...
This commit is contained in:
Caner Candan
parent
2b9402d3f5
commit
27552a573e
11 changed files with 414 additions and 71 deletions
23
.gitignore
vendored
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23
.gitignore
vendored
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@ -0,0 +1,23 @@
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# ignore html files
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*.html
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# ignore all textual files
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*.txt
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# ignore object and archive files
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*.[oa]
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# ignore auto-saved files
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*~
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\#*\#
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# excepted these manually configured files
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!CMakeLists.txt
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!README.txt
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!application/
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!build/
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!doc/
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!lib/
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!src/
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!test/
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build/
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112
CMakeLists.txt
112
CMakeLists.txt
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@ -16,60 +16,96 @@ SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT
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######################################################################################
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### 2) Include the install configuration file where are defined the main variables
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### 2) Prepare some useful variables
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######################################################################################
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INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/install.cmake)
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######################################################################################
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#####################################################################################
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### 3) Include required modules & utilities
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#####################################################################################
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INCLUDE(CMakeBackwardCompatibilityCXX)
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#INCLUDE(FindDoxygen)
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INCLUDE(CheckLibraryExists)
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#INCLUDE(Dart OPTIONAL)
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FIND_PACKAGE(Doxygen)
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FIND_PACKAGE(MPI REQUIRED)
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FIND_PACKAGE(Gnuplot REQUIRED)
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# Set a special flag if the environment is windows (should do the same in a config.g file)
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IF (WIN32)
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ADD_DEFINITIONS(-D_WINDOWS=1)
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ENDIF (WIN32)
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######################################################################################
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#####################################################################################
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### 4) Manage the build type
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#####################################################################################
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INCLUDE(${CMAKE_SOURCE_DIR}/BuildConfig.cmake)
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SET(DO_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
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SET(DO_BIN_DIR "${CMAKE_CURRENT_BINARY_DIR}")
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######################################################################################
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######################################################################################
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### 5) Now where we go ???
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### 3) Include useful features
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######################################################################################
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INCLUDE(FindDoxygen)
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INCLUDE(FindPkgConfig)
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PKG_CHECK_MODULES(EO eo REQUIRED)
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INCLUDE_DIRECTORIES(${EO_INCLUDE_DIR})
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LINK_DIRECTORIES(${EO_LIBRARY_DIRS})
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######################################################################################
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######################################################################################
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### 4) Include header files path
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######################################################################################
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INCLUDE_DIRECTORIES(
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${CMAKE_CURRENT_SOURCE_DIR}/src
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)
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######################################################################################
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######################################################################################
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### 5) Set compiler definitions
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######################################################################################
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IF(UNIX)
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# enable warnings
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ADD_DEFINITIONS( -Wall -W -Wextra )
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# ADD_DEFINITIONS( -Weffc++)
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# ADD_DEFINITIONS( -g3 )
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ENDIF()
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######################################################################################
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######################################################################################
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### 6) Prepare some variables for CMAKE usage
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######################################################################################
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SET(SAMPLE_SRCS)
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######################################################################################
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######################################################################################
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### 7) Now where we go ?
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######################################################################################
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# warning: you have to compile libraries before bopo sources because of dependencies.
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ADD_SUBDIRECTORY(lib)
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ADD_SUBDIRECTORY(doc)
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ADD_SUBDIRECTORY(src)
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ADD_SUBDIRECTORY(test)
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ADD_SUBDIRECTORY(application)
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ADD_SUBDIRECTORY(test)
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ADD_SUBDIRECTORY(doc)
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######################################################################################
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######################################################################################
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### 6) Include packaging
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### 8) Create executable, link libraries and prepare target
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######################################################################################
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SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
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LINK_DIRECTORIES(${LIBRARY_OUTPUT_PATH})
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ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS})
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#ADD_LIBRARY(${PROJECT_NAME} SHARED ${SAMPLE_SRCS})
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# INSTALL(
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# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a
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# DESTINATION lib
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# COMPONENT libraries
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# )
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######################################################################################
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### 9) Include packaging
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######################################################################################
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INCLUDE(Packaging.cmake)
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1
COPYING
Normal file
1
COPYING
Normal file
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@ -0,0 +1 @@
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Private license
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57
README
Normal file
57
README
Normal file
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@ -0,0 +1,57 @@
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This package contains the source code for BOPO problems.
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# Step 1 - Configuration
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------------------------
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Rename the "install.cmake-dist" file as "install.cmake" and edit it, inserting the FULL PATH
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to your ParadisEO distribution.
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On Windows write your path with double antislash (ex: C:\\Users\\...)
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# Step 2 - Build process
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------------------------
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ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/.
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Go to the BOPO/build/ directory and lunch cmake:
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(Unix) > cmake ..
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(Windows) > cmake .. -G"Visual Studio 9 2008"
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Note for windows users: if you don't use VisualStudio 9, enter the name of your generator instead of "VisualStudio 9 2008".
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# Step 3 - Compilation
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----------------------
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In the bopo/build/ directory:
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(Unix) > make
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(Windows) Open the VisualStudio solution and compile it, compile also the target install.
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You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
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# Step 4 - Execution
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---------------------
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A toy example is given to test the components. You can run these tests as following.
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To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/.
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In the bopo/build/ directory:
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(Unix) > ctest
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Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
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In the directory "application", there are several directory such as p_eoco which instantiate NSGAII on BOPO problems.
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(Unix) After compilation you can run the script "bopo/run.sh" and see results in "NSGAII.out". Parameters can be modified in the script.
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(Windows) Add argument "NSGAII.param" and execute the corresponding algorithms.
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Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
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# Documentation
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---------------
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The API-documentation is available in doc/html/index.html
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# Things to keep in mind when using BOPO
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----------------------------------------
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* By default, the EO random generator's seed is initialized by the number of seconds since the epoch (with time(0)). It is available in the status file dumped at each execution. Please, keep in mind that if you start two run at the same second without modifying the seed, you will get exactly the same results.
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* Execution times are measured with the boost:timer, that measure wallclock time. Additionaly, it could not measure times larger than approximatively 596.5 hours (or even less). See http://www.boost.org/doc/libs/1_33_1/libs/timer/timer.htm
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|
||||
* The q-quantile computation use averaging at discontinuities (in R, it correspond to the R-2 method, in SAS, SAS-5). For more explanations, see http://en.wikipedia.org/wiki/Quantile#Estimating_the_quantiles_of_a_population and http://stat.ethz.ch/R-manual/R-devel/library/stats/html/quantile.html
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|
||||
* You can send a SIGUSR1 to a process to get some information (written down in the log file) on the current state of the search.
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||||
7
application/CMakeLists.txt
Normal file
7
application/CMakeLists.txt
Normal file
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@ -0,0 +1,7 @@
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|||
######################################################################################
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||||
### 1) Where do we go now ?!?
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||||
######################################################################################
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||||
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||||
ADD_SUBDIRECTORY(cma_sa)
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||||
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||||
######################################################################################
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||||
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@ -1,5 +1,3 @@
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FIND_PACKAGE(Boost 1.33.0 REQUIRED)
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INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
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SET(RESOURCES
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@ -15,21 +13,7 @@ FOREACH(file ${RESOURCES})
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)
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ENDFOREACH(file)
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||||
ADD_EXECUTABLE(cma_sa main.cpp)
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FILE(GLOB SOURCES *.cpp)
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TARGET_LINK_LIBRARIES(cma_sa
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${Boost_LIBRARIES}
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BOPO
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eoutils
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pthread
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||||
moeo
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eo
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peo
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rmc_mpi
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eometah
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nklandscapes
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BOPO
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#${MPICH2_LIBRARIES}
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${LIBXML2_LIBRARIES}
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${MPI_LIBRARIES}
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)
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ADD_EXECUTABLE(cma_sa ${SOURCES})
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TARGET_LINK_LIBRARIES(cma_sa DO ${EO_LIBRARIES})
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@ -1,12 +1,3 @@
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|||
// #include <boost/numeric/ublas/matrix.hpp>
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// #include <boost/numeric/ublas/io.hpp>
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||||
#ifndef HAVE_GNUPLOT
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||||
// FIXME: temporary define to force use of gnuplot without compiling
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// again EO.
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# define HAVE_GNUPLOT
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#endif
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||||
#include <eo>
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#include <mo>
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@ -18,15 +9,12 @@
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#include <do/make_continue.h>
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||||
#include <do/make_checkpoint.h>
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||||
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||||
//#include "BopoRosenbrock.h"
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#include <do>
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#include "Rosenbrock.h"
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#include "Sphere.h"
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||||
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||||
#include <do>
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||||
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||||
typedef eoReal<eoMinimizingFitness> EOT;
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||||
//typedef doUniform< EOT > Distrib;
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||||
//typedef doNormal< EOT > Distrib;
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||||
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||||
int main(int ac, char** av)
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||||
{
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||||
|
|
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|||
26
doc/CMakeLists.txt
Normal file
26
doc/CMakeLists.txt
Normal file
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@ -0,0 +1,26 @@
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|||
#######################################################################################
|
||||
### Doc generation using Doxygen
|
||||
#######################################################################################
|
||||
|
||||
IF (DOXYGEN_FOUND)
|
||||
SET(DOC_DIR ${CMAKE_BINARY_DIR}/doc CACHE PATH "documentation directory")
|
||||
SET(DOC_CONFIG_FILE "doxyfile" CACHE PATH "documentation configuration file")
|
||||
|
||||
# define the doc target
|
||||
IF (DOXYGEN_EXECUTABLE)
|
||||
ADD_CUSTOM_TARGET(doc
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||||
COMMAND ${DOXYGEN_EXECUTABLE} ${DOC_CONFIG_FILE}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
)
|
||||
ENDIF (DOXYGEN_EXECUTABLE)
|
||||
|
||||
# configure doxyfile file
|
||||
CONFIGURE_FILE(
|
||||
"${CMAKE_CURRENT_SOURCE_DIR}/${DOC_CONFIG_FILE}.cmake"
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||||
"${CMAKE_CURRENT_BINARY_DIR}/${DOC_CONFIG_FILE}"
|
||||
)
|
||||
ELSE (DOXYGEN_FOUND)
|
||||
MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found")
|
||||
ENDIF (DOXYGEN_FOUND)
|
||||
|
||||
#######################################################################################
|
||||
229
doc/doxyfile.cmake
Normal file
229
doc/doxyfile.cmake
Normal file
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|
@ -0,0 +1,229 @@
|
|||
# Doxyfile 1.5.1
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Project related configuration options
|
||||
#---------------------------------------------------------------------------
|
||||
PROJECT_NAME = @PACKAGE_NAME@
|
||||
PROJECT_NUMBER = @PACKAGE_VERSION@
|
||||
OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/doc
|
||||
CREATE_SUBDIRS = NO
|
||||
OUTPUT_LANGUAGE = English
|
||||
BRIEF_MEMBER_DESC = YES
|
||||
REPEAT_BRIEF = YES
|
||||
ABBREVIATE_BRIEF = "The $name class" \
|
||||
"The $name widget" \
|
||||
"The $name file" \
|
||||
is \
|
||||
provides \
|
||||
specifies \
|
||||
contains \
|
||||
represents \
|
||||
a \
|
||||
an \
|
||||
the
|
||||
ALWAYS_DETAILED_SEC = NO
|
||||
INLINE_INHERITED_MEMB = NO
|
||||
FULL_PATH_NAMES = NO
|
||||
STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@
|
||||
STRIP_FROM_INC_PATH =
|
||||
SHORT_NAMES = NO
|
||||
JAVADOC_AUTOBRIEF = YES
|
||||
MULTILINE_CPP_IS_BRIEF = NO
|
||||
#DETAILS_AT_TOP = NO
|
||||
INHERIT_DOCS = YES
|
||||
SEPARATE_MEMBER_PAGES = NO
|
||||
TAB_SIZE = 8
|
||||
ALIASES =
|
||||
OPTIMIZE_OUTPUT_FOR_C = NO
|
||||
OPTIMIZE_OUTPUT_JAVA = NO
|
||||
BUILTIN_STL_SUPPORT = NO
|
||||
DISTRIBUTE_GROUP_DOC = NO
|
||||
SUBGROUPING = YES
|
||||
#---------------------------------------------------------------------------
|
||||
# Build related configuration options
|
||||
#---------------------------------------------------------------------------
|
||||
EXTRACT_ALL = NO
|
||||
EXTRACT_PRIVATE = YES
|
||||
EXTRACT_STATIC = YES
|
||||
EXTRACT_LOCAL_CLASSES = YES
|
||||
EXTRACT_LOCAL_METHODS = NO
|
||||
HIDE_UNDOC_MEMBERS = YES
|
||||
HIDE_UNDOC_CLASSES = YES
|
||||
HIDE_FRIEND_COMPOUNDS = NO
|
||||
HIDE_IN_BODY_DOCS = NO
|
||||
INTERNAL_DOCS = NO
|
||||
CASE_SENSE_NAMES = YES
|
||||
HIDE_SCOPE_NAMES = NO
|
||||
SHOW_INCLUDE_FILES = YES
|
||||
INLINE_INFO = YES
|
||||
SORT_MEMBER_DOCS = NO
|
||||
SORT_BRIEF_DOCS = NO
|
||||
SORT_BY_SCOPE_NAME = NO
|
||||
GENERATE_TODOLIST = YES
|
||||
GENERATE_TESTLIST = YES
|
||||
GENERATE_BUGLIST = YES
|
||||
GENERATE_DEPRECATEDLIST= YES
|
||||
ENABLED_SECTIONS =
|
||||
MAX_INITIALIZER_LINES = 30
|
||||
SHOW_USED_FILES = YES
|
||||
SHOW_DIRECTORIES = NO
|
||||
FILE_VERSION_FILTER =
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to warning and progress messages
|
||||
#---------------------------------------------------------------------------
|
||||
QUIET = YES
|
||||
WARNINGS = NO
|
||||
WARN_IF_UNDOCUMENTED = NO
|
||||
WARN_IF_DOC_ERROR = YES
|
||||
WARN_NO_PARAMDOC = NO
|
||||
WARN_FORMAT = "$file:$line: $text"
|
||||
WARN_LOGFILE =
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the input files
|
||||
#---------------------------------------------------------------------------
|
||||
INPUT = @CMAKE_SOURCE_DIR@
|
||||
FILE_PATTERNS = *.cpp \
|
||||
*.h \
|
||||
NEWS README
|
||||
RECURSIVE = YES
|
||||
EXCLUDE =
|
||||
EXCLUDE_SYMLINKS = NO
|
||||
EXCLUDE_PATTERNS =
|
||||
EXAMPLE_PATH =
|
||||
EXAMPLE_PATTERNS = *
|
||||
EXAMPLE_RECURSIVE = NO
|
||||
IMAGE_PATH =
|
||||
INPUT_FILTER =
|
||||
FILTER_PATTERNS =
|
||||
FILTER_SOURCE_FILES = NO
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to source browsing
|
||||
#---------------------------------------------------------------------------
|
||||
SOURCE_BROWSER = YES
|
||||
INLINE_SOURCES = NO
|
||||
STRIP_CODE_COMMENTS = YES
|
||||
REFERENCED_BY_RELATION = YES
|
||||
REFERENCES_RELATION = YES
|
||||
REFERENCES_LINK_SOURCE = YES
|
||||
USE_HTAGS = NO
|
||||
VERBATIM_HEADERS = YES
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the alphabetical class index
|
||||
#---------------------------------------------------------------------------
|
||||
ALPHABETICAL_INDEX = YES
|
||||
COLS_IN_ALPHA_INDEX = 3
|
||||
IGNORE_PREFIX = moeo
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the HTML output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_HTML = YES
|
||||
HTML_OUTPUT = html
|
||||
HTML_FILE_EXTENSION = .html
|
||||
HTML_HEADER =
|
||||
HTML_FOOTER =
|
||||
HTML_STYLESHEET =
|
||||
HTML_ALIGN_MEMBERS = YES
|
||||
GENERATE_HTMLHELP = NO
|
||||
CHM_FILE =
|
||||
HHC_LOCATION =
|
||||
GENERATE_CHI = NO
|
||||
BINARY_TOC = NO
|
||||
TOC_EXPAND = NO
|
||||
DISABLE_INDEX = NO
|
||||
ENUM_VALUES_PER_LINE = 4
|
||||
GENERATE_TREEVIEW = YES
|
||||
TREEVIEW_WIDTH = 250
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the LaTeX output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_LATEX = YES
|
||||
LATEX_OUTPUT = latex
|
||||
LATEX_CMD_NAME = latex
|
||||
MAKEINDEX_CMD_NAME = makeindex
|
||||
COMPACT_LATEX = NO
|
||||
PAPER_TYPE = a4wide
|
||||
EXTRA_PACKAGES =
|
||||
LATEX_HEADER =
|
||||
PDF_HYPERLINKS = NO
|
||||
USE_PDFLATEX = NO
|
||||
LATEX_BATCHMODE = NO
|
||||
LATEX_HIDE_INDICES = NO
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the RTF output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_RTF = NO
|
||||
RTF_OUTPUT = rtf
|
||||
COMPACT_RTF = NO
|
||||
RTF_HYPERLINKS = NO
|
||||
RTF_STYLESHEET_FILE =
|
||||
RTF_EXTENSIONS_FILE =
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the man page output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_MAN = YES
|
||||
MAN_OUTPUT = man
|
||||
MAN_EXTENSION = .3
|
||||
MAN_LINKS = NO
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the XML output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_XML = NO
|
||||
XML_OUTPUT = xml
|
||||
XML_SCHEMA =
|
||||
XML_DTD =
|
||||
XML_PROGRAMLISTING = YES
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options for the AutoGen Definitions output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_AUTOGEN_DEF = NO
|
||||
#---------------------------------------------------------------------------
|
||||
# configuration options related to the Perl module output
|
||||
#---------------------------------------------------------------------------
|
||||
GENERATE_PERLMOD = NO
|
||||
PERLMOD_LATEX = NO
|
||||
PERLMOD_PRETTY = YES
|
||||
PERLMOD_MAKEVAR_PREFIX =
|
||||
#---------------------------------------------------------------------------
|
||||
# Configuration options related to the preprocessor
|
||||
#---------------------------------------------------------------------------
|
||||
ENABLE_PREPROCESSING = YES
|
||||
MACRO_EXPANSION = NO
|
||||
EXPAND_ONLY_PREDEF = NO
|
||||
SEARCH_INCLUDES = YES
|
||||
INCLUDE_PATH =
|
||||
INCLUDE_FILE_PATTERNS =
|
||||
PREDEFINED =
|
||||
EXPAND_AS_DEFINED =
|
||||
SKIP_FUNCTION_MACROS = YES
|
||||
#---------------------------------------------------------------------------
|
||||
# Configuration::additions related to external references
|
||||
#---------------------------------------------------------------------------
|
||||
#---------------------------------------------------------------------------
|
||||
# Configuration options related to the dot tool
|
||||
#---------------------------------------------------------------------------
|
||||
CLASS_DIAGRAMS = YES
|
||||
HIDE_UNDOC_RELATIONS = YES
|
||||
HAVE_DOT = NO
|
||||
CLASS_GRAPH = YES
|
||||
COLLABORATION_GRAPH = YES
|
||||
GROUP_GRAPHS = YES
|
||||
UML_LOOK = NO
|
||||
TEMPLATE_RELATIONS = NO
|
||||
INCLUDE_GRAPH = YES
|
||||
INCLUDED_BY_GRAPH = YES
|
||||
CALL_GRAPH = NO
|
||||
CALLER_GRAPH = NO
|
||||
GRAPHICAL_HIERARCHY = YES
|
||||
DIRECTORY_GRAPH = YES
|
||||
DOT_IMAGE_FORMAT = png
|
||||
DOT_PATH =
|
||||
DOTFILE_DIRS =
|
||||
MAX_DOT_GRAPH_DEPTH = 0
|
||||
DOT_TRANSPARENT = NO
|
||||
DOT_MULTI_TARGETS = NO
|
||||
GENERATE_LEGEND = YES
|
||||
DOT_CLEANUP = YES
|
||||
#---------------------------------------------------------------------------
|
||||
# Configuration::additions related to the search engine
|
||||
#---------------------------------------------------------------------------
|
||||
SEARCHENGINE = YES
|
||||
0
doc/index.h
Normal file
0
doc/index.h
Normal file
|
|
@ -2,7 +2,7 @@
|
|||
### 1) Include useful packages
|
||||
######################################################################################
|
||||
|
||||
FIND_PACKAGE(Boost 1.33.0 REQUIRED)
|
||||
#FIND_PACKAGE(Boost 1.33.0 REQUIRED)
|
||||
|
||||
######################################################################################
|
||||
|
||||
|
|
@ -11,16 +11,7 @@ FIND_PACKAGE(Boost 1.33.0 REQUIRED)
|
|||
### 2) Include the sources
|
||||
######################################################################################
|
||||
|
||||
INCLUDE_DIRECTORIES(
|
||||
${PARADISEO_EO_SRC_DIR}/src
|
||||
${PARADISEO_MO_SRC_DIR}/src
|
||||
${PARADISEO_MOEO_SRC_DIR}/src
|
||||
${PARADISEO_PEO_SRC_DIR}/src
|
||||
${CMAKE_SOURCE_DIR}/src
|
||||
${CMAKE_SOURCE_DIR}/lib/eometah
|
||||
${CMAKE_SOURCE_DIR}/lib/nk-landscapes
|
||||
${Boost_INCLUDE_DIRS}
|
||||
)
|
||||
#INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
|
||||
|
||||
######################################################################################
|
||||
|
||||
|
|
@ -32,8 +23,9 @@ INCLUDE_DIRECTORIES(
|
|||
SET(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
|
||||
|
||||
FILE(GLOB SOURCES *.cpp)
|
||||
SET(SAMPLE_SRCS ${SOURCES} PARENT_SCOPE)
|
||||
|
||||
ADD_LIBRARY(${PROJECT_NAME} STATIC ${SOURCES})
|
||||
ADD_LIBRARY(${PROJECT_NAME} STATIC ${SAMPLE_SRCS})
|
||||
|
||||
# INSTALL(
|
||||
# TARGETS ${LIBRARY_OUTPUT_PATH}/lib${PROJECT_NAME}.a
|
||||
|
|
|
|||
Reference in a new issue