manual merge on eoPop.h
This commit is contained in:
commit
36f30db313
29 changed files with 1946 additions and 332 deletions
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@ -9,23 +9,19 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
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######################################################################################
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IF(WITH_MPI)
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MESSAGE("[EO] Compilation with MPI and BoostMPI.")
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MESSAGE("[EO] Compilation with MPI.")
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SET(CMAKE_CXX_COMPILER "${MPI_DIR}/bin/mpicxx")
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# headers location
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INCLUDE_DIRECTORIES(${MPI_DIR}/include)
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INCLUDE_DIRECTORIES(${BOOST_DIR}/include)
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# lib location
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LINK_DIRECTORIES(${MPI_DIR}/lib)
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LINK_DIRECTORIES(${BOOST_DIR}/lib)
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# for conditional compilation in code
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ADD_DEFINITIONS(-DWITH_MPI)
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LINK_LIBRARIES(boost_mpi boost_serialization)
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ADD_SUBDIRECTORY(mpi)
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ENDIF()
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@ -67,4 +67,43 @@ public:
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}
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};
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/**
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* Termination condition with a count condition (totalGenerations). This continuator contains
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* a count of cycles, which can be retrieved or set.
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*
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* @ingroup Continuators
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* @ingroup Core
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*/
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template< class EOT >
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class eoCountContinue : public eoContinue< EOT >
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{
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public:
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eoCountContinue( ) :
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thisGenerationPlaceholder( 0 ),
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thisGeneration( thisGenerationPlaceholder )
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{
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// empty
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}
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eoCountContinue( unsigned long& currentGen ) :
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thisGenerationPlaceholder( 0 ),
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thisGeneration( currentGen )
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{
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// empty
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}
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virtual std::string className( void ) const { return "eoCountContinue"; }
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virtual void reset( )
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{
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thisGeneration = 0;
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}
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protected:
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unsigned long thisGenerationPlaceholder;
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unsigned long& thisGeneration;
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};
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#endif
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@ -35,24 +35,24 @@
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@ingroup Continuators
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*/
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template< class EOT>
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class eoGenContinue: public eoContinue<EOT>, public eoValueParam<unsigned>
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class eoGenContinue: public eoCountContinue<EOT>, public eoValueParam<unsigned>
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{
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public:
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using eoCountContinue<EOT>::thisGeneration;
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using eoCountContinue<EOT>::thisGenerationPlaceholder;
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/// Ctor for setting a
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eoGenContinue( unsigned long _totalGens)
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: eoValueParam<unsigned>(0, "Generations", "Generations"),
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repTotalGenerations( _totalGens ),
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thisGenerationPlaceHolder(0),
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thisGeneration(thisGenerationPlaceHolder)
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: eoCountContinue<EOT>( ),
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eoValueParam<unsigned>(0, "Generations", "Generations"),
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repTotalGenerations( _totalGens )
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{};
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/// Ctor for enabling the save/load the no. of generations counted
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eoGenContinue( unsigned long _totalGens, unsigned long& _currentGen)
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: eoValueParam<unsigned>(0, "Generations", "Generations"),
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repTotalGenerations( _totalGens ),
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thisGenerationPlaceHolder(0),
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thisGeneration(_currentGen)
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: eoCountContinue<EOT>( _currentGen ), eoValueParam<unsigned>(0, "Generations", "Generations"),
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repTotalGenerations( _totalGens )
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{};
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/** Returns false when a certain number of generations is
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@ -77,7 +77,7 @@ public:
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*/
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virtual void totalGenerations( unsigned long _tg ) {
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repTotalGenerations = _tg;
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thisGeneration = 0;
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eoCountContinue<EOT>::reset();
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};
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/** Returns the number of generations to reach*/
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@ -86,7 +86,6 @@ public:
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return repTotalGenerations;
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};
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virtual std::string className(void) const { return "eoGenContinue"; }
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/** Read from a stream
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@ -107,8 +106,6 @@ public:
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private:
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unsigned long repTotalGenerations;
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unsigned long thisGenerationPlaceHolder;
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unsigned long& thisGeneration;
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};
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#endif
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@ -221,10 +221,11 @@ class eoPop: public std::vector<EOT>, public eoObject, public eoPersistent
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#else
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typename eoPop<EOT>::const_iterator it = std::max_element(begin(), end());
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#endif
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if( it == end() )
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throw std::runtime_error("eoPop<EOT>: Empty population, when calling best_element().");
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return (*it);
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}
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/** returns a const reference to the worse individual DOES NOT MOVE ANYBODY */
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const EOT & worse_element() const
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{
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@ -35,23 +35,26 @@
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@ingroup Continuators
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*/
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template< class EOT>
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class eoSteadyFitContinue: public eoContinue<EOT>
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class eoSteadyFitContinue: public eoCountContinue<EOT>
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{
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public:
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typedef typename EOT::Fitness Fitness;
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using eoCountContinue<EOT>::thisGenerationPlaceholder;
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using eoCountContinue<EOT>::thisGeneration;
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/// Ctor for setting a
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eoSteadyFitContinue( unsigned long _minGens, unsigned long _steadyGens)
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: repMinGenerations( _minGens ), repSteadyGenerations( _steadyGens),
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steadyState(false), thisGenerationPlaceHolder(0),
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thisGeneration(thisGenerationPlaceHolder){};
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: eoCountContinue<EOT>( ), repMinGenerations( _minGens ), repSteadyGenerations( _steadyGens),
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steadyState(false)
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{};
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/// Ctor for enabling the save/load the no. of generations counted
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eoSteadyFitContinue( unsigned long _minGens, unsigned long _steadyGen,
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unsigned long& _currentGen)
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: repMinGenerations( _minGens ), repSteadyGenerations( _steadyGen),
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steadyState(_currentGen>_minGens), thisGenerationPlaceHolder(0),
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thisGeneration(_currentGen){};
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: eoCountContinue<EOT>( _currentGen ), repMinGenerations( _minGens ), repSteadyGenerations( _steadyGen),
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steadyState(_currentGen>_minGens)
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{};
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/** Returns false when a certain number of generations is
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* reached withtout improvement */
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@ -96,7 +99,7 @@ public:
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/// Resets the state after it's been reached
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virtual void reset () {
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steadyState=false;
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thisGeneration = 0;
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eoCountContinue<EOT>::reset();
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}
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/** accessors*/
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@ -110,8 +113,6 @@ private:
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unsigned long repMinGenerations;
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unsigned long repSteadyGenerations;
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bool steadyState;
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unsigned long thisGenerationPlaceHolder;
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unsigned long& thisGeneration;
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unsigned int lastImprovement;
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Fitness bestSoFar;
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};
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@ -14,6 +14,9 @@ SET(LIBRARY_OUTPUT_PATH ${EOMPI_LIB_OUTPUT_PATH})
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SET(EOMPI_SOURCES
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eoMpi.cpp
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eoMpiAssignmentAlgorithm.cpp
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eoMpiNode.cpp
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implMpi.cpp
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)
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ADD_LIBRARY(eompi STATIC ${EOMPI_SOURCES})
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@ -1,11 +1,48 @@
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/*
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(c) Thales group, 2012
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
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License as published by the Free Software Foundation;
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version 2 of the License.
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public
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License along with this library; if not, write to the Free Software
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Contact: http://eodev.sourceforge.net
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Authors:
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Benjamin Bouvier <benjamin.bouvier@gmail.com>
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*/
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# include "eoMpi.h"
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namespace eo
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{
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namespace mpi
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{
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bmpi::communicator Node::_comm;
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/**********************************************
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* *********** GLOBALS ************************
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* *******************************************/
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eoTimerStat timerStat;
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namespace Channel
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{
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const int Commands = 0;
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const int Messages = 1;
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}
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namespace Message
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{
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const int Continue = 0;
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const int Finish = 1;
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const int Kill = 2;
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}
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const int DEFAULT_MASTER = 0;
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}
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}
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@ -143,8 +143,8 @@ namespace eo
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*/
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namespace Channel
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{
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const int Commands = 0;
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const int Messages = 1;
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extern const int Commands;
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extern const int Messages;
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}
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/**
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@ -157,9 +157,9 @@ namespace eo
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*/
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namespace Message
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{
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const int Continue = 0;
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const int Finish = 1;
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const int Kill = 2;
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extern const int Continue;
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extern const int Finish;
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extern const int Kill;
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}
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/**
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@ -167,7 +167,7 @@ namespace eo
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*
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* @ingroup MPI
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*/
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const int DEFAULT_MASTER = 0;
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extern const int DEFAULT_MASTER;
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/**
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* @brief Base class for the 4 algorithm functors.
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224
eo/src/mpi/eoMpiAssignmentAlgorithm.cpp
Normal file
224
eo/src/mpi/eoMpiAssignmentAlgorithm.cpp
Normal file
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@ -0,0 +1,224 @@
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# include "eoMpiAssignmentAlgorithm.h"
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/*
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(c) Thales group, 2012
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This library is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public
|
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License as published by the Free Software Foundation;
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version 2 of the License.
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|
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This library is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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Lesser General Public License for more details.
|
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|
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You should have received a copy of the GNU Lesser General Public
|
||||
License along with this library; if not, write to the Free Software
|
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Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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Contact: http://eodev.sourceforge.net
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Authors:
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Benjamin Bouvier <benjamin.bouvier@gmail.com>
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*/
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# include "eoMpiNode.h"
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namespace eo
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{
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namespace mpi
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{
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const int REST_OF_THE_WORLD = -1;
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/********************************************************
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* DYNAMIC ASSIGNMENT ALGORITHM *************************
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*******************************************************/
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DynamicAssignmentAlgorithm::DynamicAssignmentAlgorithm( )
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{
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for(int i = 1; i < Node::comm().size(); ++i)
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{
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availableWrk.push_back( i );
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}
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}
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DynamicAssignmentAlgorithm::DynamicAssignmentAlgorithm( int unique )
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{
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availableWrk.push_back( unique );
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}
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DynamicAssignmentAlgorithm::DynamicAssignmentAlgorithm( const std::vector<int> & workers )
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{
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availableWrk = workers;
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}
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DynamicAssignmentAlgorithm::DynamicAssignmentAlgorithm( int first, int last )
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{
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if( last == REST_OF_THE_WORLD )
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{
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last = Node::comm().size() - 1;
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}
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for( int i = first; i <= last; ++i)
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{
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availableWrk.push_back( i );
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}
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}
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int DynamicAssignmentAlgorithm::get( )
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{
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int assignee = -1;
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if (! availableWrk.empty() )
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{
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assignee = availableWrk.back();
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availableWrk.pop_back();
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}
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return assignee;
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}
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int DynamicAssignmentAlgorithm::availableWorkers()
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{
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return availableWrk.size();
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}
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void DynamicAssignmentAlgorithm::confirm( int rank )
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{
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availableWrk.push_back( rank );
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}
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std::vector<int> DynamicAssignmentAlgorithm::idles( )
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{
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return availableWrk;
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}
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void DynamicAssignmentAlgorithm::reinit( int _ )
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{
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++_;
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// nothing to do
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}
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/********************************************************
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* STATIC ASSIGNMENT ALGORITHM **************************
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*******************************************************/
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StaticAssignmentAlgorithm::StaticAssignmentAlgorithm( std::vector<int>& workers, int runs )
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{
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init( workers, runs );
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}
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StaticAssignmentAlgorithm::StaticAssignmentAlgorithm( int first, int last, int runs )
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{
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std::vector<int> workers;
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if( last == REST_OF_THE_WORLD )
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{
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last = Node::comm().size() - 1;
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}
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for(int i = first; i <= last; ++i)
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{
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workers.push_back( i );
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}
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init( workers, runs );
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}
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StaticAssignmentAlgorithm::StaticAssignmentAlgorithm( int runs )
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{
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std::vector<int> workers;
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for(int i = 1; i < Node::comm().size(); ++i)
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{
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workers.push_back( i );
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}
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init( workers, runs );
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}
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StaticAssignmentAlgorithm::StaticAssignmentAlgorithm( int unique, int runs )
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{
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std::vector<int> workers;
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workers.push_back( unique );
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init( workers, runs );
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}
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void StaticAssignmentAlgorithm::init( std::vector<int> & workers, int runs )
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{
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unsigned int nbWorkers = workers.size();
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freeWorkers = nbWorkers;
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busy.clear();
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busy.resize( nbWorkers, false );
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realRank = workers;
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if( runs <= 0 )
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{
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return;
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}
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attributions.clear();
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attributions.reserve( nbWorkers );
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// Let be the euclidean division of runs by nbWorkers :
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// runs == q * nbWorkers + r, 0 <= r < nbWorkers
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// This one liner affects q requests to each worker
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for (unsigned int i = 0; i < nbWorkers; attributions[i++] = runs / nbWorkers) ;
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// The first line computes r and the one liner affects the remaining
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// r requests to workers, in ascending order
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unsigned int diff = runs - (runs / nbWorkers) * nbWorkers;
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for (unsigned int i = 0; i < diff; ++attributions[i++]);
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}
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int StaticAssignmentAlgorithm::get( )
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||||
{
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int assignee = -1;
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for( unsigned i = 0; i < busy.size(); ++i )
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{
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if( !busy[i] && attributions[i] > 0 )
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||||
{
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busy[i] = true;
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--freeWorkers;
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assignee = realRank[ i ];
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break;
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}
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}
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return assignee;
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}
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int StaticAssignmentAlgorithm::availableWorkers( )
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{
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return freeWorkers;
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}
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std::vector<int> StaticAssignmentAlgorithm::idles()
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||||
{
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std::vector<int> ret;
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||||
for(unsigned int i = 0; i < busy.size(); ++i)
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||||
{
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if( !busy[i] )
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{
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ret.push_back( realRank[i] );
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}
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}
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return ret;
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||||
}
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void StaticAssignmentAlgorithm::confirm( int rank )
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||||
{
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int i = -1; // i is the real index in table
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||||
for( unsigned int j = 0; j < realRank.size(); ++j )
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||||
{
|
||||
if( realRank[j] == rank )
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||||
{
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i = j;
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||||
break;
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||||
}
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||||
}
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||||
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--attributions[ i ];
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busy[ i ] = false;
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++freeWorkers;
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||||
}
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||||
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||||
void StaticAssignmentAlgorithm::reinit( int runs )
|
||||
{
|
||||
init( realRank, runs );
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||||
}
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||||
}
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||||
}
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||||
|
|
@ -23,7 +23,6 @@ Authors:
|
|||
# define __MPI_ASSIGNMENT_ALGORITHM_H__
|
||||
|
||||
# include <vector> // std::vector
|
||||
# include "eoMpiNode.h"
|
||||
|
||||
namespace eo
|
||||
{
|
||||
|
|
@ -35,7 +34,7 @@ namespace eo
|
|||
*
|
||||
* @ingroup MPI
|
||||
*/
|
||||
const int REST_OF_THE_WORLD = -1;
|
||||
extern const int REST_OF_THE_WORLD;
|
||||
|
||||
/**
|
||||
* @brief Contains informations on the available workers and allows to find assignees for jobs.
|
||||
|
|
@ -115,33 +114,21 @@ namespace eo
|
|||
/**
|
||||
* @brief Uses all the hosts whose rank is higher to 1, inclusive, as workers.
|
||||
*/
|
||||
DynamicAssignmentAlgorithm( )
|
||||
{
|
||||
for(int i = 1; i < Node::comm().size(); ++i)
|
||||
{
|
||||
availableWrk.push_back( i );
|
||||
}
|
||||
}
|
||||
DynamicAssignmentAlgorithm( );
|
||||
|
||||
/**
|
||||
* @brief Uses the unique host with given rank as a worker.
|
||||
*
|
||||
* @param unique MPI rank of the unique worker.
|
||||
*/
|
||||
DynamicAssignmentAlgorithm( int unique )
|
||||
{
|
||||
availableWrk.push_back( unique );
|
||||
}
|
||||
DynamicAssignmentAlgorithm( int unique );
|
||||
|
||||
/**
|
||||
* @brief Uses the workers whose ranks are present in the argument as workers.
|
||||
*
|
||||
* @param workers std::vector containing MPI ranks of workers.
|
||||
*/
|
||||
DynamicAssignmentAlgorithm( const std::vector<int> & workers )
|
||||
{
|
||||
availableWrk = workers;
|
||||
}
|
||||
DynamicAssignmentAlgorithm( const std::vector<int> & workers );
|
||||
|
||||
/**
|
||||
* @brief Uses a range of ranks as workers.
|
||||
|
|
@ -150,50 +137,17 @@ namespace eo
|
|||
* @param last The last worker to be included (inclusive). If last == eo::mpi::REST_OF_THE_WORLD, all
|
||||
* hosts whose rank is higher than first are taken.
|
||||
*/
|
||||
DynamicAssignmentAlgorithm( int first, int last )
|
||||
{
|
||||
if( last == REST_OF_THE_WORLD )
|
||||
{
|
||||
last = Node::comm().size() - 1;
|
||||
}
|
||||
DynamicAssignmentAlgorithm( int first, int last );
|
||||
|
||||
for( int i = first; i <= last; ++i)
|
||||
{
|
||||
availableWrk.push_back( i );
|
||||
}
|
||||
}
|
||||
virtual int get( );
|
||||
|
||||
virtual int get( )
|
||||
{
|
||||
int assignee = -1;
|
||||
if (! availableWrk.empty() )
|
||||
{
|
||||
assignee = availableWrk.back();
|
||||
availableWrk.pop_back();
|
||||
}
|
||||
return assignee;
|
||||
}
|
||||
int availableWorkers();
|
||||
|
||||
int availableWorkers()
|
||||
{
|
||||
return availableWrk.size();
|
||||
}
|
||||
void confirm( int rank );
|
||||
|
||||
void confirm( int rank )
|
||||
{
|
||||
availableWrk.push_back( rank );
|
||||
}
|
||||
std::vector<int> idles( );
|
||||
|
||||
std::vector<int> idles( )
|
||||
{
|
||||
return availableWrk;
|
||||
}
|
||||
|
||||
void reinit( int _ )
|
||||
{
|
||||
++_;
|
||||
// nothing to do
|
||||
}
|
||||
void reinit( int _ );
|
||||
|
||||
protected:
|
||||
std::vector< int > availableWrk;
|
||||
|
|
@ -223,10 +177,7 @@ namespace eo
|
|||
* @param workers std::vector of MPI ranks of workers which will be used.
|
||||
* @param runs Fixed amount of runs, strictly positive.
|
||||
*/
|
||||
StaticAssignmentAlgorithm( std::vector<int>& workers, int runs )
|
||||
{
|
||||
init( workers, runs );
|
||||
}
|
||||
StaticAssignmentAlgorithm( std::vector<int>& workers, int runs );
|
||||
|
||||
/**
|
||||
* @brief Uses a range of workers.
|
||||
|
|
@ -236,21 +187,7 @@ namespace eo
|
|||
* workers from the first one are taken as workers.
|
||||
* @param runs Fixed amount of runs, strictly positive.
|
||||
*/
|
||||
StaticAssignmentAlgorithm( int first, int last, int runs )
|
||||
{
|
||||
std::vector<int> workers;
|
||||
|
||||
if( last == REST_OF_THE_WORLD )
|
||||
{
|
||||
last = Node::comm().size() - 1;
|
||||
}
|
||||
|
||||
for(int i = first; i <= last; ++i)
|
||||
{
|
||||
workers.push_back( i );
|
||||
}
|
||||
init( workers, runs );
|
||||
}
|
||||
StaticAssignmentAlgorithm( int first, int last, int runs );
|
||||
|
||||
/**
|
||||
* @brief Uses all the hosts whose rank is higher than 1 (inclusive) as workers.
|
||||
|
|
@ -258,16 +195,7 @@ namespace eo
|
|||
* @param runs Fixed amount of runs, strictly positive. If it's not set, you'll have to call reinit()
|
||||
* later.
|
||||
*/
|
||||
StaticAssignmentAlgorithm( int runs = 0 )
|
||||
{
|
||||
std::vector<int> workers;
|
||||
for(int i = 1; i < Node::comm().size(); ++i)
|
||||
{
|
||||
workers.push_back( i );
|
||||
}
|
||||
|
||||
init( workers, runs );
|
||||
}
|
||||
StaticAssignmentAlgorithm( int runs = 0 );
|
||||
|
||||
/**
|
||||
* @brief Uses an unique host as worker.
|
||||
|
|
@ -275,12 +203,7 @@ namespace eo
|
|||
* @param unique The MPI rank of the host which will be the worker.
|
||||
* @param runs Fixed amount of runs, strictly positive.
|
||||
*/
|
||||
StaticAssignmentAlgorithm( int unique, int runs )
|
||||
{
|
||||
std::vector<int> workers;
|
||||
workers.push_back( unique );
|
||||
init( workers, runs );
|
||||
}
|
||||
StaticAssignmentAlgorithm( int unique, int runs );
|
||||
|
||||
private:
|
||||
/**
|
||||
|
|
@ -292,89 +215,18 @@ namespace eo
|
|||
* @param workers Vector of hosts' ranks
|
||||
* @param runs Fixed amount of runs, strictly positive.
|
||||
*/
|
||||
void init( std::vector<int> & workers, int runs )
|
||||
{
|
||||
unsigned int nbWorkers = workers.size();
|
||||
freeWorkers = nbWorkers;
|
||||
|
||||
busy.clear();
|
||||
busy.resize( nbWorkers, false );
|
||||
realRank = workers;
|
||||
|
||||
if( runs <= 0 )
|
||||
{
|
||||
return;
|
||||
}
|
||||
|
||||
attributions.clear();
|
||||
attributions.reserve( nbWorkers );
|
||||
|
||||
// Let be the euclidean division of runs by nbWorkers :
|
||||
// runs == q * nbWorkers + r, 0 <= r < nbWorkers
|
||||
// This one liner affects q requests to each worker
|
||||
for (unsigned int i = 0; i < nbWorkers; attributions[i++] = runs / nbWorkers) ;
|
||||
// The first line computes r and the one liner affects the remaining
|
||||
// r requests to workers, in ascending order
|
||||
unsigned int diff = runs - (runs / nbWorkers) * nbWorkers;
|
||||
for (unsigned int i = 0; i < diff; ++attributions[i++]);
|
||||
}
|
||||
void init( std::vector<int> & workers, int runs );
|
||||
|
||||
public:
|
||||
int get( )
|
||||
{
|
||||
int assignee = -1;
|
||||
for( unsigned i = 0; i < busy.size(); ++i )
|
||||
{
|
||||
if( !busy[i] && attributions[i] > 0 )
|
||||
{
|
||||
busy[i] = true;
|
||||
--freeWorkers;
|
||||
assignee = realRank[ i ];
|
||||
break;
|
||||
}
|
||||
}
|
||||
return assignee;
|
||||
}
|
||||
int get( );
|
||||
|
||||
int availableWorkers( )
|
||||
{
|
||||
return freeWorkers;
|
||||
}
|
||||
int availableWorkers( );
|
||||
|
||||
std::vector<int> idles()
|
||||
{
|
||||
std::vector<int> ret;
|
||||
for(unsigned int i = 0; i < busy.size(); ++i)
|
||||
{
|
||||
if( !busy[i] )
|
||||
{
|
||||
ret.push_back( realRank[i] );
|
||||
}
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
std::vector<int> idles();
|
||||
|
||||
void confirm( int rank )
|
||||
{
|
||||
int i = -1; // i is the real index in table
|
||||
for( unsigned int j = 0; j < realRank.size(); ++j )
|
||||
{
|
||||
if( realRank[j] == rank )
|
||||
{
|
||||
i = j;
|
||||
break;
|
||||
}
|
||||
}
|
||||
void confirm( int rank );
|
||||
|
||||
--attributions[ i ];
|
||||
busy[ i ] = false;
|
||||
++freeWorkers;
|
||||
}
|
||||
|
||||
void reinit( int runs )
|
||||
{
|
||||
init( realRank, runs );
|
||||
}
|
||||
void reinit( int runs );
|
||||
|
||||
private:
|
||||
std::vector<int> attributions;
|
||||
|
|
|
|||
40
eo/src/mpi/eoMpiNode.cpp
Normal file
40
eo/src/mpi/eoMpiNode.cpp
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
/*
|
||||
(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>
|
||||
*/
|
||||
# include "eoMpiNode.h"
|
||||
|
||||
namespace eo
|
||||
{
|
||||
namespace mpi
|
||||
{
|
||||
void Node::init( int argc, char** argv )
|
||||
{
|
||||
static bmpi::environment env( argc, argv );
|
||||
}
|
||||
|
||||
bmpi::communicator& Node::comm()
|
||||
{
|
||||
return _comm;
|
||||
}
|
||||
|
||||
bmpi::communicator Node::_comm;
|
||||
}
|
||||
}
|
||||
|
|
@ -22,17 +22,17 @@ Authors:
|
|||
# ifndef __MPI_NODE_H__
|
||||
# define __MPI_NODE_H__
|
||||
|
||||
# include <boost/mpi.hpp>
|
||||
namespace bmpi = boost::mpi;
|
||||
# include "implMpi.h"
|
||||
namespace bmpi = mpi;
|
||||
|
||||
namespace eo
|
||||
{
|
||||
namespace mpi
|
||||
{
|
||||
/**
|
||||
* @brief Global object used to reach boost::mpi::communicator everywhere.
|
||||
* @brief Global object used to reach mpi::communicator everywhere.
|
||||
*
|
||||
* boost::mpi::communicator is the main object used to send and receive messages between the different hosts of
|
||||
* mpi::communicator is the main object used to send and receive messages between the different hosts of
|
||||
* a MPI algorithm.
|
||||
*
|
||||
* @ingroup MPI
|
||||
|
|
@ -49,18 +49,12 @@ namespace eo
|
|||
* @param argc Main's argc
|
||||
* @param argv Main's argv
|
||||
*/
|
||||
static void init( int argc, char** argv )
|
||||
{
|
||||
static bmpi::environment env( argc, argv );
|
||||
}
|
||||
static void init( int argc, char** argv );
|
||||
|
||||
/**
|
||||
* @brief Returns the global boost::mpi::communicator
|
||||
* @brief Returns the global mpi::communicator
|
||||
*/
|
||||
static bmpi::communicator& comm()
|
||||
{
|
||||
return _comm;
|
||||
}
|
||||
static bmpi::communicator& comm();
|
||||
|
||||
protected:
|
||||
static bmpi::communicator _comm;
|
||||
|
|
|
|||
491
eo/src/mpi/eoMultiStart.h
Normal file
491
eo/src/mpi/eoMultiStart.h
Normal file
|
|
@ -0,0 +1,491 @@
|
|||
# ifndef __EO_MULTISTART_H__
|
||||
# define __EO_MULTISTART_H__
|
||||
|
||||
# include <eo>
|
||||
# include "eoMpi.h"
|
||||
|
||||
/**
|
||||
* @ingroup MPI
|
||||
* @{
|
||||
*/
|
||||
|
||||
/**
|
||||
* @file eoMultiStart.h
|
||||
*
|
||||
* Contains implementation of a MPI job which consists in a multi start, which basically consists in the following:
|
||||
* the same eoAlgo is launched on computers of a clusters, with different seeds for each. As the eoAlgo are most of
|
||||
* the time stochastics, the results won't be the same. It is fully equivalent to launch the same program but with
|
||||
* different seeds.
|
||||
*
|
||||
* It follows the structure of a MPI job, as described in eoMpi.h. The basic algorithm is trivial:
|
||||
* - Loop while we have a run to perform.
|
||||
* - Worker performs runs and send their best solution (individual with best fitness) to the master.
|
||||
* - Master retrieves the best solution and adds it to a eoPop of best solutions (the user can chooses what he does
|
||||
* with this population, for instance: retrieve the best element, etc.)
|
||||
*
|
||||
* The principal concerns about this algorithm are:
|
||||
* - How do we reinitialize the algorithm? An eoAlgo can have several forms, and initializations have to be performed
|
||||
* before each "start". We can hence decide whether we reinits the population or keep the same population obtained
|
||||
* after the previous start, we have to reinitialize continuator, etc. This is customizable in the store.
|
||||
*
|
||||
* - Which seeds should be chosen? If we want the run to be re-runnable with the same results, we need to be sure that
|
||||
* the seeds are the same. But user can not care about this, and just want random seeds. This is customizable in the
|
||||
* store.
|
||||
*
|
||||
* These concerns are handled by functors, inheriting from MultiStartStore<EOT>::ResetAlgo (for the first concern), and
|
||||
* MultiStartStore<EOT>::GetSeeds (for the second one). There are default implementations, but there is no problem about
|
||||
* specializing them or coding your own, by directly inheriting from them.
|
||||
*
|
||||
* @ingroup MPI
|
||||
*/
|
||||
|
||||
namespace eo
|
||||
{
|
||||
namespace mpi
|
||||
{
|
||||
/**
|
||||
* @brief Data used by the Multi Start job.
|
||||
*
|
||||
* This data is shared between the different Job functors. More details are given for each attribute.
|
||||
*/
|
||||
template< class EOT >
|
||||
struct MultiStartData
|
||||
{
|
||||
typedef eoUF< eoPop<EOT>&, void> ResetAlgo;
|
||||
|
||||
MultiStartData( bmpi::communicator& _comm, eoAlgo<EOT>& _algo, int _masterRank, ResetAlgo & _resetAlgo )
|
||||
:
|
||||
runs( 0 ), pop(), bests(),
|
||||
comm( _comm ), algo( _algo ), masterRank( _masterRank ), resetAlgo( _resetAlgo )
|
||||
{
|
||||
// empty
|
||||
}
|
||||
|
||||
// dynamic parameters
|
||||
/**
|
||||
* @brief Total remaining number of runs.
|
||||
*
|
||||
* It's decremented as the runs are performed.
|
||||
*/
|
||||
int runs;
|
||||
|
||||
/**
|
||||
* @brief eoPop of the best individuals, which are the one sent by the workers.
|
||||
*/
|
||||
eoPop< EOT > bests;
|
||||
|
||||
/**
|
||||
* @brief eoPop on which the worker is working.
|
||||
*/
|
||||
eoPop< EOT > pop;
|
||||
|
||||
// static parameters
|
||||
/**
|
||||
* @brief Communicator, used to send and retrieve messages.
|
||||
*/
|
||||
bmpi::communicator& comm;
|
||||
|
||||
/**
|
||||
* @brief Algorithm which will be performed by the worker.
|
||||
*/
|
||||
eoAlgo<EOT>& algo;
|
||||
|
||||
/**
|
||||
* @brief Reset Algo functor, which defines how to reset the algo (above) before re running it.
|
||||
*/
|
||||
ResetAlgo& resetAlgo;
|
||||
|
||||
// Rank of master
|
||||
int masterRank;
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Send task (master side) in the Multi Start job.
|
||||
*
|
||||
* It only consists in decrementing the number of runs, as the worker already have the population and
|
||||
* all the necessary parameters to run the eoAlgo.
|
||||
*/
|
||||
template< class EOT >
|
||||
class SendTaskMultiStart : public SendTaskFunction< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
using SendTaskFunction< MultiStartData< EOT > >::_data;
|
||||
|
||||
void operator()( int wrkRank )
|
||||
{
|
||||
wrkRank++; // unused
|
||||
--(_data->runs);
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Handle Response (master side) in the Multi Start job.
|
||||
*
|
||||
* It consists in retrieving the best solution sent by the worker and adds it to a population of best
|
||||
* solutions.
|
||||
*/
|
||||
template< class EOT >
|
||||
class HandleResponseMultiStart : public HandleResponseFunction< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
using HandleResponseFunction< MultiStartData< EOT > >::_data;
|
||||
|
||||
void operator()( int wrkRank )
|
||||
{
|
||||
EOT individual;
|
||||
MultiStartData< EOT >& d = *_data;
|
||||
d.comm.recv( wrkRank, 1, individual );
|
||||
d.bests.push_back( individual );
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Process Task (worker side) in the Multi Start job.
|
||||
*
|
||||
* Consists in resetting the algorithm and launching it on the population, then
|
||||
* send the best individual (the one with the best fitness) to the master.
|
||||
*/
|
||||
template< class EOT >
|
||||
class ProcessTaskMultiStart : public ProcessTaskFunction< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
using ProcessTaskFunction< MultiStartData<EOT > >::_data;
|
||||
|
||||
void operator()()
|
||||
{
|
||||
_data->resetAlgo( _data->pop );
|
||||
_data->algo( _data->pop );
|
||||
_data->comm.send( _data->masterRank, 1, _data->pop.best_element() );
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Is Finished (master side) in the Multi Start job.
|
||||
*
|
||||
* The job is finished if and only if all the runs have been performed.
|
||||
*/
|
||||
template< class EOT >
|
||||
class IsFinishedMultiStart : public IsFinishedFunction< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
using IsFinishedFunction< MultiStartData< EOT > >::_data;
|
||||
|
||||
bool operator()()
|
||||
{
|
||||
return _data->runs <= 0;
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Store for the Multi Start job.
|
||||
*
|
||||
* Contains the data used by the workers (algo,...) and functor to
|
||||
* send the seeds.
|
||||
*/
|
||||
template< class EOT >
|
||||
class MultiStartStore : public JobStore< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
|
||||
/**
|
||||
* @brief Generic functor to reset an algorithm before it's launched by
|
||||
* the worker.
|
||||
*
|
||||
* This reset algorithm should reinits population (if necessary), continuator, etc.
|
||||
*/
|
||||
typedef typename MultiStartData<EOT>::ResetAlgo ResetAlgo;
|
||||
|
||||
/**
|
||||
* @brief Generic functor which returns a vector of seeds for the workers.
|
||||
*
|
||||
* If this vector hasn't enough seeds to send, random ones are generated and
|
||||
* sent to the workers.
|
||||
*/
|
||||
typedef eoUF< int, std::vector<int> > GetSeeds;
|
||||
|
||||
/**
|
||||
* @brief Default ctor for MultiStartStore.
|
||||
*
|
||||
* @param algo The algorithm to launch in parallel
|
||||
* @param masterRank The MPI rank of the master
|
||||
* @param resetAlgo The ResetAlgo functor
|
||||
* @param getSeeds The GetSeeds functor
|
||||
*/
|
||||
MultiStartStore(
|
||||
eoAlgo<EOT> & algo,
|
||||
int masterRank,
|
||||
ResetAlgo & resetAlgo,
|
||||
GetSeeds & getSeeds
|
||||
)
|
||||
: _data( eo::mpi::Node::comm(), algo, masterRank, resetAlgo ),
|
||||
_getSeeds( getSeeds ),
|
||||
_masterRank( masterRank )
|
||||
{
|
||||
// Default job functors for this one.
|
||||
this->_iff = new IsFinishedMultiStart< EOT >;
|
||||
this->_iff->needDelete(true);
|
||||
this->_stf = new SendTaskMultiStart< EOT >;
|
||||
this->_stf->needDelete(true);
|
||||
this->_hrf = new HandleResponseMultiStart< EOT >;
|
||||
this->_hrf->needDelete(true);
|
||||
this->_ptf = new ProcessTaskMultiStart< EOT >;
|
||||
this->_ptf->needDelete(true);
|
||||
}
|
||||
|
||||
/**
|
||||
* @brief Send new seeds to the workers before a job.
|
||||
*
|
||||
* Uses the GetSeeds functor given in constructor. If there's not
|
||||
* enough seeds to send, random seeds are sent to the workers.
|
||||
*
|
||||
* @param workers Vector of MPI ranks of the workers
|
||||
* @param runs The number of runs to perform
|
||||
*/
|
||||
void init( const std::vector<int>& workers, int runs )
|
||||
{
|
||||
_data.runs = runs;
|
||||
|
||||
int nbWorkers = workers.size();
|
||||
std::vector< int > seeds = _getSeeds( nbWorkers );
|
||||
if( eo::mpi::Node::comm().rank() == _masterRank )
|
||||
{
|
||||
if( seeds.size() < nbWorkers )
|
||||
{
|
||||
// Random seeds
|
||||
for( int i = seeds.size(); i < nbWorkers; ++i )
|
||||
{
|
||||
seeds.push_back( eo::rng.rand() );
|
||||
}
|
||||
}
|
||||
|
||||
for( int i = 0 ; i < nbWorkers ; ++i )
|
||||
{
|
||||
int wrkRank = workers[i];
|
||||
eo::mpi::Node::comm().send( wrkRank, 1, seeds[ i ] );
|
||||
}
|
||||
} else
|
||||
{
|
||||
int seed;
|
||||
eo::mpi::Node::comm().recv( _masterRank, 1, seed );
|
||||
eo::log << eo::debug << eo::mpi::Node::comm().rank() << "- Seed: " << seed << std::endl;
|
||||
eo::rng.reseed( seed );
|
||||
}
|
||||
}
|
||||
|
||||
MultiStartData<EOT>* data()
|
||||
{
|
||||
return &_data;
|
||||
}
|
||||
|
||||
private:
|
||||
MultiStartData< EOT > _data;
|
||||
GetSeeds & _getSeeds;
|
||||
int _masterRank;
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief MultiStart job, created for convenience.
|
||||
*
|
||||
* This is an OneShotJob, which means workers leave it along with
|
||||
* the master.
|
||||
*/
|
||||
template< class EOT >
|
||||
class MultiStart : public OneShotJob< MultiStartData< EOT > >
|
||||
{
|
||||
public:
|
||||
|
||||
MultiStart( AssignmentAlgorithm & algo,
|
||||
int masterRank,
|
||||
MultiStartStore< EOT > & store,
|
||||
// dynamic parameters
|
||||
int runs,
|
||||
const std::vector<int>& seeds = std::vector<int>() ) :
|
||||
OneShotJob< MultiStartData< EOT > >( algo, masterRank, store )
|
||||
{
|
||||
store.init( algo.idles(), runs );
|
||||
}
|
||||
|
||||
/**
|
||||
* @brief Returns the best solution, at the end of the job.
|
||||
*
|
||||
* Warning: if you call this function from a worker, or from the master before the
|
||||
* launch of the job, you will only get an empty population!
|
||||
*
|
||||
* @return Population of best individuals retrieved by the master.
|
||||
*/
|
||||
eoPop<EOT>& best_individuals()
|
||||
{
|
||||
return this->store.data()->bests;
|
||||
}
|
||||
};
|
||||
|
||||
/*************************************
|
||||
* DEFAULT GET SEEDS IMPLEMENTATIONS *
|
||||
************************************/
|
||||
|
||||
/**
|
||||
* @brief Uses the internal default seed generator to get seeds,
|
||||
* which means: random seeds are sent.
|
||||
*/
|
||||
template<class EOT>
|
||||
struct DummyGetSeeds : public MultiStartStore<EOT>::GetSeeds
|
||||
{
|
||||
std::vector<int> operator()( int n )
|
||||
{
|
||||
return std::vector<int>();
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Sends seeds to the workers, which are multiple of a number
|
||||
* given by the master. If no number is given, a random one is used.
|
||||
*
|
||||
* This functor ensures that even if the same store is used with
|
||||
* different jobs, the seeds will be different.
|
||||
*/
|
||||
template<class EOT>
|
||||
struct MultiplesOfNumber : public MultiStartStore<EOT>::GetSeeds
|
||||
{
|
||||
MultiplesOfNumber ( int n = 0 )
|
||||
{
|
||||
while( n == 0 )
|
||||
{
|
||||
n = eo::rng.rand();
|
||||
}
|
||||
_seed = n;
|
||||
_i = 0;
|
||||
}
|
||||
|
||||
std::vector<int> operator()( int n )
|
||||
{
|
||||
std::vector<int> ret;
|
||||
for( unsigned int i = 0; i < n; ++i )
|
||||
{
|
||||
ret.push_back( (++_i) * _seed );
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
|
||||
private:
|
||||
|
||||
unsigned int _seed;
|
||||
unsigned int _i;
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Returns random seeds to the workers. We can controle which seeds are generated
|
||||
* by precising the seed of the master.
|
||||
*/
|
||||
template<class EOT>
|
||||
struct GetRandomSeeds : public MultiStartStore<EOT>::GetSeeds
|
||||
{
|
||||
GetRandomSeeds( int seed )
|
||||
{
|
||||
eo::rng.reseed( seed );
|
||||
}
|
||||
|
||||
std::vector<int> operator()( int n )
|
||||
{
|
||||
std::vector<int> ret;
|
||||
for(int i = 0; i < n; ++i)
|
||||
{
|
||||
ret.push_back( eo::rng.rand() );
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
};
|
||||
|
||||
/**************************************
|
||||
* DEFAULT RESET ALGO IMPLEMENTATIONS *
|
||||
**************************************
|
||||
|
||||
/**
|
||||
* @brief For a Genetic Algorithm, reinits the population by copying the original one
|
||||
* given in constructor, and reinits the continuator.
|
||||
*
|
||||
* The evaluator should also be given, as the population needs to be evaluated
|
||||
* before each run.
|
||||
*/
|
||||
template<class EOT>
|
||||
struct ReuseOriginalPopEA: public MultiStartStore<EOT>::ResetAlgo
|
||||
{
|
||||
ReuseOriginalPopEA(
|
||||
eoCountContinue<EOT> & continuator,
|
||||
const eoPop<EOT>& originalPop,
|
||||
eoEvalFunc<EOT>& eval) :
|
||||
_continuator( continuator ),
|
||||
_originalPop( originalPop ),
|
||||
_eval( eval )
|
||||
{
|
||||
// empty
|
||||
}
|
||||
|
||||
void operator()( eoPop<EOT>& pop )
|
||||
{
|
||||
pop = _originalPop; // copies the original population
|
||||
for(unsigned i = 0, size = pop.size(); i < size; ++i)
|
||||
{
|
||||
_eval( pop[i] );
|
||||
}
|
||||
_continuator.reset();
|
||||
}
|
||||
|
||||
private:
|
||||
eoCountContinue<EOT> & _continuator;
|
||||
const eoPop<EOT>& _originalPop;
|
||||
eoEvalFunc<EOT>& _eval;
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief For a Genetic Algorithm, reuses the same population without
|
||||
* modifying it after a run.
|
||||
*
|
||||
* This means, if you launch a run after another one, you'll make evolve
|
||||
* the same population.
|
||||
*
|
||||
* The evaluator should also be sent, as the population needs to be evaluated
|
||||
* at the first time.
|
||||
*/
|
||||
template< class EOT >
|
||||
struct ReuseSamePopEA : public MultiStartStore<EOT>::ResetAlgo
|
||||
{
|
||||
ReuseSamePopEA(
|
||||
eoCountContinue<EOT>& continuator,
|
||||
const eoPop<EOT>& originalPop,
|
||||
eoEvalFunc<EOT>& eval
|
||||
) :
|
||||
_continuator( continuator ),
|
||||
_originalPop( originalPop ),
|
||||
_firstTime( true )
|
||||
{
|
||||
for( unsigned i = 0, size = originalPop.size();
|
||||
i < size; ++i )
|
||||
{
|
||||
eval(_originalPop[i]);
|
||||
}
|
||||
}
|
||||
|
||||
void operator()( eoPop<EOT>& pop )
|
||||
{
|
||||
if( _firstTime )
|
||||
{
|
||||
pop = _originalPop;
|
||||
_firstTime = false;
|
||||
}
|
||||
_continuator.reset();
|
||||
}
|
||||
|
||||
protected:
|
||||
|
||||
eoCountContinue<EOT>& _continuator;
|
||||
eoPop<EOT> _originalPop;
|
||||
bool _firstTime;
|
||||
};
|
||||
} // namespace mpi
|
||||
} // namespace eo
|
||||
|
||||
/**
|
||||
* @}
|
||||
*/
|
||||
|
||||
# endif // __EO_MULTISTART_H__
|
||||
166
eo/src/mpi/implMpi.cpp
Normal file
166
eo/src/mpi/implMpi.cpp
Normal file
|
|
@ -0,0 +1,166 @@
|
|||
/*
|
||||
(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>
|
||||
*/
|
||||
# include "implMpi.h"
|
||||
|
||||
namespace mpi
|
||||
{
|
||||
const int any_source = MPI_ANY_SOURCE;
|
||||
const int any_tag = MPI_ANY_TAG;
|
||||
|
||||
environment::environment(int argc, char**argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
}
|
||||
|
||||
environment::~environment()
|
||||
{
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
||||
status::status( const MPI_Status & s )
|
||||
{
|
||||
_source = s.MPI_SOURCE;
|
||||
_tag = s.MPI_TAG;
|
||||
_error = s.MPI_ERROR;
|
||||
}
|
||||
|
||||
communicator::communicator( )
|
||||
{
|
||||
_rank = -1;
|
||||
_size = -1;
|
||||
|
||||
_buf = 0;
|
||||
_bufsize = -1;
|
||||
}
|
||||
|
||||
communicator::~communicator()
|
||||
{
|
||||
if( _buf )
|
||||
{
|
||||
delete _buf;
|
||||
_buf = 0;
|
||||
}
|
||||
}
|
||||
|
||||
int communicator::rank()
|
||||
{
|
||||
if ( _rank == -1 )
|
||||
{
|
||||
MPI_Comm_rank( MPI_COMM_WORLD, &_rank );
|
||||
}
|
||||
return _rank;
|
||||
}
|
||||
|
||||
int communicator::size()
|
||||
{
|
||||
if ( _size == -1 )
|
||||
{
|
||||
MPI_Comm_size( MPI_COMM_WORLD, &_size );
|
||||
}
|
||||
return _size;
|
||||
}
|
||||
|
||||
/*
|
||||
* SEND / RECV INT
|
||||
*/
|
||||
void communicator::send( int dest, int tag, int n )
|
||||
{
|
||||
MPI_Send( &n, 1, MPI_INT, dest, tag, MPI_COMM_WORLD );
|
||||
}
|
||||
|
||||
void communicator::recv( int src, int tag, int& n )
|
||||
{
|
||||
MPI_Status stat;
|
||||
MPI_Recv( &n, 1, MPI_INT, src, tag, MPI_COMM_WORLD , &stat );
|
||||
}
|
||||
|
||||
/*
|
||||
* SEND / RECV STRING
|
||||
*/
|
||||
void communicator::send( int dest, int tag, const std::string& str )
|
||||
{
|
||||
int size = str.size() + 1;
|
||||
send( dest, tag, size );
|
||||
MPI_Send( (char*)str.c_str(), size, MPI_CHAR, dest, tag, MPI_COMM_WORLD);
|
||||
}
|
||||
|
||||
void communicator::recv( int src, int tag, std::string& str )
|
||||
{
|
||||
int size = -1;
|
||||
MPI_Status stat;
|
||||
recv( src, tag, size );
|
||||
|
||||
if( _buf == 0 )
|
||||
{
|
||||
_buf = new char[ size ];
|
||||
_bufsize = size;
|
||||
} else if( _bufsize < size )
|
||||
{
|
||||
delete [] _buf;
|
||||
_buf = new char[ size ];
|
||||
_bufsize = size;
|
||||
}
|
||||
MPI_Recv( _buf, size, MPI_CHAR, src, tag, MPI_COMM_WORLD, &stat );
|
||||
str.assign( _buf );
|
||||
}
|
||||
|
||||
/*
|
||||
* SEND / RECV Objects
|
||||
*/
|
||||
void communicator::send( int dest, int tag, const eoserial::Persistent & persistent )
|
||||
{
|
||||
eoserial::Object* obj = persistent.pack();
|
||||
std::stringstream ss;
|
||||
obj->print( ss );
|
||||
delete obj;
|
||||
send( dest, tag, ss.str() );
|
||||
}
|
||||
|
||||
void communicator::recv( int src, int tag, eoserial::Persistent & persistent )
|
||||
{
|
||||
std::string asText;
|
||||
recv( src, tag, asText );
|
||||
eoserial::Object* obj = eoserial::Parser::parse( asText );
|
||||
persistent.unpack( obj );
|
||||
delete obj;
|
||||
}
|
||||
|
||||
/*
|
||||
* Other methods
|
||||
*/
|
||||
status communicator::probe( int src, int tag )
|
||||
{
|
||||
MPI_Status stat;
|
||||
MPI_Probe( src, tag, MPI_COMM_WORLD , &stat );
|
||||
return status( stat );
|
||||
}
|
||||
|
||||
void communicator::barrier()
|
||||
{
|
||||
MPI_Barrier( MPI_COMM_WORLD );
|
||||
}
|
||||
|
||||
void broadcast( communicator & comm, int value, int root )
|
||||
{
|
||||
MPI_Bcast( &value, 1, MPI_INT, root, MPI_COMM_WORLD );
|
||||
}
|
||||
}
|
||||
322
eo/src/mpi/implMpi.h
Normal file
322
eo/src/mpi/implMpi.h
Normal file
|
|
@ -0,0 +1,322 @@
|
|||
/*
|
||||
(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>
|
||||
*/
|
||||
# ifndef __EO_IMPL_MPI_HPP__
|
||||
# define __EO_IMPL_MPI_HPP__
|
||||
|
||||
# include <mpi.h>
|
||||
# include <serial/eoSerial.h>
|
||||
|
||||
/**
|
||||
* This namespace contains reimplementations of some parts of the Boost::MPI API in C++, so as to be used in
|
||||
* EO without any dependance to Boost. Historically, EO's parallelization module used the
|
||||
* boost library to add a layer over MPI. After having noticed that just some functions
|
||||
* were really used, we decided to reimplement our own C++-like implementation of MPI.
|
||||
*
|
||||
* Because the Boost::MPI API is really clean, we reused it in this module. However, all
|
||||
* the functions of Boost::MPI were not used, hence a subset of the API is reused. For
|
||||
* instance, users can just send integer, std::string or eoserial::Persistent objects;
|
||||
* furthermore, only eoserial::Persistent objects can sent in a table.
|
||||
*
|
||||
* The documentation of the functions is exactly the same as the official Boost::MPI
|
||||
* documentation. You can find it on www.boost.org/doc/libs/1_49_0/doc/html/mpi/
|
||||
* The entities are here shortly described, if you need further details, don't hesitate
|
||||
* to visit the boost URL.
|
||||
*/
|
||||
|
||||
namespace mpi
|
||||
{
|
||||
/**
|
||||
* @ingroup Parallel
|
||||
* @{
|
||||
*/
|
||||
|
||||
/**
|
||||
* @brief Constant indicating that a message can come from any process.
|
||||
*/
|
||||
extern const int any_source;
|
||||
|
||||
/**
|
||||
* @brief Constant indicating that a message can come from any tag (channel).
|
||||
*/
|
||||
extern const int any_tag;
|
||||
|
||||
/**
|
||||
* @brief Wrapper class to have a MPI environment.
|
||||
*
|
||||
* Instead of calling MPI_Init and MPI_Finalize, it is only necessary to instantiate
|
||||
* this class once, in the global context.
|
||||
*/
|
||||
class environment
|
||||
{
|
||||
public:
|
||||
|
||||
/**
|
||||
* @brief Inits MPI context.
|
||||
*
|
||||
* @param argc Number of params in command line (same as one in main)
|
||||
* @param argv Strings containing params (same as one in main)
|
||||
*/
|
||||
environment(int argc, char**argv);
|
||||
|
||||
/**
|
||||
* @brief Closes MPI context.
|
||||
*/
|
||||
~environment();
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Wrapper class for MPI_Status
|
||||
*
|
||||
* Consists only in a C++ wrapper class, giving getters on status attributes.
|
||||
*/
|
||||
class status
|
||||
{
|
||||
public:
|
||||
|
||||
/**
|
||||
* @brief Converts a MPI_Status into a status.
|
||||
*/
|
||||
status( const MPI_Status & s );
|
||||
|
||||
/**
|
||||
* @brief Returns the tag of the associated communication.
|
||||
*/
|
||||
int tag() { return _tag; }
|
||||
|
||||
/**
|
||||
* @brief Indicates which error number we obtained in the associated communication.
|
||||
*/
|
||||
int error() { return _error; }
|
||||
|
||||
/**
|
||||
* @brief Returns the MPI rank of the source of the associated communication.
|
||||
*/
|
||||
int source() { return _source; }
|
||||
|
||||
private:
|
||||
int _source;
|
||||
int _tag;
|
||||
int _error;
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Main object, used to send / receive messages, get informations about the rank and the size of the world,
|
||||
* etc.
|
||||
*/
|
||||
class communicator
|
||||
{
|
||||
public:
|
||||
|
||||
/**
|
||||
* Creates the communicator, using the whole world as a MPI_Comm.
|
||||
*
|
||||
* @todo Allow the user to precise which MPI_Comm to use
|
||||
*/
|
||||
communicator( );
|
||||
|
||||
~communicator();
|
||||
|
||||
/**
|
||||
* @brief Returns the MPI rank of the current process.
|
||||
*/
|
||||
int rank();
|
||||
|
||||
/**
|
||||
* @brief Returns the size of the MPI cluster.
|
||||
*/
|
||||
int size();
|
||||
|
||||
/*
|
||||
* SEND / RECV INT
|
||||
*/
|
||||
|
||||
/**
|
||||
* @brief Sends an integer to dest on channel "tag".
|
||||
*
|
||||
* @param dest MPI rank of the receiver
|
||||
* @param tag MPI tag of message
|
||||
* @param n The integer to send
|
||||
*/
|
||||
void send( int dest, int tag, int n );
|
||||
|
||||
/*
|
||||
* @brief Receives an integer from src on channel "tag".
|
||||
*
|
||||
* @param src MPI rank of the sender
|
||||
* @param tag MPI tag of message
|
||||
* @param n Where to save the received integer
|
||||
*/
|
||||
void recv( int src, int tag, int& n );
|
||||
|
||||
/*
|
||||
* SEND / RECV STRING
|
||||
*/
|
||||
|
||||
/**
|
||||
* @brief Sends a string to dest on channel "tag".
|
||||
*
|
||||
* @param dest MPI rank of the receiver
|
||||
* @param tag MPI tag of message
|
||||
* @param str The std::string to send
|
||||
*/
|
||||
void send( int dest, int tag, const std::string& str );
|
||||
|
||||
/*
|
||||
* @brief Receives a string from src on channel "tag".
|
||||
*
|
||||
* @param src MPI rank of the sender
|
||||
* @param tag MPI tag of message
|
||||
* @param std::string Where to save the received string
|
||||
*/
|
||||
void recv( int src, int tag, std::string& str );
|
||||
|
||||
/*
|
||||
* SEND / RECV Objects
|
||||
*/
|
||||
|
||||
/**
|
||||
* @brief Sends an eoserial::Persistent to dest on channel "tag".
|
||||
*
|
||||
* @param dest MPI rank of the receiver
|
||||
* @param tag MPI tag of message
|
||||
* @param persistent The object to send (it must absolutely implement eoserial::Persistent)
|
||||
*/
|
||||
void send( int dest, int tag, const eoserial::Persistent & persistent );
|
||||
|
||||
/**
|
||||
* @brief Sends an array of eoserial::Persistent to dest on channel "tag".
|
||||
*
|
||||
* @param dest MPI rank of the receiver
|
||||
* @param tag MPI tag of message
|
||||
* @param table The array of eoserial::Persistent objects
|
||||
* @param size The number of elements to send (no check is done, the user has to be sure that the size won't
|
||||
* overflow!)
|
||||
*/
|
||||
template< class T >
|
||||
void send( int dest, int tag, T* table, int size )
|
||||
{
|
||||
// Puts all the values into an array
|
||||
eoserial::Array* array = new eoserial::Array;
|
||||
|
||||
for( int i = 0; i < size; ++i )
|
||||
{
|
||||
array->push_back( table[i].pack() );
|
||||
}
|
||||
|
||||
// Encapsulates the array into an object
|
||||
eoserial::Object* obj = new eoserial::Object;
|
||||
obj->add( "array", array );
|
||||
std::stringstream ss;
|
||||
obj->print( ss );
|
||||
delete obj;
|
||||
|
||||
// Sends the object as a string
|
||||
send( dest, tag, ss.str() );
|
||||
}
|
||||
|
||||
/*
|
||||
* @brief Receives an eoserial::Persistent object from src on channel "tag".
|
||||
*
|
||||
* @param src MPI rank of the sender
|
||||
* @param tag MPI tag of message
|
||||
* @param persistent Where to unpack the serialized object?
|
||||
*/
|
||||
void recv( int src, int tag, eoserial::Persistent & persistent );
|
||||
|
||||
/*
|
||||
* @brief Receives an array of eoserial::Persistent from src on channel "tag".
|
||||
*
|
||||
* @param src MPI rank of the sender
|
||||
* @param tag MPI tag of message
|
||||
* @param table The table in which we're saving the received objects. It must have been allocated by the user,
|
||||
* as no allocation is performed here.
|
||||
* @param size The number of elements to receive (no check is done, the user has to be sure that the size won't
|
||||
* overflow!)
|
||||
*/
|
||||
template< class T >
|
||||
void recv( int src, int tag, T* table, int size )
|
||||
{
|
||||
// Receives the string which contains the object
|
||||
std::string asText;
|
||||
recv( src, tag, asText );
|
||||
|
||||
// Parses the object and retrieves the table
|
||||
eoserial::Object* obj = eoserial::Parser::parse( asText );
|
||||
eoserial::Array* array = static_cast<eoserial::Array*>( (*obj)["array"] );
|
||||
|
||||
// Retrieves all the values from the array
|
||||
for( int i = 0; i < size; ++i )
|
||||
{
|
||||
eoserial::unpackObject( *array, i, table[i] );
|
||||
}
|
||||
delete obj;
|
||||
}
|
||||
|
||||
/*
|
||||
* Other methods
|
||||
*/
|
||||
|
||||
/**
|
||||
* @brief Wrapper for MPI_Probe
|
||||
*
|
||||
* Waits for a message to come from process having rank src, on the channel
|
||||
* tag.
|
||||
*
|
||||
* @param src MPI rank of the sender (any_source if it can be any sender)
|
||||
* @param tag MPI tag of the expected message (any_tag if it can be any tag)
|
||||
*/
|
||||
status probe( int src = any_source, int tag = any_tag );
|
||||
|
||||
/**
|
||||
* @brief Wrapper for MPI_Barrier
|
||||
*
|
||||
*
|
||||
*/
|
||||
void barrier();
|
||||
|
||||
private:
|
||||
int _rank;
|
||||
int _size;
|
||||
|
||||
char* _buf; // temporary buffer for sending and receiving strings. Avoids reallocations
|
||||
int _bufsize; // size of the above temporary buffer
|
||||
};
|
||||
|
||||
/**
|
||||
* @brief Wrapper for MPI_Bcast
|
||||
*
|
||||
* Broadcasts an integer value on the communicator comm, from the process having the MPI rank root.
|
||||
*
|
||||
* @param comm The communicator on which to broadcast
|
||||
* @param value The integer value to send
|
||||
* @param root The MPI rank of the broadcaster
|
||||
*
|
||||
* @todo Actually comm isn't used and broadcast is performed on the whole MPI_COMM_WORLD. TODO: Use comm instead
|
||||
*/
|
||||
void broadcast( communicator & comm, int value, int root );
|
||||
|
||||
/**
|
||||
* @}
|
||||
*/
|
||||
} // namespace mpi
|
||||
|
||||
# endif //__EO_IMPL_MPI_HPP__
|
||||
|
|
@ -30,12 +30,7 @@ Authors:
|
|||
|
||||
# include "utils/eoParallel.h" // eo::parallel
|
||||
|
||||
# ifdef WITH_MPI
|
||||
// For serialization purposes
|
||||
# include <boost/serialization/access.hpp>
|
||||
# include <boost/serialization/vector.hpp>
|
||||
# include <boost/serialization/map.hpp>
|
||||
# endif
|
||||
# include "serial/eoSerial.h" // eo::Persistent
|
||||
|
||||
/**
|
||||
* @brief Timer allowing to measure time between a start point and a stop point.
|
||||
|
|
@ -202,6 +197,9 @@ class eoTimer
|
|||
* @ingroup Utilities
|
||||
*/
|
||||
class eoTimerStat
|
||||
# ifdef WITH_MPI
|
||||
: public eoserial::Persistent
|
||||
# endif
|
||||
{
|
||||
public:
|
||||
|
||||
|
|
@ -215,41 +213,63 @@ class eoTimerStat
|
|||
* It can readily be serialized with boost when compiling with mpi.
|
||||
*/
|
||||
struct Stat
|
||||
# ifdef WITH_MPI
|
||||
: public eoserial::Persistent
|
||||
# endif
|
||||
{
|
||||
std::vector<long int> utime;
|
||||
std::vector<long int> stime;
|
||||
std::vector<double> wtime;
|
||||
#ifdef WITH_MPI
|
||||
// Gives access to boost serialization
|
||||
friend class boost::serialization::access;
|
||||
void unpack( const eoserial::Object* obj )
|
||||
{
|
||||
utime.clear();
|
||||
static_cast< eoserial::Array* >(obj->find("utime")->second)
|
||||
->deserialize< std::vector<long int>, eoserial::Array::UnpackAlgorithm >( utime );
|
||||
|
||||
/**
|
||||
* Serializes the single statistic in a boost archive (useful for boost::mpi).
|
||||
* Just serializes the 3 vectors.
|
||||
*/
|
||||
template <class Archive>
|
||||
void serialize( Archive & ar, const unsigned int version )
|
||||
{
|
||||
ar & utime & stime & wtime;
|
||||
(void) version; // avoid compilation warning
|
||||
}
|
||||
stime.clear();
|
||||
static_cast< eoserial::Array* >(obj->find("stime")->second)
|
||||
->deserialize< std::vector<long int>, eoserial::Array::UnpackAlgorithm >( stime );
|
||||
|
||||
wtime.clear();
|
||||
static_cast< eoserial::Array* >(obj->find("wtime")->second)
|
||||
->deserialize< std::vector<double>, eoserial::Array::UnpackAlgorithm >( wtime );
|
||||
}
|
||||
|
||||
eoserial::Object* pack( void ) const
|
||||
{
|
||||
eoserial::Object* obj = new eoserial::Object;
|
||||
obj->add("utime", eoserial::makeArray< std::vector<long int>, eoserial::MakeAlgorithm >( utime ) );
|
||||
obj->add("stime", eoserial::makeArray< std::vector<long int>, eoserial::MakeAlgorithm >( stime ) );
|
||||
obj->add("wtime", eoserial::makeArray< std::vector<double>, eoserial::MakeAlgorithm >( wtime ) );
|
||||
return obj;
|
||||
}
|
||||
# endif
|
||||
};
|
||||
|
||||
#ifdef WITH_MPI
|
||||
// Gives access to boost serialization
|
||||
friend class boost::serialization::access;
|
||||
|
||||
/**
|
||||
* Serializes the timerStat object in a boost archive (useful for boost::mpi).
|
||||
* Just serializes the map.
|
||||
*/
|
||||
template <class Archive>
|
||||
void serialize( Archive & ar, const unsigned int version )
|
||||
void unpack( const eoserial::Object* obj )
|
||||
{
|
||||
_stats.clear();
|
||||
for( eoserial::Object::const_iterator it = obj->begin(), final = obj->end();
|
||||
it != final;
|
||||
++it)
|
||||
{
|
||||
ar & _stats;
|
||||
(void) version; // avoid compilation warning
|
||||
eoserial::unpackObject( *obj, it->first, _stats[ it->first ] );
|
||||
}
|
||||
}
|
||||
|
||||
eoserial::Object* pack( void ) const
|
||||
{
|
||||
eoserial::Object* obj = new eoserial::Object;
|
||||
for( std::map<std::string, Stat >::const_iterator it = _stats.begin(), final = _stats.end();
|
||||
it != final;
|
||||
++it)
|
||||
{
|
||||
obj->add( it->first, it->second.pack() );
|
||||
}
|
||||
return obj;
|
||||
}
|
||||
# endif
|
||||
|
||||
/**
|
||||
|
|
|
|||
Reference in a new issue