example fixed

CHANGELOG.md

@@ -9,9 +9,9 @@ All notable changes to this project will be documented in this file.
 - Increaded performance for grid ghost get
 - Introduced forms to increase the performance of the grid iterator in case of stencil code (see example 5_GrayScott)
 - EMatrix wrapped eigen matrices compatibles with vector_dist_id
-- General tuning for high dimension vector_dist_id (up to 50 dimensions)
+- General tuning for high dimension vector_dist_id (up to 50 dimensions) + PS_CMA_ES (Particle-Swarm Covariant Matrix Adaptation Evolution Strategy) example in Numerics
 - Added Discrete element Method example (8_DEM)
-- Introduced map(LOCAL) for fast communication in case we have small moovement
+- Introduced map(LOCAL) for fast communication in case we have small movement
 
 ### Fixed
 

example/Debugging/1_classes/main.cpp

@@ -17,7 +17,6 @@
 #define SE_CLASS3
 #define THROW_ON_ERROR
 #include "Memleak_check.hpp"
-#include "data_type/scalar.hpp"
 #include "Grid/grid_dist_id.hpp"
 #include "Decomposition/CartDecomposition.hpp"
 #include "Point_test.hpp"
@@ -72,7 +71,7 @@ int main(int argc, char* argv[])
 	// * g: ghost extension
 	//
 	//
-	grid_dist_id<3, float, scalar<float[3]>, CartDecomposition<3,float>> * g_dist = new grid_dist_id<3, float, scalar<float[3]>, CartDecomposition<3,float>>(sz,domain,g);
+	grid_dist_id<3, float, aggregate<float[3]>, CartDecomposition<3,float>> * g_dist = new grid_dist_id<3, float, aggregate<float[3]> >(sz,domain,g);
 
 	//
 	// ### WIKI 6 ###

example/Grid/3_gray_scott_3d/main.cpp

@@ -166,7 +166,7 @@ int main(int argc, char* argv[])
 	for (size_t i = 0; i < timeSteps; ++i)
 	{
 		if (i % 300 == 0)
-			std::cout << "STEP: " << i << std::endl;
+		{std::cout << "STEP: " << i << std::endl;}
 
 		//! \cond [stencil get and use] \endcond
 
@@ -175,15 +175,15 @@ int main(int argc, char* argv[])
 		while (it.isNext())
 		{
 			// center point
-			auto Cp = it.getStencilGrid<0>();
+			auto Cp = it.getStencil<0>();
 
 			// plus,minus X,Y,Z
-			auto mx = it.getStencilGrid<1>();
-			auto px = it.getStencilGrid<2>();
-			auto my = it.getStencilGrid<3>();
-			auto py = it.getStencilGrid<4>();
-			auto mz = it.getStencilGrid<5>();
-			auto pz = it.getStencilGrid<6>();
+			auto mx = it.getStencil<1>();
+			auto px = it.getStencil<2>();
+			auto my = it.getStencil<3>();
+			auto py = it.getStencil<4>();
+			auto mz = it.getStencil<5>();
+			auto pz = it.getStencil<6>();
 
 			// update based on Eq 2
 			New.get<U>(Cp) = Old.get<U>(Cp) + uFactor * (

example/Grid/3_gray_scott_3d_vectorization/main.cpp

@@ -167,7 +167,7 @@ void step(grid_dist_id<3, double, aggregate<double>> & OldU,
 
 			out1.store(&U_new.get<0>(Cp),Vc::Unaligned);
 			out2.store(&V_new.get<0>(Cp),Vc::Unaligned);
-	END_LOOP_M
+	END_LOOP_M(Vc::double_v::Size)
 
 	//! \cond [cpp_update] \endcond
 

example/Numerics/PSE/0_Derivative_approx_1D/main.cpp

@@ -100,7 +100,7 @@ int main(int argc, char* argv[])
 	// we create a set of N+1 particles to have a fully covered domain of particles between 0.0 and 4.0
 	// Suppose we have a spacing given by 1.0 you need 4 +1 particles to cover your domain
 	//
-	vector_dist<1,double, aggregate<double>, CartDecomposition<1,double> > vd(Npart+1,box,bc,g);
+	vector_dist<1,double, aggregate<double> > vd(Npart+1,box,bc,g);
 
 	//
 	// ### WIKI 4 ###

example/Vector/1_HDF5_save_load/Makefile

@@ -11,7 +11,7 @@ all: hdf5
 
 
 %.o: %.cpp
-	$(CC) -O0 $(OPT) -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+	$(CC) -O3 $(OPT) -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
 
 hdf5: $(OBJ)
 	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)

example/Vector/3_molecular_dynamic/main_vl.cpp

@@ -62,7 +62,7 @@ constexpr int force = 1;
 
 //! \cond [arg diff] \endcond
 
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, Mem_fast<>, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
 {
 	//! \cond [arg diff] \endcond
 
@@ -150,7 +150,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ve
 
 //! \cond [calc energy vl] \endcond
 
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, Mem_fast<>, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
 {
 	double E = 0.0;
 

example/Vector/4_complex_prop/Makefile

@@ -10,7 +10,7 @@ OBJ_SER = main_ser.o
 all: vect_cp vect_ser
 
 %.o: %.cpp
-	$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+	$(CC) -O0 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
 
 vect_cp: $(OBJ)
 	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)

example/Vector/4_complex_prop/main_ser.cpp

@@ -112,6 +112,15 @@ public:
 
 	//! \cond [pack request] \endcond
 
+	//! \cond [noPointers] \endcond
+
+	static bool noPointers()
+	{
+		return false;
+	}
+
+	//! \cond [noPointers] \endcond
+
 	//! \cond [pack serialize] \endcond
 
 	//! Serialize the data structure
@@ -210,11 +219,12 @@ public:
  *
  * \page Vector_4_complex_prop_ser Vector 4 property serialization
  *
- * In order to make my_struct serializable we need 3 methods
+ * In order to make my_struct serializable we need 4 methods
  *
  * * **packRequest** This method indicate how many byte are needed to serialize this structure
  * * **pack** This method serialize the data-structure
  * * **unpack** This method de-serialize the data structure
+ * * **noPointers()** a static method that inform the OpenFPM sub-system that the structure has no pointers inside 
  *
  * ### packRequest ###
  *
@@ -294,6 +304,12 @@ public:
  *
  * \snippet Vector/4_complex_prop/main_ser.cpp unpacker ser other
  *
+ * ### noPointers ###
+ *
+ * This method inform the sub-system that the custom structure does not have pointers
+ *
+ * \snippet Vector/4_complex_prop/main_ser.cpp noPointers
+ *
  * ### Constructor and destructor and operator= ###
  *
  * Constructor and destructor are not releated to serialization and de-serialization concept.

example/Vector/4_multiphase_celllist_verlet/Makefile

@@ -7,7 +7,7 @@ LDIR =
 OBJ = main.o
 
 %.o: %.cpp
-	$(CC) -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+	$(CC) -O0 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
 
 multip: $(OBJ)
 	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)

example/Vector/4_multiphase_celllist_verlet/main.cpp

@@ -237,7 +237,11 @@ int main(int argc, char* argv[])
 	//! \cond [create multi-phase multi verlet] \endcond
 
 	// This function create an "Empty" Multiphase Cell List from all the phases
-	auto CL_all = createCellListM<2>(phases,r_cut);
+
+	// We just create a cell list with slightly bigget r_cut to avoid error in Verlet creation
+	// because of round off errors
+	float r_cut2 = r_cut*1.00001;
+	auto CL_all = createCellListM<2>(phases,r_cut2);
 
 	// This create a Verlet-list between phase0 and all the other phases
 	auto NNver0_all = createVerletM<2>(0,phases.get(0),phases,CL_all,r_cut);

example/Vector/5_molecular_dynamic_sym/main.cpp

@@ -76,7 +76,8 @@ constexpr int force = 1;
 
 //! \cond [calc forces vl] \endcond
 
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+template<typename VerletList>
+void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList & NN, double sigma12, double sigma6, double r_cut)
 {
 	// Reset force on the ghost
 
@@ -186,7 +187,8 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ve
 
 //! \cond [calc energy vl] \endcond
 
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+template<typename VerletList>
+double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList & NN, double sigma12, double sigma6, double r_cut)
 {
 	double E = 0.0;
 

example/Vector/5_molecular_dynamic_sym_crs/main.cpp

@@ -127,7 +127,8 @@ constexpr int force = 1;
 
 //! \cond [calc forces vl] \endcond
 
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+template<typename VerletList>
+void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList & NN, double sigma12, double sigma6, double r_cut)
 {
 	// Reset force on the ghost
 
@@ -163,7 +164,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ve
 
 		// Get an iterator over the neighborhood particles of p
 		// Note that in case of symmetric
-		auto Np = NN.getNNIterator<NO_CHECK>(p);
+		auto Np = NN.template getNNIterator<NO_CHECK>(p);
 
 		// For each neighborhood particle ...
 		while (Np.isNext())
@@ -242,7 +243,8 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ve
 
 //! \cond [calc energy vl] \endcond
 
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
+template<typename VerletList>
+double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList & NN, double sigma12, double sigma6, double r_cut)
 {
 	double E = 0.0;
 
@@ -262,7 +264,7 @@ double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd,
 		Point<3,double> xp = vd.getPos(p);
 
 		// Get an iterator over the neighborhood particles of p
-		auto Np = NN.getNNIterator<NO_CHECK>(p);
+		auto Np = NN.template getNNIterator<NO_CHECK>(p);
 
 		double Ep = E;
 

src/Decomposition/Distribution/parmetis_util.hpp

@@ -14,7 +14,7 @@
 #include "VCluster/VCluster.hpp"
 #include "Graph/ids.hpp"
 
-#define PARMETSI_ERROR_OBJECT std::runtime_error("Runtime Parmetis error");
+#define PARMETIS_ERROR_OBJECT std::runtime_error("Runtime Parmetis error");
 
 
 /*! \brief Metis graph structure
@@ -213,6 +213,16 @@ public:
 	Parmetis(Vcluster & v_cl, size_t nc)
 	:v_cl(v_cl), nc(nc),n_dec(0)
 	{
+#ifdef SE_CLASS1
+
+		if (sizeof(idx_t) != 8)
+		{
+			std::cerr << __FILE__ << ":" << __LINE__ << " Error detected invalid installation of Parmetis. OpenFPM support Parmetis/Metis version with 64 bit idx_t" << std::endl;
+			ACTION_ON_ERROR(PARMETIS_ERROR_OBJECT);
+		}
+
+#endif
+
 		// TODO Move into VCluster
 		MPI_Comm_dup(MPI_COMM_WORLD, &comm);
 
@@ -246,16 +256,6 @@ public:
 	 */
 	~Parmetis()
 	{
-#ifdef SE_CLASS1
-
-		if (sizeof(idx_t) != 8)
-		{
-			std::cerr << __FILE__ << ":" << __LINE__ << " Error detected invalid installation of Parmetis. OpenFPM support Parmetis/Metis version with 64 bit idx_t" << std::endl;
-			ACTION_ON_ERROR(PARMETIS_ERROR_OBJECT);
-		}
-
-#endif
-
 		// Deallocate the Mg structure
 		if (Mg.nvtxs != NULL)
 		{

src/Grid/Iterators/grid_dist_id_iterator.hpp

@@ -59,9 +59,6 @@ class grid_dist_iterator<dim,device_grid,FREE,stencil>
 	//! stop point (is the grid size)
 	grid_key_dx<dim> stop;
 
-	// device grid pointer
-	device_grid * dg;
-
 	/*! \brief from g_c increment g_c until you find a valid grid
 	 *
 	 */
@@ -244,18 +241,6 @@ class grid_dist_iterator<dim,device_grid,FREE,stencil>
 	{
 		return grid_dist_lin_dx(g_c,a_it.template getStencil<id>());
 	}
-
-	/*! \brief Return the stencil point offset
-	 *
-	 * \tparam id
-	 *
-	 * \return linearized distributed key
-	 *
-	 */
-	template<unsigned int id> inline grid_dist_g_dx<device_grid> getStencilGrid()
-	{
-		return grid_dist_g_dx<device_grid>(dg,a_it.template getStencil<id>());
-	}
 };