Distributed vector and grid compiling and passing the test

src/.deps/pdata-main.Po

@@ -1293,8 +1293,12 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
  ../../OpenFPM_data/src/Space/SpaceBox.hpp \
  ../../OpenFPM_data/src/Space/Shape/Point.hpp \
  ../../OpenFPM_data/src/Space/Shape/Box.hpp \
- ../../OpenFPM_data/src/Space/Ghost.hpp Grid/grid_dist_id_iterator.hpp \
- Grid/grid_dist_key.hpp ../../OpenFPM_data/src/Point_test.hpp \
+ ../../OpenFPM_data/src/Space/Ghost.hpp \
+ ../../OpenFPM_data/src/Space/SpaceBox.hpp Grid/grid_dist_id_iterator.hpp \
+ Grid/grid_dist_key.hpp \
+ ../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
+ ../../OpenFPM_data/src/Space/Matrix.hpp \
+ ../../OpenFPM_data/src/Point_test.hpp \
  ../../OpenFPM_data/src/base_type.hpp \
  ../../OpenFPM_data/src/Point_orig.hpp \
  ../../OpenFPM_data/src/Grid/Encap.hpp \
@@ -1367,8 +1371,6 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
  /usr/include/boost/iostreams/detail/path.hpp \
  /usr/include/boost/config/abi_prefix.hpp \
  /usr/include/boost/config/abi_suffix.hpp dec_optimizer.hpp \
- ../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
- ../../OpenFPM_data/src/Space/Matrix.hpp \
  /usr/include/c++/4.8.3/unordered_map \
  /usr/include/c++/4.8.3/bits/hashtable.h \
  /usr/include/c++/4.8.3/bits/hashtable_policy.h \
@@ -4254,10 +4256,16 @@ Grid/grid_dist_id.hpp:
 
 ../../OpenFPM_data/src/Space/Ghost.hpp:
 
+../../OpenFPM_data/src/Space/SpaceBox.hpp:
+
 Grid/grid_dist_id_iterator.hpp:
 
 Grid/grid_dist_key.hpp:
 
+../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp:
+
+../../OpenFPM_data/src/Space/Matrix.hpp:
+
 ../../OpenFPM_data/src/Point_test.hpp:
 
 ../../OpenFPM_data/src/base_type.hpp:
@@ -4414,10 +4422,6 @@ metis_util.hpp:
 
 dec_optimizer.hpp:
 
-../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp:
-
-../../OpenFPM_data/src/Space/Matrix.hpp:
-
 /usr/include/c++/4.8.3/unordered_map:
 
 /usr/include/c++/4.8.3/bits/hashtable.h:

src/Decomposition/CartDecomposition.hpp

@@ -687,7 +687,7 @@ p1[0]<-----+         +----> p2[0]
 		{
 			if (ghost.template getLow(i) >= domain.template getHigh(i) / gr.size(i) || ghost.template getHigh(i)  >= domain.template getHigh(i) / gr.size(i))
 			{
-				std::cerr << "Error: Ghost are bigger that one domain" << "\n";
+				std::cerr << "Error " << __FILE__ << ":" << __LINE__  << " : Ghost are bigger than one domain" << "\n";
 			}
 		}
 #endif
@@ -1186,6 +1186,7 @@ p1[0]<-----+         +----> p2[0]
 	 * 1) p_sub_X.vtk domain for the processor X as union of sub-domain
 	 * 2) sub_np_c_X.vtk sub-domain of the near processors contiguous to the processor X (Color encoded)
 	 * 3) sub_X_inte_g_np.vtk Intersection between the ghosts of the near processors and the processors X sub-domains (Color encoded)
+	 * 4) sub_X_ghost.vtk ghost for the processor X (Color encoded)
 	 *
 	 * where X is the processor number
 	 *
@@ -1216,11 +1217,22 @@ p1[0]<-----+         +----> p2[0]
 		{
 			for (size_t s = 0 ; s < box_nn_processor_int.get(p).size() ; s++)
 			{
-				auto & diocane = box_nn_processor_int.get(p).get(s).nbx;
-				vtk_box3.add(diocane);
+				vtk_box3.add(box_nn_processor_int.get(p).get(s).nbx);
 			}
 		}
 		vtk_box3.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_inte_g_np") + std::string(".vtk"));
+
+
+		//! sub_X_ghost.vtk ghost for the processor X (Color encoded)
+		VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box4;
+		for (size_t p = 0 ; p < box_nn_processor_int.size() ; p++)
+		{
+			for (size_t s = 0 ; s < box_nn_processor_int.get(p).size() ; s++)
+			{
+				vtk_box4.add(box_nn_processor_int.get(p).get(s).bx);
+			}
+		}
+		vtk_box4.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_ghost") + std::string(".vtk"));
 	}
 };
 

src/Grid/grid_dist_id.hpp

@@ -8,36 +8,35 @@
 #include "mathutil.hpp"
 #include "grid_dist_id_iterator.hpp"
 #include "grid_dist_key.hpp"
+#include "NN/CellList/CellDecomposer.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]
+ * Implementation of a distributed grid with decomposition on the ids.
+ * A distributed grid is a grid distributed across processors.
+ * The decomposition is performed on the ids of the elements
  *
- * 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 St Type of space where the grid is living
+ * \param T object the grid is storing
  * \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> >
+template<unsigned int dim, typename St, typename T, typename Decomposition,typename Memory=HeapMemory , typename device_grid=grid_cpu<dim,T> >
 class grid_dist_id
 {
+	// Domain
+	Box<dim,St> domain;
+
 	// Ghost expansion
-	Box<dim,size_t> ghost;
+	Ghost<dim,St> ghost;
 
 	//! Local grids
 	Vcluster_object_array<device_grid> loc_grid;
@@ -48,8 +47,10 @@ class grid_dist_id
 	//! Size of the grid on each dimension
 	size_t g_sz[dim];
 
-	//! Communicator class
+	//! Structure that divide the space into cells
+	CellDecomposer_sm<dim,St> cd_sm;
 
+	//! Communicator class
 	Vcluster & v_cl;
 
 	/*! \brief Get the grid size
@@ -99,8 +100,8 @@ class grid_dist_id
 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)
+	grid_dist_id(Vcluster v_cl, Decomposition & dec, const size_t (& g_sz)[dim], const Box<dim,St> & domain, const Ghost<dim,T> & ghost)
+	:domain(domain),cd_sm(domain,g_sz,0),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];}
@@ -123,9 +124,14 @@ public:
 		Create();
 	}
 
-	//! constructor
-	grid_dist_id(size_t (& g_sz)[dim])
-	:dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
+	/*! \brief Constrcuctor
+	 *
+	 * \param g_sz array with the grid size on each dimension
+	 * \param domain
+	 *
+	 */
+	grid_dist_id(const size_t (& g_sz)[dim],const Box<dim,St> & domain)
+	:domain(domain),cd_sm(domain,g_sz,0),ghost(0),dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
 	{
 		// fill the global size of the grid
 		for (int i = 0 ; i < dim ; i++)	{this->g_sz[i] = g_sz[i];}
@@ -141,11 +147,8 @@ public:
 		for (int i = 0 ; i < dim ; i++)
 		{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/dim));}
 
-		// Box
-		Box<dim,size_t> b(g_sz);
-
 		// Create the sub-domains
-		dec.setParameters(div,b);
+		dec.setParameters(div,domain);
 
 		// Create local grid
 		Create();
@@ -168,10 +171,13 @@ public:
 
 	void Create()
 	{
+		// Box used for rounding error
+		Box<dim,St> rnd_box;
+		for (size_t i = 0 ; i < dim ; i++)	{rnd_box.setHigh(i,0.5); rnd_box.setLow(i,0.5);}
+
 		// ! 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
@@ -188,15 +194,34 @@ public:
 		for (size_t i = 0 ; i < n_grid ; i++)
 		{
 			// Get the local hyper-cube
+			SpaceBox<dim,St> sp = dec.getLocalHyperCube(i);
 
-			SpaceBox<dim,size_t> sp = dec.getLocalHyperCube(i);
+			// Convert sp into grid units
+			sp /= cd_sm.getCellBox().getP2();
 
-			// Calculate the local grid size
+			// enlarge by 0.5 for rounding
+			sp.enlarge(rnd_box);
 
-			getGridSize(sp,l_res);
+			// Convert from SpaceBox<dim,float> to SpaceBox<dim,size_t>
+			SpaceBox<dim,size_t> sp_t = sp;
 
-			// Set the dimensions of the local grid
+			// convert the ghost from space coordinate to grid units
+			Ghost<dim,St> g_int = ghost;
+			g_int /= cd_sm.getCellBox().getP2();
+
+			// enlarge by 0.5 for rounding
+			g_int.enlarge(rnd_box);
+
+			// convert from Ghost<dim,St> to Ghost<dim,size_t>
+			Ghost<dim,size_t> g_int_t = g_int;
 
+			// Enlarge sp with the Ghost size
+			sp_t.enlarge(g_int_t);
+
+			// Get the local size
+			for (size_t i = 0 ; i < dim ; i++) {l_res[i] = sp_t.getHigh(i) - sp_t.getLow(i);}
+
+			// Set the dimensions of the local grid
 			loc_grid.get(i).template resize<Memory>(l_res);
 		}
 	}
@@ -251,13 +276,7 @@ public:
  * 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
+ * 1D specialization
  *
  * \param dim Dimensionality of the grid
  * \param T type of grid
@@ -270,8 +289,8 @@ public:
 template<typename T, typename Decomposition,typename Memory , typename device_grid >
 class grid_dist_id<1,T,Decomposition,Memory,device_grid>
 {
-	// Ghost expansion
-	Box<1,size_t> ghost;
+	// Ghost
+	Ghost<1,T> ghost;
 
 	//! Local grids
 	Vcluster_object_array<device_grid> loc_grid;
@@ -327,7 +346,7 @@ class grid_dist_id<1,T,Decomposition,Memory,device_grid>
 public:
 
 	//! constructor
-	grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[1], Box<1,size_t> & ghost)
+	grid_dist_id(Vcluster v_cl, Decomposition & dec, size_t (& g_sz)[1], Box<1,T> & ghost)
 	:ghost(ghost),loc_grid(NULL),v_cl(v_cl)
 	{
 		// fill the global size of the grid
@@ -339,7 +358,7 @@ public:
 
 	//! constructor
 	grid_dist_id(size_t (& g_sz)[1])
-	:v_cl(*global_v_cluster)
+	:v_cl(*global_v_cluster),ghost(0)
 	{
 		// fill the global size of the grid
 		for (int i = 0 ; i < 1 ; i++)	{this->g_sz[i] = g_sz[i];}

src/Grid/grid_dist_id_unit_test.hpp

@@ -6,10 +6,10 @@
 
 BOOST_AUTO_TEST_SUITE( grid_dist_id_test )
 
-template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2, scalar<float>, CartDecomposition<2,size_t>> & g_dist)
+template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> & g_dist)
 {
 	// scalar
-	typedef scalar<size_t> S;
+	typedef scalar<float> S;
 
 	// iterator
 
@@ -30,6 +30,9 @@ template<typename iterator> void jacobi_iteration(iterator g_it, grid_dist_id<2,
 
 BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
 {
+	// Domain
+	Box<2,float> domain({0.0,0.0},{1.0,1.0});
+
 	// Initialize the global VCluster
 	init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
 
@@ -38,7 +41,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
 
 	// Distributed grid with id decomposition
 
-	grid_dist_id<2, scalar<float>, CartDecomposition<2,size_t>> g_dist(sz);
+	grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> g_dist(sz,domain);
 
 	// get the domain iterator
 

src/Vector/vector_dist_unit_test.hpp

@@ -94,9 +94,10 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 		++it;
 	}
 
-	// set the ghost based on the radius cut off
-	Ghost<2,float> g(spacing.get(0));
+	// set the ghost based on the radius cut off (make just a little bit smaller than the spacing)
+	Ghost<2,float> g(spacing.get(0) - spacing .get(0) * 0.0001);
 
+	// set the ghost
 	vd.setGhost(g);
 
 	//! Output the decomposition
@@ -131,20 +132,30 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 
 		bool is_in = false;
 		size_t b = 0;
+		size_t lb = 0;
 
 		// check if the received data is in one of the ghost boxes
 		for ( ; b < dec.getNGhostBox() ; b++)
 		{
 			if (dec.getGhostBox(b).isInside(vd.getPos<s::x>(key)) == true)
-			{is_in = true; break;}
+			{
+				is_in = true;
+
+				// Add
+				vb.get(b)++;
+				lb = b;
+			}
 		}
 		BOOST_REQUIRE_EQUAL(is_in,true);
 
 		// Check that the particle come from the correct processor
-		BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getGhostBoxProcessor(b));
+		BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getGhostBoxProcessor(lb));
 
-		// Add
-		vb.get(b)++;
+		if (b == 0)
+		{
+			int debug = 0;
+			debug++;
+		}
 
 		++g_it;
 	}