Fixes in CartDecomposition and latest changes

configure.ac

@@ -38,7 +38,7 @@ m4_ifdef([AX_BLAS],,[m4_include([m4/ax_blas.m4])])
 m4_ifdef([AX_LAPACK],,[m4_include([m4/ax_lapack.m4])])
 m4_ifdef([AX_SUITESPARSE],,[m4_include([m4/ax_suitesparse.m4])])
 m4_ifdef([AX_EIGEN],,[m4_include([m4/ax_eigen.m4])])
-
+m4_ifdef([AX_LIB_HDF5],,[m4_include([m4/ax_lib_hdf5.m4])]])
 
 case $host_os in
    *cygwin*)
@@ -111,6 +111,17 @@ fi
 IMMDX_LIB_METIS([],[echo "Cannot detect metis, use the --with-metis option if it is not installed in the default location"
                     exit 201])
 
+#########
+
+## Check for HDF5
+
+AX_LIB_HDF5([parallel])
+
+if test x"$with_hdf5" = x"no"; then
+    echo "Cannot detect hdf5, use the --with-hdf5 option if it is not installed in the default location"
+    exit 207
+fi
+
 ########
 
 ## Enable scan coverty
@@ -134,7 +145,7 @@ fi
 ## Check for parMetis
 
 IMMDX_LIB_PARMETIS([],[echo "Cannot detect parmetis, use the --with-parmetis option if it is not installed in the default location"
-                    exit 203])
+                    exit 208])
 
 ####### include OpenFPM_devices include path
 

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

@@ -204,7 +204,7 @@ int main(int argc, char* argv[])
 	}
 
 	//
-	// ### WIKI 6 ###
+	// ### WIKI 7 ###
 	//
 	// We create a CellList with cell spacing 12 sigma
 	//
@@ -218,14 +218,13 @@ int main(int argc, char* argv[])
     double linf = 0.0;
 
 	//
-	// ### WIKI 6 ###
+	// ### WIKI 8 ###
 	//
     // For each particle get the neighborhood of each particle
     //
     // This cycle is literally the formula from PSE operator approximation
-	//
-    //
     //
+    // \$ \frac{1}{\epsilon^{2}} h (u_{q} - u_{p}) \eta_{\epsilon}(x_q - x_p) \$
     //
 
     auto it_p = vd.getDomainIterator();
@@ -288,7 +287,7 @@ int main(int argc, char* argv[])
     }
 
 	//
-	// ### WIKI 7 ###
+	// ### WIKI 9 ###
 	//
     // Calculate the maximum infinity norm across processors and
     // print it
@@ -301,7 +300,7 @@ int main(int argc, char* argv[])
     	std::cout << "Norm infinity: " << linf << "\n";
 
 	//
-	// ### WIKI 8 ###
+	// ### WIKI 10 ###
 	//
 	// Deinitialize the library
 	//

example/Vector/1_celllist/Makefile

+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+	$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+cell: $(OBJ)
+	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: cell
+
+.PHONY: clean all
+
+clean:
+	rm -f *.o *~ core cell
+

example/Vector/1_verlet/Makefile

+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+	$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+verlet: $(OBJ)
+	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: vect
+
+.PHONY: clean all
+
+clean:
+	rm -f *.o *~ core verlet
+

install

-#! /bin/bash
-
-source script/help
-source script/discover_os
-source script/show_solutions
-source script/pre_req
-source script/remove_old
-
-##
-
-install_req=1
-i_dir=" "
-sq=0
-
-while getopts :di:shc: FLAG; do
-  case $FLAG in
-    d)
-      echo "Disable depencencies installation"
-      install_req=0
-      ;;
-    i)
-      echo "Setting dependencies installation dir: $OPTARG"
-      i_dir=$OPTARG
-      ;;
-    s)
-      echo "Skipping user cin"
-      sq=1
-      ;;
-    c)
-      echo "Fowarding options $OPTARG to configure script"
-      configure_options=$OPTARG
-      ;;
-    h)  #show help
+	#! /bin/bash
+
+	source script/help
+	source script/discover_os
+	source script/show_solutions
+	source script/pre_req
+	source script/remove_old
+
+	##
+
+	install_req=1
+	i_dir=" "
+	sq=0
+
+	while getopts :di:shc: FLAG; do
+	  case $FLAG in
+	    d)
+	      echo "Disable depencencies installation"
+	      install_req=0
+	      ;;
+	    i)
+	      echo "Setting dependencies installation dir: $OPTARG"
+	      i_dir=$OPTARG
+	      ;;
+	    s)
+	      echo "Skipping user cin"
+	      sq=1
+	      ;;
+	    c)
+	      echo "Fowarding options $OPTARG to configure script"
+	      configure_options=$OPTARG
+	      ;;
+	    h)  #show help
       HELP
       ;;
     \?) #unrecognized option - are fowarded to configure
@@ -143,6 +143,8 @@ BOOST_installed=0
 LAPACK_installed=0
 SUITESPARSE_installed=0
 EIGEN_installed=0
+HDF5_installed=0
+H5PART_installed=0
 blas_options=""
 conf_err=1
 
@@ -219,15 +221,24 @@ else
             ./script/install_EIGEN.sh $i_dir $compiler_opt
             configure_options=" $configure_options --with-eigen=$i_dir/EIGEN "
             EIGEN_installed=1
-	elif [ $conf_err -ne 207 ]; then
+	elif [ $conf_err -eq 208 ]; then
             echo "ParMetis not found try to install"
             if [ $PARMETIS_installed -eq 1  ]; then
                 echo "Error the installation of ParMETIS failed"
                 exit 1
             fi
-            ./script/install_ParMetis.sh $i_dir $compiler_gcc $compiler_gpp
+            ./script/install_Parmetis.sh $i_dir $compiler_gcc $compiler_gpp
             PARMETIS_installed=1
             configure_options=" $configure_options --with-parmetis=$i_dir/PARMETIS "
+        elif [ $conf_err -eq 207 ]; then
+            echo "HDF5 not found try to install"
+            if [ $HDF5_installed -eq 1 ]; then
+                echo "Error the installation of HDF5 failed"
+                exit 1	
+            fi
+            ./script/install_HDF5.sh $i_dir $compiler_opt
+            configure_options=" $configure_options --with-hdf5=$i_dir/HDF5/bin/h5pcc "
+            HDF5_installed=1
         elif [ $conf_err -ne 0 ]; then
             echo "I do not know how to recover from this error"
             exit 1
@@ -326,6 +337,20 @@ if [ $SUITESPARSE_installed -eq 1 ]; then
     echo -e "\033[1m  export DYLD_LIBRARY_PATH=\"\$DYLD_LIBRARY_PATH:$i_dir/SUITESPARSE/lib\" \033[0m"
   fi
 fi
+if [ $EIGEN_installed -eq 1 ]; then
+  echo ""
+  echo -e "\033[1;34;5m ---------------------------------------  \033[0m"
+  echo -e "\033[1;34;5m --------------- EIGEN ----------------- \033[0m"
+  echo -e "  EIGEN has been installed into: \033[1m $i_dir/EIGEN \033[0m"
+  echo ""
+fi
+if [ $HDF5_installed -eq 1 ]; then
+  echo ""
+  echo -e "\033[1;34;5m ---------------------------------------  \033[0m"
+  echo -e "\033[1;34;5m ---------------- HDF5 ----------------- \033[0m"
+  echo -e "  HDF5 has been installed into: \033[1m $i_dir/HDF5 \033[0m"
+  echo ""
+fi
 echo ""
 echo ""
 if [ $conf_err -ne 0 ]; then

openfpm_data @ 2fe8dee2

-Subproject commit a0c140b7772c3b39a817f03d3da76b7a60a9c074
+Subproject commit 2fe8dee2be9e818c1ff8d876bf99a6ce8f591d17

openfpm_io @ 59f5019f

-Subproject commit d5d691407e392ca64094d1b2a6008b5ca33eefe9
+Subproject commit 59f5019f8f3acc6401af7422f19d61dd225e1a21

script/detect_fortran

@@ -8,8 +8,6 @@ function detect_fortran()
       return
     fi
 
-    echo -e "$1 \033[92;1m SUCCESS \033[0m"
-
     dgc_ret=1
 }
 

script/install_HDF5.sh

+#! /bin/bash
+
+# check if the directory $1/HDF5 exist
+
+if [ -d "$1/HDF5" ]; then
+  echo "HDF5 already installed"
+  exit 0
+fi
+
+wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.8.16.tar.bz2
+tar -xf hdf5-1.8.16.tar.bz2
+cd hdf5-1.8.16
+CC=mpicc ./configure --enable-parallel --prefix=$1/HDF5
+make -j 4
+mkdir $1/HDF5
+make install

script/install_MPI.sh

@@ -7,7 +7,7 @@ if [ -d "$1/MPI" ]; then
   exit 0
 fi
 
-wget http://www.open-mpi.de/software/ompi/v1.8/downloads/openmpi-1.8.7.tar.bz2
+wget http://ppmcore.mpi-cbg.de/upload/openmpi-1.8.7.tar.bz2
 tar -xvf openmpi-1.8.7.tar.bz2
 cd openmpi-1.8.7
 

script/install_Parmetis.sh

@@ -10,8 +10,9 @@ fi
 wget http://ppmcore.mpi-cbg.de/upload/parmetis-4.0.3.tar.gz
 tar -xf parmetis-4.0.3.tar.gz
 cd parmetis-4.0.3
+make config prefix=$1/PARMETIS
 make -j 4
-if [ $? -eq 0 ]; then
+if [ $? -ne 0 ]; then
     echo "PARMETIS error installing"
     exit 0
 fi

src/Decomposition/CartDecomposition_ext.hpp

+/*
+ * CartDecomposition_ext.hpp
+ *
+ *  Created on: Mar 6, 2016
+ *      Author: i-bird
+ */
+
+#ifndef SRC_DECOMPOSITION_CARTDECOMPOSITION_EXT_HPP_
+#define SRC_DECOMPOSITION_CARTDECOMPOSITION_EXT_HPP_
+
+template<unsigned int dim, typename T, typename Memory = HeapMemory, typename Distribution = ParMetisDistribution<dim, T>>
+class CartDecomposition;
+
+/**
+ * \brief This class decompose a space into sub-sub-domains and distribute them across processors
+ *
+ * \tparam dim is the dimensionality of the physical domain we are going to decompose.
+ * \tparam T type of the space we decompose, Real, Integer, Complex ...
+ * \tparam Memory Memory factory used to allocate memory
+ * \tparam Distribution type of distribution, can be ParMetisDistribution or MetisDistribution
+ *
+ * Most of the functionality is the same as CartDecomposition so refer to that class for more information
+ *
+ * The additional functionality is the possibility to produce an extended decomposition, in figure is
+ * show what we mean with extended
+ *
+ * \see CartDecomposition
+ *
+ *
+ *
+ * ### Create a Cartesian decomposition object on a Box space, distribute, calculate internal and external ghost boxes
+ * \snippet CartDecomposition_unit_test.hpp Create CartDecomposition
+ *
+ */
+
+template<unsigned int dim, typename T, typename Memory = HeapMemory, typename Distribution = ParMetisDistribution<dim, T>>
+class CartDecomposition_ext: public CartDecomposition<dim,T,Memory,Distribution>
+{
+private:
+
+	/*! \brief It copy the sub-domains into another CartesianDecomposition object extending them
+	 *
+	 * \see duplicate (in case of extended domain)
+	 *
+	 * \param cart Cartesian decomposition object
+	 * \param box Extended domain
+	 *
+	 */
+	void extend_subdomains(const CartDecomposition<dim,T,Memory,Distribution> & dec, const ::Box<dim,T> & ext_dom)
+	{
+		// Box
+		typedef ::Box<dim,T> b;
+
+		this->bbox.zero();
+
+		for (size_t i = 0 ; i < dim ; i++)
+		{
+			this->ss_box.setLow(i,0.0);
+			this->ss_box.setHigh(i,ext_dom.getHigh(i) - ext_dom.getLow(i));
+		}
+
+		// Extend sub-domains
+		for (size_t i = 0 ; i < dec.sub_domains.size() ; i++)
+		{
+			::Box<dim,T> box;
+
+			// Calculate the extended box
+			for (size_t j = 0 ; j < dim ; j++)
+			{
+				if (dec.sub_domains.template get<b::p1>(i)[j] == dec.domain.getLow(j))
+					box.setLow(j,ext_dom.getLow(j));
+				else
+					box.setLow(j,dec.sub_domains.template get<b::p1>(i)[j]);
+
+				if (dec.sub_domains.template get<b::p2>(i)[j] == dec.domain.getHigh(j))
+					box.setHigh(j,ext_dom.getHigh(j));
+				else
+					box.setHigh(j,dec.sub_domains.template get<b::p2>(i)[j]);
+			}
+
+			// add the subdomain
+			this->sub_domains.add(box);
+
+			// Calculate the bound box
+			this->bbox.enclose(box);
+
+			// Create the smallest box contained in all sub-domain
+			this->ss_box.contained(box);
+		}
+	}
+
+	/*! \brief Extend the fines for the new Cartesian decomposition
+	 *
+	 * \param new_fines extended fine_s
+	 * \param old_fines old fine_s
+	 *
+	 */
+	void extend_fines(const CartDecomposition<dim,T> & dec)
+	{
+		// Extension, first we calculate the extensions of the new domain compared
+		// to the old one in cell units (each cell unit is a sub-sub-domain)
+		::Box<dim,size_t> ext;
+		// Extension of the new fines structure
+		::Box<dim,size_t> n_fines_ext;
+		// Extension of the old fines structure
+		::Box<dim,size_t> o_fines_ext;
+
+		size_t sz_new[dim];
+		size_t sz_old[dim];
+
+		for (size_t i = 0; i < dim ; i++)
+		{
+			size_t p1 = (dec.domain.getLow(i) - dec.domain.getLow(i)) / dec.cd.getCellBox().getHigh(i) + 1;
+			size_t p2 = (dec.domain.getLow(i) - dec.domain.getLow(i)) / dec.cd.getCellBox().getHigh(i) + 1;
+
+			ext.setLow(i,p1);
+			ext.setHigh(i,p2);
+			sz_new[i] = p1+p2+dec.cd.getGrid().size(i);
+			sz_old[i] = dec.cd.getGrid().size(i);
+		}
+
+		grid_sm<dim,void> info_new(sz_new);
+		grid_sm<dim,void> info_old(sz_old);
+
+		// resize the new fines
+		this->fine_s.resize(info_new.size());
+
+		// we create an iterator that iterate across the full new fines
+		grid_key_dx_iterator<dim> fines_t(info_new);
+
+		while (fines_t.isNext())
+		{
+			auto key = fines_t.get();
+
+			// new_fines is bigger than old_fines structure
+			// out of bound key must be adjusted
+			// The adjustment produce a natural extension
+			// a representation can be seen in the figure of
+			// CartDecomposition duplicate function with extended domains
+
+			grid_key_dx<dim> key_old;
+			for (size_t i = 0 ; i < dim ; i++)
+			{
+				key_old.set_d(i,(long int)key.get(i) - ext.getLow(i));
+				if (key_old.get(i) < 0)
+					key_old.set_d(i,0);
+				else if(key_old.get(i) >= (long int)info_old.size(i) )
+					key_old.set_d(i,info_old.size(i)-1);
+			}
+
+			this->fine_s.get(info_new.LinId(key)) = dec.fine_s.get(info_old.LinId(key_old));
+
+			++fines_t;
+		}
+
+		this->gr.setDimensions(sz_new);
+
+		// the new extended CellDecomposer must be consistent with the old cellDecomposer.
+		this->cd.setDimensions(dec.cd,ext);
+	}
+
+public:
+
+	/*! \brief Cartesian decomposition constructor
+	 *
+	 * \param v_cl VCluster
+	 *
+	 */
+	CartDecomposition_ext(Vcluster & v_cl)
+	:CartDecomposition<dim,T,Memory,Distribution>(v_cl)
+	{
+	}
+
+	typedef CartDecomposition<dim,T,Memory,Distribution> base_type;
+
+	/*! \brief It create another object that contain the same decomposition information but with different ghost boxes and an extended domain
+	 *
+	 * The domain extension is produced extending the boxes at the border like in figure
+	 *
+	 * \verbatim
+	 *
++--------------^--------^----------^----------+
+|              |        |          |          |
+|        A     |    E   |     F    |    N     |
+|    +-----------------------------------+---->
+|    |         |        |          |     |    |
+|  A |   A     |        |     F    |     |    |
+|    |         |        |          |     |    |
+|    |         |    E   +----------+  N  |  N |
+<--------------+        |          |     |    |
+|    |         |        |          |     |    |
+|    |         |        |     G    |     |    |
+|    |         |        |          +---------->
+|  B |   B     |        +----------+     |    |
+|    |         +--------+          |  M  |  M |
+|    |         |        |     H    |     |    |
+|    |         |        +-----+----+---------->
+<--------------+    D   |     |          |    |
+|    |         |        |  I  |     L    |  L |
+|  C |   C     |        |     |          |    |
+|    |         |        |     |          |    |
+|    +-----------------------------------+    |
+|              |        |     |               |
+|        C     |    D   |  I  |     L         |
++--------------v--------v-----v---------------+
+
+	 *
+	 * \endverbatim
+	 *
+	 * \param g ghost
+	 * \param domain extended domain (MUST be extended)
+	 *
+	 * \return a duplicated decomposition with different ghost boxes and an extended domain
+	 *
+	 */
+	void setParameters(const CartDecomposition<dim,T,Memory,Distribution> & dec, const Ghost<dim,T> & g, const ::Box<dim,T> & ext_domain)
+	{
+		this->box_nn_processor = dec.box_nn_processor;
+
+		// Calculate new sub-domains for extended domain
+		extend_subdomains(dec,ext_domain);
+
+		// Calculate fine_s structure for the extended domain
+		// update the cell decomposer and gr
+		extend_fines(dec);
+
+		// Get the old sub-sub-domain grid extension
+
+		this->domain = ext_domain;
+
+		// spacing does not change
+		std::copy(dec.spacing,dec.spacing+3,this->spacing);
+
+		//! Runtime virtual cluster
+		this->v_cl = dec.v_cl;
+
+		this->ghost = g;
+		this->dist = dec.dist;
+
+		for (size_t i = 0 ; i < dim ; i++)
+			this->bc[i] = dec.bc[i];
+
+		(static_cast<nn_prcs<dim,T> &>(*this)).create(this->box_nn_processor, this->sub_domains);
+		(static_cast<nn_prcs<dim,T> &>(*this)).applyBC(ext_domain,g,this->bc);
+
+		this->Initialize_geo_cell_lists();
+		this->calculateGhostBoxes();
+	}
+
+};
+
+
+
+#endif /* SRC_DECOMPOSITION_CARTDECOMPOSITION_EXT_HPP_ */

src/Decomposition/Distribution/Distribution_unit_tests.hpp

@@ -51,6 +51,83 @@ template<unsigned int dim, typename Distribution> void setSphereComputationCosts
 	}
 }
 
+struct animal
+{
+	typedef boost::fusion::vector<float[2], size_t, size_t, size_t> type;
+
+	//! Attributes name
+	struct attributes
+	{
+		static const std::string name[];
+	};
+
+	//! type of the positional field
+	typedef float s_type;
+
+	//! The data
+	type data;
+
+	//! position property id in boost::fusion::vector
+	static const unsigned int pos = 0;
+	//! genre of animal property id in boost::fusion::vector
+	static const unsigned int genre = 1;
+	//! state property id in boost::fusion::vector
+	static const unsigned int status = 2;
+	//! alive time property id in boost::fusion::vector
+	static const unsigned int time_a = 3;
+
+	//! total number of properties boost::fusion::vector
+	static const unsigned int max_prop = 4;
+
+	animal()
+	{
+	}
+
+	inline animal(const animal & p)
+	{
+		boost::fusion::at_c<0>(data)[0] = boost::fusion::at_c<0>(p.data)[0];
+		boost::fusion::at_c<0>(data)[1] = boost::fusion::at_c<0>(p.data)[1];
+		//boost::fusion::at_c<0>(data)[2] = boost::fusion::at_c<0>(p.data)[2];
+		boost::fusion::at_c<1>(data) = boost::fusion::at_c<1>(p.data);
+		boost::fusion::at_c<2>(data) = boost::fusion::at_c<2>(p.data);
+		boost::fusion::at_c<3>(data) = boost::fusion::at_c<3>(p.data);
+	}
+
+	template<unsigned int id> inline auto get() -> decltype(boost::fusion::at_c < id > (data))
+	{
+		return boost::fusion::at_c<id>(data);
+	}
+
+	template<unsigned int id> inline auto get() const -> const decltype(boost::fusion::at_c < id > (data))
+	{
+		return boost::fusion::at_c<id>(data);
+	}
+
+	template<unsigned int dim, typename Mem> inline animal(const encapc<dim, animal, Mem> & p)
+	{
+		this->operator=(p);
+	}
+
+	template<unsigned int dim, typename Mem> inline animal & operator=(const encapc<dim, animal, Mem> & p)
+	{
+		boost::fusion::at_c<0>(data)[0] = p.template get<0>()[0];
+		boost::fusion::at_c<0>(data)[1] = p.template get<0>()[1];
+		//boost::fusion::at_c<0>(data)[2] = p.template get<0>()[2];
+		boost::fusion::at_c<1>(data) = p.template get<1>();
+		boost::fusion::at_c<2>(data) = p.template get<2>();
+		boost::fusion::at_c<3>(data) = p.template get<3>();
+
+		return *this;
+	}
+
+	static bool noPointers()
+	{
+		return true;
+	}
+};
+
+const std::string animal::attributes::name[] = { "pos"