[mlpack-git] [mlpack] Problem Linking MLPACK on Mac (#441)

[Emmanuel John]

`Graph::sparsifyGraph()` is my function. 

    void Graph::sparsifyGraph(){
        for(Node& nod: nodes){
		std::vector<Edge> edges;
		double total =0;
		for(Neighbor& nb:neighbors(nod.getNodeId())){
			if(nod.getNodeId() > nb.nodeId) continue;
			Edge edge(nod, getNode(nb.nodeId), nb.algebraicDist);
			total+=nb.algebraicDist;
			edges.push_back(edge);
		}

		/*const double mean = total/edges.size();
		//sort the edges according to the algebraic distance
		sort(edges.begin(), edges.end(),SortByAlgebraicDistance());
		int p = edges.size() * 0.5;
		double median =0;
		if(p%2==0){
			median = (edges[p-1].weight + edges[p].weight) *0.5;
		}else{
			median = edges[p-1].weight;
		}
		std::cout<<mean<<" "<<median<<std::endl;*/

		//lets try k-means
		using namespace mlpack::kmeans;
		using namespace mlpack::metric;
		// The dataset we are clustering.
		arma::mat data(1, edges.size());
		int col =0;
		for(Edge& e: edges){
			//std::cout<<e<<std::endl;
			data(0,col) = e.weight;
			col++;
		}
		
		// The number of clusters we are getting.
		size_t clusters = 5;
		// The centroids will be stored in this matrix.
		// The assignments will be stored in this vector.
		arma::Col<size_t> assignments;

		// Initialize with the default arguments.
		//KMeans<SquaredEuclideanDistance,RefinedStart, MaxVarianceNewCluster> k;
		KMeans<> k;
		//RefinedStart k;
		k.Cluster(data, clusters, assignments);

		for(int i =0;i<edges.size();i++){
			std::cout<<edges[i].weight<<" "<<assignments(i)<<std::endl;
		}
		//std::cout<<edges.size()<<" "<<assignments.size()<<std::endl;
		//exit(0);
	}
    }

This is what my Makefile look like:


     # Warnings frequently signal eventual errors:
     CXXFLAGS=-std=c++11 -g -O3 #-W -Wall -Weffc++ -Wextra -pedantic -O3

     #Includes
     INCLUDES=-I/usr/include/libxml2/ -I/usr/local/include/mlpack -I/Users/emmanueljohn/libs/NetworKit/include
     LFLAGS=-L/Users/emmanueljohn/libs/NetworKit

    #Linker flags for both OS X and Linux
    LDFLAGS=-lexpat -fopenmp -lmlpack #-lNetworKit 

    # Generates list of object files from all the
    #   source files in directory
    OBJS = $(addsuffix .o, $(basename $(shell find *.cpp)))
    DEPS = $(OBJS:.o=.d)

    # Set executable name
    EXEC = run

    # Declare the phony targets
    .PHONY: echo clean r clang gcc setclang setgcc vg

    # Phony targets to run dependencies in order
    gcc: | setgcc $(EXEC)
    clang: | setclang $(EXEC)

    # For use with the clang static analyzer by
    #  using the environment variable for CXX
    sb: | $(clean) $(EXEC)

    vg: $(EXEC)
	    valgrind ./$(EXEC)

    # Run the executable
    r:
	./$(EXEC)

    clean:
	rm -rf $(OBJS)
	rm -rf $(DEPS)
	rm -rf $(EXEC)

    # Phony target to use clang for compile and linking
    setclang:
	@echo "Setting clang"
	$(eval CXX = clang++)
	$(eval CXX_LINK = clang++)

    # Phony target to use g++ for compile and linking
    setgcc:
	@echo "Setting g++"
	$(eval CXX = g++-4.8)
	$(eval CXX_LINK = g++-4.8)

    # $< refers to the first dependency
    # Uses static pattern rule to keep from compiling all
    #   objects every time.
    $(OBJS): %.o: %.cpp
	$(CXX) $(CXXFLAGS) $(INCLUDES) $(LFLAGS) -c $< -o $@ 

    $(DEPS): %.d: %.cpp
	@echo "Generating "$@
	@set -e; rm -f $@; \
      g++-4.8 -MM $(CPPFLAGS) $< > $@.$$$$; \
      sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@; \
      rm -f $@.$$$$
    #g++ -o LibDemo -std=c++11 -I/home/emmanuj/libs/networkit/include -    L/home/emmanuj/libs/networkit/ LibDemo.cpp -lNetworKit -fopenmp
    # $@ refers to the target
    $(EXEC): $(OBJS)
	$(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(INCLUDES) $(LFLAGS) $(LDFLAGS)

    include $(DEPS)



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Reply to this email directly or view it on GitHub:
https://github.com/mlpack/mlpack/issues/441#issuecomment-109643580
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