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kpsc59
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Changes for Hellbender
1 parent bd23cc9 commit f1a5045

23 files changed

+64
-33
lines changed

‎.gitignore

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*.exe
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*.out
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*.app
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.nfs*

‎Makefile

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@@ -8,12 +8,10 @@ LIBFORMAT = static_pic
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#
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#---------------------------------------------------------------------------------------------------
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CPLEXDIR = /opt/ibm/ILOG/CPLEX_Studio221/cplex
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CONCERTDIR = /opt/ibm/ILOG/CPLEX_Studio221/concert
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#CPLEXDIR = /cluster/software/cplex-studio/cplex-studio-12.7.0/cplex
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#CONCERTDIR = /cluster/software/cplex-studio/cplex-studio-12.7.0/concert
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# CPLEXDIR = /Applications/CPLEX_Studio128/cplex
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# CONCERTDIR = /Applications/CPLEX_Studio128/concert
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#CPLEXDIR = /opt/ibm/ILOG/CPLEX_Studio221/cplex
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#CONCERTDIR = /opt/ibm/ILOG/CPLEX_Studio221/concert
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CPLEXDIR = /cluster/software/cplex_studio/v2211/cplex
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CONCERTDIR = /cluster/software/cplex_studio/v2211/concert
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#---------------------------------------------------------------------------------------------------
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# Compiler selection
@@ -57,9 +55,9 @@ CXXFLAGS = -O3 -Wall -fPIC -fexceptions -DIL_STD -std=c++11 -fno-strict-aliasing
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CPLEXLIBDIR = $(CPLEXDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
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CONCERTLIBDIR = $(CONCERTDIR)/lib/$(SYSTEM)/$(LIBFORMAT)
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OPENMPIT = /usr/lib/lam/lib
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#OPENMPIT = /usr/lib/lam/lib
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CXXLNDIRS = -L$(CPLEXLIBDIR) -L$(CONCERTLIBDIR) -L$(OPENMPIT)
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CXXLNDIRS = -L$(CPLEXLIBDIR) -L$(CONCERTLIBDIR)
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CXXLNFLAGS = -lconcert -lilocplex -lcplex -lm -lpthread -ldl
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#---------------------------------------------------------------------------------------------------
@@ -88,10 +86,10 @@ $(OBJDIR)/main.o: $(addprefix $(SRCDIR)/, main.cpp main.h) \
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$(OBJDIR)/ConfigParser.o: $(addprefix $(SRCDIR)/, ConfigParser.cpp ConfigParser.h) \
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$(addprefix $(OBJDIR)/, CSFS_Utils.o)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/Cut.o: $(addprefix $(SRCDIR)/, Cut.cpp Cut.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/CutAndSolveController.o: $(addprefix $(SRCDIR)/, CutAndSolveController.cpp CutAndSolveController.h) \
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$(addprefix $(OBJDIR)/, CutCreator.o CSFS.o \
@@ -105,48 +103,48 @@ $(OBJDIR)/CutAndSolveWorker.o: $(addprefix $(SRCDIR)/, CutAndSolveWorker.cpp Cut
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$(OBJDIR)/CutCreator.o: $(addprefix $(SRCDIR)/, CutCreator.cpp CutCreator.h) \
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$(addprefix $(OBJDIR)/, CutSet.o Individual.o Marker.o CSFS_Data.o)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/CutSet.o: $(addprefix $(SRCDIR)/, CutSet.cpp CutSet.h) \
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$(addprefix $(OBJDIR)/, Cut.o)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/Individual.o: $(addprefix $(SRCDIR)/, Individual.cpp Individual.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/Marker.o: $(addprefix $(SRCDIR)/, Marker.cpp Marker.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/CSFS.o: $(addprefix $(SRCDIR)/, CSFS.cpp CSFS.h) \
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$(addprefix $(OBJDIR)/, CSFS_Data.o Solution.o)
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$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(OBJDIR)/CSFS_Data.o: $(addprefix $(SRCDIR)/, CSFS_Data.cpp CSFS_Data.h) \
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$(addprefix $(OBJDIR)/, ConfigParser.o CSFS_Utils.o Timer.o)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/CSFS_Utils.o: $(addprefix $(SRCDIR)/, CSFS_Utils.cpp CSFS_Utils.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/Parallel.o: $(addprefix $(SRCDIR)/, Parallel.cpp Parallel.h)
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/SparseSolver.o: $(addprefix $(SRCDIR)/, SparseSolver.cpp SparseSolver.h) \
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$(addprefix $(OBJDIR)/, CutSet.o CSFS.o Solution.o Timer.o)
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$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(OBJDIR)/RelaxationSolver.o: $(addprefix $(SRCDIR)/, RelaxationSolver.cpp RelaxationSolver.h) \
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$(addprefix $(OBJDIR)/, CutSet.o CSFS_Data.o Solution.o Timer.o)
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$(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
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$(OBJDIR)/Solution.o: $(addprefix $(SRCDIR)/, Solution.cpp Solution.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/Timer.o: $(addprefix $(SRCDIR)/, Timer.cpp Timer.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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$(OBJDIR)/VariableEqualities.o: $(addprefix $(SRCDIR)/, VariableEqualities.cpp VariableEqualities.h)
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$(CXX) $(CXXFLAGS) -c -o $@ $<
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$(MPICXX) $(CXXFLAGS) -c -o $@ $<
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#---------------------------------------------------------------------------------------------------
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.PHONY: clean cleanest

‎compile.sh

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#! /bin/bash
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#SBATCH -p general # use the general partition
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#SBATCH -J compile_csfs # job name
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#SBATCH -o results-%j.out # output file name
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#SBATCH -t 0-00:10 # time limit
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#SBATCH -N 1 # number of nodes
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#SBATCH -n 1 # number of cores (AKA tasks)
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#SBATCH [email protected] # email address for notifications
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#SBATCH --mail-type=BEGIN,END,FAIL # which type of notifications to send
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# load modules
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module load openmpi/4.1.5_gcc_12.3.0
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module load cplex/2211
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module list
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# Comple program
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srun make

‎csfs

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‎src/CSFS.cpp

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#include "CSFS.h"
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#include <iomanip>
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#include <iostream>
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#include <cassert>
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//------------------------------------------------------------------------------
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// Returns the next coordinates by reference.

‎src/CSFS_Utils.cpp

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#include "CSFS_Utils.h"
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#include <iostream>
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#include <sstream>
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//------------------------------------------------------------------------------
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// Binomial coefficient. "n choose k"
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// Adapted from:
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// https://www.geeksforgeeks.org/space-and-time-efficient-binomial-coefficient/
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//------------------------------------------------------------------------------
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/*
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boost::multiprecision::cpp_int CSFSUtils::C(const std::size_t n, std::size_t k)
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{
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if (k > n)
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return result;
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}
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*/
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//------------------------------------------------------------------------------

‎src/CSFS_Utils.h

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#ifndef CSFS_UTILS_H
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#define CSFS_UTILS_H
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#include <assert.h>
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#include <boost/multiprecision/cpp_int.hpp>
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//#include <boost/multiprecision/cpp_int.hpp>
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#include <random>
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namespace CSFSUtils
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{
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boost::multiprecision::cpp_int C(const std::size_t, std::size_t);
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//boost::multiprecision::cpp_int C(const std::size_t, std::size_t);
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std::mt19937 createRng();
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std::size_t genRand();
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std::string getNthWord(const std::string &, std::size_t);

‎src/ConfigParser.cpp

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//------------------------------------------------------------------------------
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// Returns the value mapped to the parameter as a boost::multiprecision::cpp_int
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//------------------------------------------------------------------------------
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/*
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boost::multiprecision::cpp_int ConfigParser::getMultiprecisionInt(const std::string &parameterName) const
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{
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std::string value = findValue(parameterName);
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boost::multiprecision::cpp_int returnValue(value);
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return returnValue;
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}
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*/
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//------------------------------------------------------------------------------

‎src/ConfigParser.h

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#ifndef CONFIG_PARSER
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#define CONFIG_PARSER
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#include <boost/multiprecision/cpp_int.hpp>
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//#include <boost/multiprecision/cpp_int.hpp>
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#include <fstream>
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#include <map>
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#include <sstream>
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double getDouble(const std::string &) const;
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float getFloat(const std::string &) const;
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int getInt(const std::string &) const;
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boost::multiprecision::cpp_int getMultiprecisionInt(const std::string &) const;
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//boost::multiprecision::cpp_int getMultiprecisionInt(const std::string &) const;
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short getShort(const std::string &) const;
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std::size_t getSizeT(const std::string &) const;
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std::string getString(const std::string &) const;

‎src/Cut.cpp

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#include "Cut.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructors

‎src/Cut.h

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#ifndef CUT_H
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#define CUT_H
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#include <assert.h>
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#include <sstream>
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#include <vector>
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‎src/CutAndSolveController.cpp

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#include "CutAndSolveController.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor

‎src/CutAndSolveController.h

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#ifndef CNS_CONTROLLER_H
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#define CNS_CONTROLLER_H
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#include <boost/multiprecision/cpp_dec_float.hpp>
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//#include <boost/multiprecision/cpp_dec_float.hpp>
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#include "CutCreator.h"
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#include "CSFS.h"

‎src/CutAndSolveWorker.cpp

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#include "CutAndSolveWorker.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor

‎src/CutCreator.cpp

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#include "CutCreator.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor

‎src/CutSet.cpp

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#include "CutSet.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor

‎src/Individual.cpp

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#include "Individual.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructors

‎src/Individual.h

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#ifndef INDIVIDUAL_H
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#define INDIVIDUAL_H
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#include <assert.h>
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#include <vector>
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class Individual

‎src/Marker.cpp

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#include "Marker.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructors

‎src/Marker.h

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#ifndef MARKER_H
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#include <assert.h>
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#include <cstddef>
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class Marker

‎src/PatfileReader.cpp

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#include "PatfileReader.h"
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#include "Cut.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructors

‎src/RelaxationSolver.cpp

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#include "RelaxationSolver.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor

‎src/SparseSolver.cpp

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#include "SparseSolver.h"
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#include "CSFS_Utils.h"
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#include <cassert>
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//------------------------------------------------------------------------------
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// Constructor
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//------------------------------------------------------------------------------

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