallelApply.h>
# include <paradiseo/eompi/eoTerminateJob.h>
# include "t-mpi-common.h"
# include <iostream>
# include <cstdlib>
# include <vector>
using namespace std;
using namespace eo::mpi;
// Job functor.
struct plusOne : public eoUF< SerializableBase<int>&, void >
{
void operator() ( SerializableBase<int>& x )
{
++x;
}
};
/*
* Shows the wrapped result of IsFinished, prints a message and returns the wrapped value.
* times is an integer counting how many time the wrapper (hence the wrapped too) has been called.
*/
template< class EOT >
struct ShowWrappedResult : public IsFinishedParallelApply<EOT>
{
using IsFinishedParallelApply<EOT>::_wrapped;
ShowWrappedResult ( IsFinishedParallelApply<EOT> * w = 0 ) : IsFinishedParallelApply<EOT>( w ), times( 0 )
{
// empty
}
bool operator()()
{
bool wrappedValue = _wrapped->operator()(); // (*_wrapped)();
cout << times << ") Wrapped function would say that it is " << ( wrappedValue ? "":"not ") << "finished" << std::endl;
++times;
return wrappedValue;
}
private:
int times;
};
int main(int argc, char** argv)
{
// eo::log << eo::setlevel( eo::debug );
eo::log << eo::setlevel( eo::quiet );
Node::init( argc, argv );
srand( time(0) );
vector< SerializableBase<int> > v;
for( int i = 0; i < 1000; ++i )
{
v.push_back( rand() );
}
int offset = 0;
vector< SerializableBase<int> > originalV = v;
plusOne plusOneInstance;
StaticAssignmentAlgorithm assign( v.size() );
ParallelApplyStore< SerializableBase<int> > store( plusOneInstance, eo::mpi::DEFAULT_MASTER, 1 );
store.data( v );
// This is the only thing which changes: we wrap the IsFinished function.
// According to RAII, we'll delete the invokated wrapper at the end of the main ; the store won't delete it
// automatically.
ShowWrappedResult< SerializableBase<int> > wrapper;
store.wrapIsFinished( &wrapper );
ParallelApply< SerializableBase<int> > job( assign, eo::mpi::DEFAULT_MASTER, store );
// Equivalent to:
// Job< ParallelApplyData<int> > job( assign, 0, store );
job.run();
EmptyJob stop( assign, eo::mpi::DEFAULT_MASTER );
if( job.isMaster() )
{
++offset;
for(unsigned i = 0; i < v.size(); ++i)
{
cout << v[i] << ' ';
if( originalV[i] + offset != v[i] )
{
cout << " <-- ERROR at this point." << endl;
exit( EXIT_FAILURE );
}
}
cout << endl;
}
return 0;
}

104
test/eompi/template-job.cpp Executable file
View file

@ -0,0 +1,104 @@
# include <paradiseo/eompi.h>
using namespace eo::mpi;
/*
* This file is a template for a new eo::mpi::Job. You have everything that should be necessary to implement a new
* parallelized algorithm.
*
* Replace __TEMPLATE__ by the name of your algorithm (for instance: MultiStart, ParallelApply, etc.).
*/
template< class EOT >
struct __TEMPLATE__Data
{
};
template< class EOT >
class SendTask__TEMPLATE__ : public SendTaskFunction< __TEMPLATE__Data< EOT > >
{
public:
using SendTaskFunction< __TEMPLATE__Data< EOT > >::_data;
void operator()( int wrkRank )
{
// TODO implement me
}
};
template< class EOT >
class HandleResponse__TEMPLATE__ : public HandleResponseFunction< __TEMPLATE__Data< EOT > >
{
public:
using HandleResponseFunction< __TEMPLATE__Data< EOT > >::_data;
void operator()( int wrkRank )
{
// TODO implement me
}
};
template< class EOT >
class ProcessTask__TEMPLATE__ : public ProcessTaskFunction< __TEMPLATE__Data< EOT > >
{
public:
using ProcessTaskFunction< __TEMPLATE__Data<EOT> >::_data;
void operator()()
{
// TODO implement me
}
};
template< class EOT >
class IsFinished__TEMPLATE__ : public IsFinishedFunction< __TEMPLATE__Data< EOT > >
{
public:
using IsFinishedFunction< __TEMPLATE__Data< EOT > >::_data;
bool operator()()
{
// TODO implement me
}
};
template< class EOT >
class __TEMPLATE__Store : public JobStore< __TEMPLATE__Data< EOT > >
{
public:
__TEMPLATE__Data<EOT>* data()
{
// TODO implement me
return 0;
}
};
template< class EOT >
class __TEMPLATE__ : public MultiJob< __TEMPLATE__Data< EOT > >
{
public:
__TEMPLATE__( AssignmentAlgorithm & algo,
int masterRank,
__TEMPLATE__Store< EOT > & store ) :
MultiJob< __TEMPLATE__Data< EOT > >( algo, masterRank, store )
{
// TODO implement me
}
};
/*
int main(int argc, char **argv)
{
Node::init( argc, argv );
DynamicAssignmentAlgorithm assignmentAlgo;
__TEMPLATE__Store<int> store;
__TEMPLATE__<int> job( assignmentAlgo, DEFAULT_MASTER, store );
}
*/

112
test/mo/CMakeLists.txt Executable file
View file

@ -0,0 +1,112 @@
######################################################################################
### 0) Include headers
######################################################################################
#include_directories(${EO_SRC_DIR}/src)
#include_directories(${MO_SRC_DIR}/src)
#include_directories(${PROBLEMS_SRC_DIR})
#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
######################################################################################
### 1) Define test list
######################################################################################
set (TEST_LIST
t-moAdaptiveWalkSampling
t-moNeighbor
t-moBitNeighbor
t-moOrderNeighborhood
t-moFullEvalByCopy
t-moFullEvalByModif
t-moNeighborComparator
t-moSolNeighborComparator
t-moTrueContinuator
t-moRndWithoutReplNeighborhood
t-moRndWithReplNeighborhood
t-moFitnessStat
t-moDistanceStat
t-moNeighborhoodStat
t-moCounterMonitorSaver
t-moSolutionStat
t-moCheckpoint
t-moDummyMemory
t-moSolVectorTabuList
t-moBestImprAspiration
t-moSimpleHCexplorer
t-moRandomBestHCexplorer
t-moNeutralHCexplorer
t-moFirstImprHCexplorer
t-moRandomWalkExplorer
t-moMetropolisHastingExplorer
t-moRandomNeutralWalkExplorer
t-moTSexplorer
t-moSolComparator
t-moDummyEval
t-moDummyNeighbor
t-moDummyNeighborhood
t-moSimpleCoolingSchedule
t-moAlwaysAcceptCrit
t-moBetterAcceptCrit
t-moCountMoveMemory
t-moMonOpPerturb
t-moRestartPerturb
t-moNeighborhoodPerturb
t-moSAexplorer
t-moSA
t-moLocalSearch
t-moILSexplorer
t-moSimpleHC
t-moFirstImprHC
t-moRandomBestHC
t-moNeighborVectorTabuList
t-moMonOpDiversification
t-moTS
t-moILS
t-moDummyLS
t-moRandomSearch
t-moMetropolisHasting
t-moNeutralHC
t-moRandomWalk
t-moRandomNeutralWalk
t-moIterContinuator
t-moFitContinuator
t-moCombinedContinuator
t-moFullEvalContinuator
t-moNeighborEvalContinuator
t-moTimeContinuator
t-moDummyExplorer
t-moLocalSearchInit
t-moSolInit
t-moEvalCounter
t-moNeighborBestStat
t-moCounterStat
t-moMinusOneCounterStat
t-moVectorMonitor
t-moRandomSearchExplorer
t-moSampling
t-moDensityOfStatesSampling
t-moAutocorrelationSampling
t-moHillClimberSampling
t-moFDCsampling
t-moNeutralDegreeSampling
t-moFitnessCloudSampling
t-moNeutralWalkSampling
t-moStatistics
t-moIndexedVectorTabuList
# t-moRndIndexedVectorTabuList
t-moDynSpanCoolingSchedule
)
######################################################################################
### 3) Create each test
######################################################################################
foreach (test ${TEST_LIST})
set ("T_${test}_SOURCES" "${test}.cpp")
add_executable(${test} ${T_${test}_SOURCES})
add_test(${test} ${test})
target_link_libraries(${test} ga es eoutils eo)
install(TARGETS ${test} RUNTIME DESTINATION share/${PROJECT_TAG}/mo/test COMPONENT tests)
endforeach (test)

251
test/mo/moTestClass.h Executable file
View file

@ -0,0 +1,251 @@
/*
<moTestClass.h>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Sébastien Verel, Arnaud Liefooghe, Jérémie Humeau
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#ifndef _moTestClass_h
#define _moTestClass_h
#include <paradiseo/eo/EO.h>
#include <paradiseo/eo/eoEvalFunc.h>
#include <paradiseo/mo/neighborhood/moNeighbor.h>
#include <paradiseo/mo/neighborhood/moBackableNeighbor.h>
#include <paradiseo/mo/neighborhood/moNeighborhood.h>
#include <paradiseo/mo/neighborhood/moRndNeighborhood.h>
#include <paradiseo/mo/eval/moEval.h>
#include <paradiseo/eo/ga/eoBit.h>
#include <paradiseo/eo/eoScalarFitness.h>
#include <paradiseo/mo/neighborhood/moOrderNeighborhood.h>
#include <paradiseo/mo/problems/bitString/moBitNeighbor.h>
#include <paradiseo/mo/neighborhood/moIndexNeighbor.h>
#include <paradiseo/eo/utils/eoMonitor.h>
#include <paradiseo/eo/utils/eoUpdater.h>
#include <paradiseo/eo/eoInit.h>
typedef eoBit<eoMinimizingFitness> bitVector;
typedef moBitNeighbor<eoMinimizingFitness> bitNeighbor;
class moDummyRndNeighborhood: public moOrderNeighborhood<bitNeighbor> ,
public moRndNeighborhood<bitNeighbor> {
public:
moDummyRndNeighborhood(unsigned int a) :
moOrderNeighborhood<bitNeighbor> (a) {
}
};
typedef moDummyRndNeighborhood bitNeighborhood;
typedef EO<int> Solution;
class moDummyNeighborTest: public moNeighbor<Solution> {
public:
virtual void move(Solution & _solution) {
}
};
class moDummyBackableNeighbor: public moBackableNeighbor<Solution> {
public:
virtual void move(Solution & _solution) {
}
virtual void moveBack(Solution & _solution) {
}
};
class moDummyNeighborhoodTest: public moNeighborhood<moDummyNeighborTest> {
public:
typedef moDummyNeighborTest Neighbor;
moDummyNeighborhoodTest() :
i(0), j(0) {
}
virtual bool hasNeighbor(EOT & _solution) {
bool res;
if (i % 3 == 0 || i == 1)
res = false;
else
res = true;
i++;
return res;
}
virtual void init(EOT & _solution, Neighbor & _current) {
}
virtual void next(EOT & _solution, Neighbor & _current) {
}
virtual bool cont(EOT & _solution) {
j++;
return (j % 10 != 0);
}
private:
int i, j;
};
class moDummyEvalTest: public eoEvalFunc<Solution> {
public:
void operator()(Solution& _sol) {
if (_sol.invalid())
_sol.fitness(100);
else
_sol.fitness(_sol.fitness() + 50);
}
};
class evalOneMax: public moEval<bitNeighbor> {
private:
unsigned size;
public:
evalOneMax(unsigned _size) :
size(_size) {
}
;
~evalOneMax(void) {
}
;
void operator()(bitVector& _sol, bitNeighbor& _n) {
unsigned int fit = _sol.fitness();
if (_sol[_n.index()])
fit--;
else
fit++;
_n.fitness(fit);
}
};
class dummyEvalOneMax: public moEval<bitNeighbor> {
private:
unsigned size;
public:
dummyEvalOneMax(unsigned _size) :
size(_size) {
}
;
~dummyEvalOneMax(void) {
}
;
void operator()(bitVector& _sol, bitNeighbor& _n) {
unsigned int fit = _sol.fitness();
_n.fitness(fit);
}
};
class monitor1: public eoMonitor {
public:
monitor1(unsigned int& _a) :
a(_a) {
}
eoMonitor& operator()() {
a++;
return *this;
}
void lastCall() {
a++;
}
private:
unsigned int& a;
};
class monitor2: public eoMonitor {
public:
monitor2(unsigned int& _a) :
a(_a) {
}
eoMonitor& operator()() {
a++;
return *this;
}
void lastCall() {
a++;
}
private:
unsigned int& a;
};
class updater1: public eoUpdater {
public:
updater1(unsigned int& _a) :
a(_a) {
}
void operator()() {
a++;
}
void lastCall() {
a++;
}
private:
unsigned int& a;
};
class dummyInit: public eoInit<bitVector> {
public:
void operator()(bitVector& sol) {
}
};
class dummyInit2: public eoInit<bitVector> {
public:
dummyInit2(unsigned int _size) :
size(_size) {
}
void operator()(bitVector& sol) {
sol.resize(0);
for (unsigned int i = 0; i < size; i++)
sol.push_back(true);
}
private:
unsigned int size;
};
#endif

77
test/mo/t-moAdaptiveWalkSampling.cpp Executable file
View file

@ -0,0 +1,77 @@
/*
<t-moAdaptiveWalkSampling.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Boufaras Karima
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <iostream>
#include <cstdlib>
#include <cassert>
#include <paradiseo/mo/sampling/moAdaptiveWalkSampling.h>
#include "moTestClass.h"
#include <paradiseo/mo/algo/moFirstImprHC.h>
#include <paradiseo/problems/eval/oneMaxEval.h>
#include <paradiseo/mo/continuator/moSolutionStat.h>
#include <paradiseo/mo/continuator/moCounterStat.h>
#include <paradiseo/mo/continuator/moIterContinuator.h>
int main() {
std::cout << "[t-moAdaptiveWalkSampling] => START" << std::endl;
bitNeighborhood nh(5);
oneMaxEval<bitVector> fullEval;
evalOneMax eval(5);
dummyInit2 init(5);
moIterContinuator<bitNeighbor> cont(2);
moAdaptiveWalkSampling<bitNeighbor> test(init,nh,fullEval,eval,3);
moCounterStat<bitVector> stat2;
test.add(stat2);
test();
std::vector<double> res;
std::vector<bitVector> res2;
res = test.getValues(1);
res2= test.getSolutions(0);
for (unsigned int i=0; i<res2.size(); i++)
assert(res2[i].fitness()==5-i);
for (unsigned int i=0; i<res.size(); i++)
assert(res[i]==i);
test.fileExport("outputTestAdaptativeWalkSampling1");
test.fileExport(1, "outputTestAdaptativeWalkSampling2");
std::cout << "[t-moAdaptiveWalkSampling] => OK" << std::endl;
return EXIT_SUCCESS;
}

51
test/mo/t-moAlwaysAcceptCrit.cpp Executable file
View file

@ -0,0 +1,51 @@
/*
<t-moAlwaysAcceptCrit.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Sébastien Verel, Arnaud Liefooghe, Jérémie Humeau
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <iostream>
#include <cstdlib>
#include <cassert>
#include <paradiseo/mo/acceptCrit/moAlwaysAcceptCrit.h>
#include "moTestClass.h"
int main() {
std::cout << "[t-moAlwaysAcceptCrit] => START" << std::endl;
bitVector sol1, sol2;
moAlwaysAcceptCrit<bitNeighbor> test;
assert(test(sol1,sol2));
std::cout << "[t-moAlwaysAcceptCrit] => OK" << std::endl;
return EXIT_SUCCESS;
}

58
test/mo/t-moAutocorrelationSampling.cpp Executable file
View file

@ -0,0 +1,58 @@
/*
<t-moAutocorrelationSampling.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Sébastien Verel, Arnaud Liefooghe, Jérémie Humeau
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <iostream>
#include <cstdlib>
#include <cassert>
#include <paradiseo/mo/sampling/moAutocorrelationSampling.h>
#include "moTestClass.h"
#include <paradiseo/problems/eval/oneMaxEval.h>
int main() {
std::cout << "[t-moAutocorrelationSampling] => START" << std::endl;
bitNeighborhood nh(4);
oneMaxEval<bitVector> fullEval;
evalOneMax eval(4);
dummyInit2 init(4);
moAutocorrelationSampling<bitNeighbor> test(init, nh, fullEval, eval, 3);
test();
test.fileExport("outputTestAutocorrelationSampling");
std::cout << "[t-moAutocorrelationSampling] => OK" << std::endl;
return EXIT_SUCCESS;
}

78
test/mo/t-moBestImprAspiration.cpp Executable file
View file

@ -0,0 +1,78 @@
/*
<t-moBestImprAspiration.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Sébastien Verel, Arnaud Liefooghe, Jérémie Humeau
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <paradiseo/mo/memory/moBestImprAspiration.h>
#include "moTestClass.h"
#include <iostream>
#include <cstdlib>
#include <cassert>
int main() {
std::cout << "[t-moBestImprAspiration] => START" << std::endl;
moBestImprAspiration<bitNeighbor> test;
eoBit<eoMinimizingFitness> sol1(4);
eoBit<eoMinimizingFitness> sol2(4);
eoBit<eoMinimizingFitness> sol3(4);
eoBit<eoMinimizingFitness> sol4(4);
bitNeighbor n1;
bitNeighbor n2;
bitNeighbor n3;
bitNeighbor n4;
sol3[0]=true;
sol4[3]=true;
sol1.fitness(4);
sol2.fitness(5);
sol3.fitness(3);
sol4.fitness(3);
n1.fitness(4);
n2.fitness(5);
n3.fitness(3);
n4.fitness(3);
//verification qu'on update bien le best so far quand il faut
test.init(sol1);
assert(test.getBest()==sol1);
assert(!test(sol2,n2));
assert(test(sol3,n3));
test.update(sol3,n3);
assert(test.getBest()==sol3);
assert(!test(sol4,n4));
test.update(sol4,n4);
assert(test.getBest()==sol3);
std::cout << "[t-moBestImprAspiration] => OK" << std::endl;
return EXIT_SUCCESS;
}

61
test/mo/t-moBetterAcceptCrit.cpp Executable file
View file

@ -0,0 +1,61 @@
/*
<t-moBetterAcceptCrit.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010
Sébastien Verel, Arnaud Liefooghe, Jérémie Humeau
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <iostream>
#include <cstdlib>
#include <cassert>
#include <paradiseo/mo/comparator/moSolComparator.h>
#include <paradiseo/mo/acceptCrit/moBetterAcceptCrit.h>
#include "moTestClass.h"
int main() {
std::cout << "[t-moBetterAcceptCrit] => START" << std::endl;
bitVector sol1, sol2, sol3;
sol1.fitness(2);
sol2.fitness(3);
sol3.fitness(3);
moSolComparator<bitVector> comparator;
moBetterAcceptCrit<bitNeighbor> test(comparator);
assert(test(sol2, sol1));
assert(!test(sol1, sol2));
assert(!test(sol2, sol3));
std::cout << "[t-moBetterAcceptCrit] => OK" << std::endl;
return EXIT_SUCCESS;
}

Some files were not shown because too many files have changed in this diff Show more