Adding detection of HDF5

configure.ac

@@ -37,6 +37,7 @@ 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])]])
 
 
 CXXFLAGS+=" --std=c++11 "
@@ -100,6 +101,13 @@ 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([],[echo "Cannot detect hdf5, use the --with-hdf5 option if it is not installed in the default location"
+                    exit 206])
+
 ########
 
 ## Enable scan coverty

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

@@ -137,6 +137,7 @@ BOOST_installed=0
 LAPACK_installed=0
 SUITESPARSE_installed=0
 EIGEN_installed=0
+HDF5_installed=0
 blas_options=""
 conf_err=1
 
@@ -213,6 +214,14 @@ else
             ./script/install_EIGEN.sh $i_dir $compiler_opt
             configure_options=" $configure_options --with-eigen=$i_dir/EIGEN "
             EIGEN_installed=1
+        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"	
+            fi
+            ./script/install_HDF5.sh $i_dir $compiler_opt
+            configure_options=" $configure_options --with-hdf5=$i_dir/HDF5 "
+            HDF5_installed=1
         elif [ $conf_err -ne 0 ]; then
             echo "I do not know how to recover from this error"
             exit 1

openfpm_data @ d99d6e28

-Subproject commit 726d347a31701409657d5bf4b45336ce47eba73e
+Subproject commit d99d6e286199f5483327a9fd86ee84277c279310

openfpm_io @ 52333293

-Subproject commit cb37b2bc9e40a02de36ed664dc0bfe43f6257f37
+Subproject commit 523332938de0a47a1ca1d652a8e171cf9b8a6f5b

openfpm_vcluster @ 0ed3620c

-Subproject commit 6e360fcbf118277ca59b2709eb2ffa0661c677a8
+Subproject commit 0ed3620ce1e91e5fa3541e01c1654dfad7515b87

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
+./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
 sh ./configure --prefix=$1/MPI --enable-opal-multi-threads --enable-mpi-f90 $2 $3

src/Vector/vector_dist.hpp

@@ -20,6 +20,8 @@
 #include "util/object_util.hpp"
 #include "memory/ExtPreAlloc.hpp"
 #include "CSVWriter/CSVWriter.hpp"
+#include "VTKWriter/VTKWriter.hpp"
+#include "H5PartWriter/H5PartWriter.hpp"
 #include "Decomposition/common.hpp"
 #include "Grid/grid_dist_id_iterator_dec.hpp"
 #include "Vector/vector_dist_ofb.hpp"
@@ -1240,15 +1242,32 @@ public:
 	 * \return if the file has been written correctly
 	 *
 	 */
-	inline bool write(std::string out, int opt = NO_GHOST)
+	inline bool write(std::string out, int opt = NO_GHOST | VTK_WRITER)
 	{
-		// CSVWriter test
-		CSVWriter<openfpm::vector<Point<dim,St>>, openfpm::vector<prop> > csv_writer;
+		if ((opt & 0xFFFF0000) == CSV_WRITER)
+		{
+			// CSVWriter test
+			CSVWriter<openfpm::vector<Point<dim,St>>, openfpm::vector<prop> > csv_writer;
+
+			std::string output = std::to_string(out + std::to_string(v_cl.getProcessUnitID()) + std::to_string(".csv"));
+
+			// Write the CSV
+			return csv_writer.write(output,v_pos,v_prp);
+		}
+		else if ((opt & 0xFFFF0000) == VTK_WRITER)
+		{
+			// CSVWriter test
+			VTKWriter<boost::mpl::pair<openfpm::vector<Point<dim,St>>, openfpm::vector<prop>>, VECTOR_POINTS> vtk_writer;
 
-		std::string output = std::to_string(out + std::to_string(v_cl.getProcessUnitID()) + std::to_string(".csv"));
+			std::string output = std::to_string(out + std::to_string(v_cl.getProcessUnitID()) + std::to_string(".csv"));
 
-		// Write the CSV
-		return csv_writer.write(output,v_pos,v_prp);
+			// Write the CSV
+			return vtk_writer.write(output,v_pos,v_prp);
+		}
+		else if ((opt & 0xFFFF0000) == H5PART_WRITER)
+		{
+
+		}
 	}
 
 	/* \brief It return the id of structure in the allocation list