Added missing files

src/Decomposition/CartDecomposition.cpp

+/*
+ * CartDecomposition.cpp
+ *
+ *  Created on: Aug 15, 2014
+ *      Author: Pietro Incardona
+ */
+
+#include "CartDecomposition.hpp"
+
+
+
+/*! \brief The the bulk part of the data set, or the data that does not depend
+ *  from the ghosts layers
+ *
+ * The the bulk part of the data set, or the data that does not depend from the
+ *  ghosts layers
+ *
+ */
+
+/*template<typename T> T CartDecomposition<T>::getBulk(T data)
+{
+	// for each element in data
+
+	for (size_t i = 0; i < data.size() ; i++)
+	{
+		if (localSpace.isInside())
+	}
+
+}
+
+template<typename T> T CartDecomposition<T>::getInternal()
+{
+
+}*/
+
+/*! \brief Check if is border or bulk
+ *
+ * \param neighboorhood define the neighboorhood of all the points
+ * \return true if border, false if bulk
+ *
+ */
+
+bool borderOrBulk(neighborhood & nb)
+{
+	device::grid<1,size_t> nbr = nb.next();
+
+	// check the neighborhood
+
+	// get neighborhood iterator
+
+	grid_key_dx_iterator<dim> iterator_nbr = nbr.getIterator();
+
+	while (iterator_nbr.hasNext())
+	{
+		grid_key_dx key_nbr = iterator_nbr.next();
+
+		// check if the neighboorhood is internal
+
+		if(subspace.isBound(data.template get<Point::x>(key_nbr)) == false)
+		{
+			// it is border
+
+			return true;
+
+			ret.bord.push_back(key);
+			break;
+		}
+	}
+
+	return false;
+}
+
+/*! \brief This function divide the data set into bulk, border, external and internal part
+ *
+ * \tparam dim dimensionality of the structure storing your data
+ *         (example if they are in 3D grid, has to be 3)
+ * \tparam T type of object we are dividing
+ * \tparam device type of layout selected
+ * \param data 1-dimensional grid of point
+ * \param nb define the neighborhood of all the points
+ * \return a structure with the set of objects divided
+ *
+ */
+
+template<unsigned int dim, typename T, template<typename> class layout, typename Memory, template<unsigned int, typename> class Domain, template<typename, typename, typename> class data_s>
+dataDiv<T> CartDecomposition<dim,T,layout>::divide(device::grid<1,Point<dim,T>> & data, neighborhood & nb)
+{
+	//! allocate the 3 subset
+
+	dataDiv<T> ret;
+
+	ret.bord = new boost::shared_ptr<T>(new T());
+	ret.inte = new boost::shared_ptr<T>(new T());
+	ret.ext = new boost::shared_ptr<T>(new T());
+
+	//! get grid iterator
+
+	grid_key_dx_iterator<dim> iterator = data.getIterator();
+
+	//! we iterate trough all the set of objects
+
+	while (iterator.hasNext())
+	{
+		grid_key_dx<dim> key = iterator.next();
+
+		//! Check if the object is inside the subspace
+
+		if (subspace.isBound(data.template get<Point<3,T>::x>(key)))
+		{
+			//! Check if the neighborhood is inside the subspace
+
+			if (borderOrBulk(nb) == true)
+			{
+				// It is border
+
+				ret.bord.push_back(key);
+			}
+			else
+			{
+				// It is bulk
+
+				ret.bulk.push_back(key);
+			}
+		}
+		else
+		{
+			//! it is external
+
+			ret.ext.push_back(key);
+		}
+	}
+}

src/Decomposition/CartDecomposition_unit_test.hpp

+#ifndef CARTDECOMPOSITION_UNIT_TEST_HPP
+#define CARTDECOMPOSITION_UNIT_TEST_HPP
+
+#include "CartDecomposition.hpp"
+#include "mathutil.hpp"
+
+BOOST_AUTO_TEST_SUITE( CartDecomposition_test )
+
+#define SUB_UNIT_FACTOR 64
+
+BOOST_AUTO_TEST_CASE( CartDecomposition_test_use)
+{
+	// Virtual cluster
+	Vcluster vcl(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+
+	CartDecomposition<3,float> dec(vcl);
+
+	// Physical domain
+	Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+	size_t div[3];
+
+	// Get the number of processor and calculate the number of sub-domain
+	// for decomposition
+	size_t n_proc = vcl.getProcessingUnits();
+	size_t n_sub = n_proc * SUB_UNIT_FACTOR;
+
+	// Calculate the number of sub-domain on each dimension
+	for (int i = 0 ; i < 3 ; i++)
+	{div[i] = round_big_2(pow(n_sub,1.0/3));}
+
+	// Decompose
+	dec.setParameters(div,box);
+
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+#endif

src/Decomposition/Decomposition.hpp

+#include "Space/SpaceBox.hpp"
+
+#ifndef DECOMPOSITION_HPP_
+#define DECOMPOSITION_HPP_
+
+/**
+ *
+ * \brief class that store Internal part external and border part of a dataset
+ *
+ */
+
+template <typename T> class dataDiv
+{
+	//! Border part of the data
+	boost::shared_ptr<T> bord;
+	//! internal part of your data
+	boost::shared_ptr<T> inte;
+	//! external part of your data
+	boost::shared_ptr<T> ext;
+};
+
+/*! \brief This class define the domain decomposition interface
+ *
+ * This class define the domain decomposition interface, its main functionality
+ * is to divide a domain in several subspaces
+ *
+ * \tparam T structure that store the dataset
+ * \tparam S type of space is decomposing Real integer complex ...
+ *
+ */
+
+template<typename T, typename S>
+class Decomposition
+{
+	/*! \brief The the internal part of the data set, or the data that
+	 * does not depend from the ghosts layers
+	 *
+	 * \return The internal part of the dataset
+	 *
+	 */
+	virtual T getInternal();
+
+
+	/*! Get the ghost part of the dataset
+	 *
+	 * \return The internal part of the dataset
+	 *
+	 */
+	virtual T getBorder();
+
+	/*! Get the external part of the dataset (outside the ghost)
+	 *
+	 * \return The external part of the dataset
+	 *
+	 */
+	virtual T getExternal();
+
+	//! divide the dataset from internal part and border
+	virtual dataDiv<T> divide();
+
+	//! Get the number of hyper-cube the space id is divided into
+	virtual size_t getNHyperCube(size_t id);
+
+	//! Get the hyper-cube margins
+	virtual std::vector<T> & getHyperCube(size_t id, size_t id_c);
+
+	//! destructor
+	virtual ~Decomposition(){}
+};
+
+#endif

src/Decomposition/DistModel.hpp

+#ifndef DIST_MODEL_HPP
+#define DIST_MODEL_HPP
+
+#include "metis.h"
+
+/*! \brief This class do graph partitioning
+ *
+ * This class do graph partitioning, it use METIS internaly
+ *
+ */
+
+template<typename Graph, typename algorithm>
+class GraphPartitioning
+{
+	//! Structure that store the graph
+	Graph & grp;
+
+	/*! Constructor
+	 *
+	 * It load the graph to partition
+	 *
+	 * \param g Graph to store
+	 *
+	 */
+	GraphPartitioning(Graph & g)
+	:grp(g)
+	{}
+};
+
+#endif

src/Grid/grid_dist_id.hpp

+#ifndef COM_UNIT_HPP
+#define COM_UNIT_HPP
+
+#include <vector>
+#include "Grid/map_grid.hpp"
+#include "VCluster.hpp"
+#include "Space/SpaceBox.hpp"
+#include "mathutil.hpp"
+#include "grid_dist_id_iterator.hpp"
+#include "grid_dist_id_iterator_margin.hpp"
+#include "grid_dist_key.hpp"
+
+#define SUB_UNIT_FACTOR 64
+
+
+/*! \brief This is a distributed grid
+ *
+ * Implementation of a distributed grid with id decomposition. A distributed grid is a grid distributed
+ * across processors. The decomposition is performed on the id of the elements
+ *
+ * [Examples]
+ *
+ * on 1D where the id is from 1 to N
+ * processor k take M contiguous elements
+ *
+ * on 3D where (for example)
+ * processor k take M id-connected elements
+ *
+ * \param dim Dimensionality of the grid
+ * \param T type of grid
+ * \param Decomposition Class that decompose the grid for example CartDecomposition
+ * \param Mem Is the allocator
+ * \param device type of base structure is going to store the data
+ *
+ */
+
+template<unsigned int dim, typename T, typename Decomposition,typename Memory=HeapMemory , typename device_grid=grid_cpu<dim,T> >
+class grid_dist_id
+{
+	// Ghost expansion
+	Box<dim,size_t> ghost;
+
+	//! Local grids
+	Vcluster_object_array<device_grid> loc_grid;
+
+	//! Space Decomposition
+	Decomposition dec;
+
+	//! Size of the grid on each dimension
+	size_t g_sz[dim];
+
+	//! Communicator class
+
+	Vcluster & v_cl;
+
+	/*! \brief Get the grid size
+	 *
+	 * Get the grid size, given a domain, the resolution on it and another spaceBox
+	 * it give the size on all directions of the local grid
+	 *
+	 * \param sp SpaceBox enclosing the local grid
+	 * \param domain Space box enclosing the physical domain or part of it
+	 * \param v_size grid size on this physical domain
+	 *
+	 * \return An std::vector representing the local grid on each dimension
+	 *
+	 */
+	std::vector<size_t> getGridSize(SpaceBox<dim,typename Decomposition::domain_type> & sp, Box<dim,typename Decomposition::domain_type> & domain, size_t (& v_size)[dim])
+	{
+		std::vector<size_t> tmp;
+		for (size_t d = 0 ; d < dim ; d++)
+		{
+			//! Get the grid size compared to the domain space and its resolution
+			typename Decomposition::domain_type dim_sz = (sp.getHigh(d) - sp.getLow(d)) / ((domain.getHigh(d) - domain.getLow(d)) / v_size[d]) + 0.5;
+
+			// push the size of the local grid
+			tmp.push_back(dim_sz);
+		}
+		return tmp;
+	}
+
+	/*! \brief Get the grid size
+	 *
+	 * Get the grid size, given a spaceBox
+	 * it give the size on all directions of the local grid
+	 *
+	 * \param sp SpaceBox enclosing the local grid
+	 * \param sz array to fill with the local grid size on each dimension
+	 *
+	 */
+	void getGridSize(SpaceBox<dim,size_t> & sp, size_t (& v_size)[dim])
+	{
+		for (size_t d = 0 ; d < dim ; d++)
+		{
+			// push the size of the local grid
+			v_size[d] = sp.getHigh(d) - sp.getLow(d);
+		}
+	}
+
+public:
+
+	//! constructor
+	grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[dim], Box<dim,size_t> & ghost)
+	:ghost(ghost),loc_grid(NULL),v_cl(v_cl),dec(dec)
+	{
+		// fill the global size of the grid
+		for (int i = 0 ; i < dim ; i++)	{this->g_sz[i] = g_sz[i];}
+
+		// Get the number of processor and calculate the number of sub-domain
+		// for decomposition
+		size_t n_proc = v_cl.getProcessingUnits();
+		size_t n_sub = n_proc * SUB_UNIT_FACTOR;
+
+		// Calculate the maximum number (before merging) of sub-domain on
+		// each dimension
+		size_t div[dim];
+		for (int i = 0 ; i < dim ; i++)
+		{div[i] = round_big_2(pow(n_sub,1.0/dim));}
+
+		// Create the sub-domains
+		dec.setParameters(div);
+	}
+
+	//! constructor
+	grid_dist_id(size_t (& g_sz)[dim])
+	:v_cl(*global_v_cluster),dec(Decomposition(v_cl))
+	{
+		// fill the global size of the grid
+		for (int i = 0 ; i < dim ; i++)	{this->g_sz[i] = g_sz[i];}
+
+		// first compute a decomposition
+		Create();
+	}
+
+	/*! \brief Get the object that store the decomposition information
+	 *
+	 * \return the decomposition object
+	 *
+	 */
+
+	Decomposition & getDecomposition()
+	{
+		return dec;
+	}
+
+	/*! \brief Create the grid on memory
+	 *
+	 */
+
+	void Create()
+	{
+		// ! Create an hyper-cube approximation.
+		// ! In order to work on grid_dist the decomposition
+		// ! has to be a set of hyper-cube
+
+		dec.hyperCube();
+
+		// Get the number of local grid needed
+
+		size_t n_grid = dec.getNLocalHyperCube();
+
+		// create local grids for each hyper-cube
+
+		loc_grid = v_cl.allocate<device_grid>(n_grid);
+
+		// Size of the grid on each dimension
+		size_t l_res[dim];
+
+		// Allocate the grids
+
+		for (size_t i = 0 ; i < n_grid ; i++)
+		{
+			// Get the local hyper-cube
+
+			SpaceBox<dim,size_t> sp = dec.getLocalHyperCube(i);
+
+			// Calculate the local grid size
+
+			getGridSize(sp,l_res);
+
+			// Set the dimensions of the local grid
+
+			loc_grid.get(i).template resize<Memory>(l_res);
+		}
+	}
+
+	/*! \brief It return an iterator of the bulk part of the grid with a specified margin
+	 *
+	 * For margin we mean that every point is at least m points far from the border
+	 *
+	 * \param m margin
+	 *
+	 * \return An iterator to a grid with specified margins
+	 *
+	 */
+	grid_dist_iterator_margin<dim,device_grid> getBulkIterator(size_t margin)
+	{
+		grid_dist_iterator_margin<dim,device_grid> it(loc_grid,margin);
+
+		return it;
+	}
+
+	//! Destructor
+	~grid_dist_id()
+	{
+	}
+};
+
+#endif

src/Grid/grid_dist_id_iterator.hpp

+/*
+ * grid_dist_id_iterator.hpp
+ *
+ *  Created on: Feb 4, 2015
+ *      Author: Pietro Incardona
+ */
+
+#ifndef GRID_DIST_ID_ITERATOR_HPP_
+#define GRID_DIST_ID_ITERATOR_HPP_
+
+#include "grid_dist_key.hpp"
+#include "Grid/grid.hpp"
+
+/*! \brief Distributed grid iterator
+ *
+ * Iterator across the local element of the distributed grid
+ *
+ */
+
+template<unsigned int dim, typename l_grid>
+class grid_dist_iterator
+{
+	//! grid list counter
+
+	size_t g_c;
+
+	//! List of the grids we are going to iterate
+	std::vector<l_grid> & gList;
+
+	//! Actual iterator
+	grid_key_dx_iterator<dim> a_it;
+
+	public:
+
+	/*! \brief Constructor of the distributed grid
+	 *
+	 * \param gk std::vector of the local grid
+	 *
+	 */
+	grid_dist_iterator(std::vector<l_grid> & gk)
+	:g_c(0),gList(gk)
+	{
+		// Initialize with the current iterator
+		// with the first grid
+
+		a_it = gList[0].getIterator();
+	}
+
+	// Destructor
+	~grid_dist_iterator()
+	{}
+
+	/*! \brief Get the next element
+	 *
+	 * \return the next grid_key
+	 *
+	 */
+
+	grid_key_dx_iterator<dim> operator++()
+	{
+		a_it++;
+
+		// check if a_it is at the end
+
+		if (a_it.isEnd() == false)
+			return *this;
+		else
+		{
+			// switch to the new grid
+
+			g_c++;
+
+			// get the next grid iterator
+
+			a_it = a_it = gList[g_c].getIterator();
+
+			// increment to a valid point
+
+			a_it++;
+		}
+
+		return *this;
+	}
+
+	/*! \brief Check if there is the next element
+	 *
+	 * \return true if there is the next, false otherwise
+	 *
+	 */
+
+	bool isEnd()
+	{
+		// If there are no other grid stop
+
+		if (g_c >= gList.size())
+			return true;
+	}
+
+	/*! \brief Get the actual key
+	 *
+	 * \return the actual key
+	 *
+	 */
+	grid_dist_key_dx<dim> get()
+	{
+		return a_it;
+	}
+};
+
+
+#endif /* GRID_DIST_ID_ITERATOR_HPP_ */

src/Grid/grid_dist_id_iterator_margin.hpp

+/*
+ * grid_dist_id_iterator_sub.hpp
+ *
+ *  Created on: Feb 4, 2015
+ *      Author: Pietro Incardona
+ */
+
+#ifndef GRID_DIST_ID_ITERATOR_SUB_HPP_
+#define GRID_DIST_ID_ITERATOR_SUB_HPP_
+
+#include "VCluster.hpp"
+
+/*! \brief Distributed grid iterator
+ *
+ * Iterator across the local element of the distributed grid
+ *
+ */
+
+template<unsigned int dim, typename device_grid>
+class grid_dist_iterator_margin
+{
+	//! grid list counter
+	size_t g_c;
+
+	//! List of the grids we are going to iterate
+	Vcluster_object_array<device_grid> & gList;
+
+	//! Actual iterator
+	grid_key_dx_iterator_sub<dim> * a_it;
+
+	//! margin of the grid iterator
+	size_t m;
+
+	public:
+
+	/*! \brief Constructor of the distributed grid
+	 *
+	 * \param gk std::vector of the local grid
+	 *
+	 */
+	grid_dist_iterator_margin(Vcluster_object_array<device_grid> & gk, size_t m)
+	:g_c(0),gList(gk),m(m)
+	{
+		// Initialize the current iterator
+		// with the first grid
+
+		a_it = new grid_key_dx_iterator_sub<dim>(gList[0].getSubIterator(m));
+	}
+
+	// Destructor