From ac5c47cdd35cebffbd8e15f9cf7053fb383aab35 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@localhost.localdomain>
Date: Wed, 24 Feb 2016 06:11:00 -0500
Subject: [PATCH] HDF5 Writer compile
---
build_io.sh | 1 +
configure.ac | 25 +-
src/CSVWriter/CSVWriter.hpp | 2 +
src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp | 24 ++
.../HDF5_XdmfWriter_point_set.hpp | 178 +++++++++++
.../HDF5_XdmfWriter_unit_tests.hpp | 64 ++++
src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp | 300 ++++++++++++++++++
src/Makefile.am | 11 +-
src/Plot/GoogleChart.hpp | 8 +
src/Plot/Plot_unit_tests.hpp | 41 +++
src/Plot/util.hpp | 45 +++
src/VTKWriter/VTKWriter.hpp | 5 +-
src/VTKWriter/VTKWriter_graph.hpp | 2 +-
src/VTKWriter/VTKWriter_unit_tests.hpp | 8 +-
src/main.cpp | 1 +
15 files changed, 702 insertions(+), 13 deletions(-)
create mode 100644 src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp
create mode 100644 src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp
create mode 100644 src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp
create mode 100644 src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp
create mode 100644 src/Plot/util.hpp
diff --git a/build_io.sh b/build_io.sh
index ea5fcd5b..9a30aeb4 100755
--- a/build_io.sh
+++ b/build_io.sh
@@ -11,6 +11,7 @@ mkdir openfpm_io/src/config
git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_devices.git openfpm_devices
git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_data.git openfpm_data
git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_pdata.git openfpm_pdata
+git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_vcluster.git openfpm_vcluster
cd "$1/openfpm_io"
diff --git a/configure.ac b/configure.ac
index 80597d77..7d879ab1 100755
--- a/configure.ac
+++ b/configure.ac
@@ -17,7 +17,18 @@ m4_ifdef([AX_BOOST_IOSTREAMS],,[m4_include([m4/ax_boost_iostreams.m4])])
m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
m4_ifdef([AX_BOOST_UNIT_TEST_FRAMEWORK],,[m4_include([m4/ax_boost_unit_test_framework.m4])])
-CXXFLAGS+=" --std=c++11 -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-unused-parameter "
+case $host_os in
+ *cygwin*)
+ # Do something specific for cygwin
+ CXXFLAGS+=" --std=gnu++11 "
+ ;;
+ *)
+ #Default Case
+ CXXFLAGS+=" --std=c++11 "
+ ;;
+esac
+
+CXXFLAGS+=" -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-unused-parameter "
NVCCFLAGS=" "
INCLUDES_PATH=" "
@@ -73,9 +84,19 @@ AC_ARG_WITH([pdata],
[pdata_dir="$withval"],
[pdata_dir="../../openfpm_pdata/src"])
+####### HDF5
+
+AX_LIB_HDF5([parallel])
+
+if test x"$with_hdf5" = x"no"; then
+ echo "Cannot detect hdf5, use the --with-hdf5 option if it is not installed in the default location"
+ exit 207
+fi
+
+
####### include openfpm_devices include path
-INCLUDES_PATH+="-I. -Iconfig -I../../openfpm_data/src -I../../openfpm_devices/src -I$pdata_dir "
+INCLUDES_PATH+="-I. -Iconfig -I../../openfpm_vcluster/src -I../../openfpm_data/src -I../../openfpm_devices/src -I$pdata_dir "
########
diff --git a/src/CSVWriter/CSVWriter.hpp b/src/CSVWriter/CSVWriter.hpp
index eb90d670..fc6822c8 100644
--- a/src/CSVWriter/CSVWriter.hpp
+++ b/src/CSVWriter/CSVWriter.hpp
@@ -18,6 +18,8 @@
#include "csv_multiarray.hpp"
#include "util.hpp"
+#define CSV_WRITER 0x30000
+
/*! \brief this class is a functor for "for_each" algorithm
*
* For each element of the boost::vector the operator() is called.
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp b/src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp
new file mode 100644
index 00000000..597c69b9
--- /dev/null
+++ b/src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp
@@ -0,0 +1,24 @@
+/*
+ * H5PartWriter.hpp
+ *
+ * Created on: Feb 7, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
+
+#define H5PART_WRITER 0x20000
+
+#define H5_POINTSET 1
+
+template <unsigned int imp>
+class HDF5_XdmfWriter
+{
+
+};
+
+#include "HDF5_XdmfWriter_point_set.hpp"
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_ */
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp
new file mode 100644
index 00000000..fd760158
--- /dev/null
+++ b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp
@@ -0,0 +1,178 @@
+/*
+ * H5PartWriter_point_set.hpp
+ *
+ * Created on: Feb 7, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
+
+#include "HDF5_XdmfWriter_util.hpp"
+#include "Vector/map_vector.hpp"
+#include "VCluster.hpp"
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to produce write each property in H5Part
+ *
+ * \tparam ele_v is the vector of properties
+ * \tparam seq, sequence of property to output
+ * \tparam has_name define if the structure define names for the properties
+ *
+ */
+
+template<typename ele_v, bool has_name>
+struct H5_prop_out
+{
+ // HDF5 file
+ hid_t file_id;
+
+ // vector that we are processing
+ ele_v & vv;
+
+ // Up to which element to write
+ size_t stop;
+
+ /*! \brief constructor
+ *
+ * \param v_out string to fill with the vertex properties
+ *
+ */
+ H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
+ :file_id(file_id),vv(vv),stop(stop)
+ {};
+
+ //! It produce an output for each property
+ template<typename T>
+ void operator()(T& t) const
+ {
+ typedef typename boost::mpl::at<typename ele_v::value_type::value_type::type,boost::mpl::int_<T::value>>::type ptype;
+
+ H5_write<ptype,T::value,ele_v>::write(file_id,std::string(ele_v::value_type::attributes::names[T::value]),vv,stop);
+ }
+};
+
+
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to produce an output for each property
+ *
+ * \tparam ele_v is the vector of properties
+ * \tparam seq, sequence of property to output
+ * \tparam has_name define if the structure define names
+ *
+ */
+template<typename ele_v>
+struct H5_prop_out<ele_v,false>
+{
+ // HDF5 file
+ hid_t file_id;
+
+ // vector that we are processing
+ ele_v & vv;
+
+ // Up to which element to write
+ size_t stop;
+
+ /*! \brief constructor
+ *
+ * \param v_out string to fill with the vertex properties
+ *
+ */
+ H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
+ :file_id(file_id),vv(vv),stop(stop)
+ {};
+
+ //! It produce an output for each property
+ template<typename T>
+ void operator()(T& t) const
+ {
+ typedef typename boost::mpl::at<typename ele_v::value_type::type,boost::mpl::int_<T::value>>::type ptype;
+
+ H5_write<ptype,T::value,ele_v>::write(file_id,std::string("attr") + std::to_string(T::value),vv,stop);
+ }
+};
+
+template <>
+class HDF5_XdmfWriter<H5_POINTSET>
+{
+ // Time step
+ int t;
+
+ //! HDF5 file
+ hid_t file_id;
+
+public:
+
+ /*!
+ *
+ * H5PartWriter constructor
+ *
+ */
+ HDF5_XdmfWriter()
+ :t(0)
+ {}
+
+
+ /*!
+ *
+ * \brief Write a set of particle position and properties into HDF5
+ *
+ * \tparam Pos Vector of positions type
+ * \taparam Prp Vector of properties type
+ * \tparam prp list of properties to output
+ *
+ * \param pos Vector with the positions
+ * \param prp Vector with the properties
+ * \param stop size of the vector to output
+ *
+ */
+ template<typename VPos, typename VPrp, int ... prp > bool write(const std::string & file, openfpm::vector<VPos> & v_pos, openfpm::vector<VPrp> & v_prp, size_t stop)
+ {
+ Vcluster & v_cl = *global_v_cluster;
+
+ // Open and HDF5 file in parallel
+
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, v_cl.getMPIComm(), MPI_INFO_NULL);
+ file_id = H5Fcreate(file.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ H5Pclose(plist_id);
+
+ // Single coordinate positional vector
+ openfpm::vector<typename VPos::coord_type> x_n;
+ x_n.resize(stop);
+
+ //for each component, fill x_n
+ for (size_t i = 0 ; i < VPos::dims ; i++)
+ {
+ //
+ for (size_t j = 0 ; j < stop ; j++)
+ x_n.get(j) = v_pos.template get<0>(j)[i];
+
+ std::stringstream str;
+ str << "x" << i;
+
+ HDF5CreateDataSet<typename VPos::coord_type>(file_id,str.str(),x_n.getPointer(),stop*sizeof(typename VPos::coord_type));
+ }
+
+ // Now we write the properties
+
+ typedef typename to_boost_vmpl<prp ... >::type v_prp_seq;
+ H5_prop_out<openfpm::vector<VPrp>,has_attributes<VPrp>::value> f(file_id,v_prp,stop);
+
+ boost::mpl::for_each_ref<v_prp_seq>(f);
+
+ H5Fclose(file_id);
+
+ return true;
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_ */
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp
new file mode 100644
index 00000000..86bd879f
--- /dev/null
+++ b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp
@@ -0,0 +1,64 @@
+/*
+ * H5PartWriter_unit_tests.hpp
+ *
+ * Created on: Feb 22, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
+
+#include "VCluster.hpp"
+#include "util/SimpleRNG.hpp"
+#include "HDF5_XdmfWriter.hpp"
+
+BOOST_AUTO_TEST_SUITE( HDF5_writer_test )
+
+
+BOOST_AUTO_TEST_CASE( HDF5_writer_use)
+{
+ openfpm::vector<Point<3,double>> pv;
+ openfpm::vector<Point_test<double>> pvp;
+
+ SimpleRNG rng;
+
+ Vcluster & v_cl = *global_v_cluster;
+
+ if (v_cl.getProcessingUnits() != 3)
+ return;
+
+ double z_base = v_cl.getProcessUnitID();
+
+ // fill 1000 particles for each processors
+
+ for (size_t i = 0 ; i < 1000 ; i++)
+ {
+ Point<3,double> p;
+ p[0] = rng.GetUniform();
+ p[1] = rng.GetUniform();
+ p[2] = z_base+rng.GetUniform();
+
+ pv.add(p);
+
+ p[0] += 2.0;
+
+ Point_test<double> pt;
+ pt.fill();
+
+ pvp.add(pt);
+ }
+
+ HDF5_XdmfWriter<H5_POINTSET> h5p;
+ h5p.template write<Point<3,double>,Point_test<double>,0,1,4,5>("h5part.h5",pv,pvp,1000);
+
+ // check that match
+
+ bool test = compare("test_h5part.h5part","test_h5part_test.h5part");
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_ */
diff --git a/src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp
new file mode 100644
index 00000000..db7acd59
--- /dev/null
+++ b/src/HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp
@@ -0,0 +1,300 @@
+/*
+ * H5PartWriteData_meta.hpp
+ *
+ * Created on: Feb 22, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
+#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
+
+#include "hdf5.h"
+#include "Vector/map_vector.hpp"
+
+/*! \brief HDF5 Create the data-set in the file
+ *
+ * \tparam type Type to write
+ *
+ * \param file_id Id of the file
+ * \param filespace id where to write
+ * \param str dataset to write
+ * \param ptr pointer with the data to write
+ * \param sz size of the data to write
+ *
+ * \return true if the function succeed
+ *
+ */
+template<typename type> bool HDF5CreateDataSet(hid_t file_id, const std::string & str ,void * ptr, size_t sz)
+{
+ hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
+ if (plist_id < 0)
+ return false;
+
+ /* Create the dataspace for the position dataset. */
+ hsize_t dimsf[1] = {sz};
+ hid_t filespace = H5Screate_simple(1, dimsf, NULL);
+ if (filespace < 0)
+ return false;
+
+ if (std::is_same<type,char>::value == true)
+ {
+ hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_CHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (dset_id < 0)
+ return false;
+
+ herr_t status = H5Dwrite(dset_id, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, plist_id, ptr);
+ if (status < 0)
+ return false;
+
+ H5Dclose(dset_id);
+ H5Dclose(filespace);
+ return true;
+ }
+/* else if (std::is_same<type,signed char>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ H5Dclose(dset_id);
+ return status;
+ }
+ else if (std::is_same<type,unsigned char>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,short>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned short>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_USHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,int>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned int>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UINT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,long long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,unsigned long long>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else if (std::is_same<type,float>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }*/
+ else if (std::is_same<type,double>::value == true)
+ {
+ hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ if (dset_id < 0)
+ return false;
+
+ herr_t status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist_id, ptr);
+ if (status < 0)
+ return false;
+
+ H5Dclose(dset_id);
+ H5Dclose(filespace);
+ return true;
+ }
+ /*else if (std::is_same<type,long double>::value == true)
+ {
+ dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LDOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }*/
+
+ return true;
+}
+
+
+/*! \brief Write an HDF5 dataset in case of scalars and vectors
+ *
+ * \tparam T type to write
+ * \tparam pid Property id
+ * \tparam V Vector containing the information
+ *
+ */
+template<typename T,size_t pid, typename V>
+struct H5_write
+{
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j);
+
+ HDF5CreateDataSet<T>(file_id,str.c_str(),buffer.getPointer(),stop*sizeof(T));
+ }
+};
+
+//! Partial specialization for N=1 1D-Array
+template<typename T,size_t pid, typename V,size_t N1>
+struct H5_write<T[N1],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1];
+
+ std::stringstream sstr;
+ sstr << "_" << i1;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+};
+
+//! Partial specialization for N=2 2D-Array
+template<typename T, size_t pid, typename V,size_t N1,size_t N2>
+struct H5_write<T[N1][N2],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2];
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=3
+template<typename T, size_t pid, typename V,size_t N1,size_t N2,size_t N3>
+struct H5_write<T[N1][N2][N3],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2][i3];
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2 << "_" << i3;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+ }
+};
+
+//! Partial specialization for N=4
+template<typename T, size_t pid, typename V ,size_t N1,size_t N2,size_t N3,size_t N4>
+struct H5_write<T[N1][N2][N3][N4],pid,V>
+{
+
+ /*! \brief write
+ *
+ * \param file_id HDF5 file
+ * \param str dataset name
+ * \param v Vector containing the information
+ * \param stop size to store
+ *
+ */
+ static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
+ {
+ for (size_t i1 = 0 ; i1 < N1 ; i1++)
+ {
+ for (size_t i2 = 0 ; i2 < N2 ; i2++)
+ {
+ for (size_t i3 = 0 ; i3 < N3 ; i3++)
+ {
+ for (size_t i4 = 0 ; i4 < N4 ; i4++)
+ {
+ // Create the buffer
+ openfpm::vector<T> buffer;
+ buffer.resize(stop);
+
+ for (size_t j = 0 ; j < stop ; j++)
+ buffer.get(j) = v.template get<pid>(j)[i1][i2][i3][i4];
+
+
+ std::stringstream sstr;
+ sstr << "_" << i1 << "_" << i2 << "_" << i3 << "_" << i4;
+
+ HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
+ }
+ }
+ }
+ }
+ }
+};
+
+#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_ */
diff --git a/src/Makefile.am b/src/Makefile.am
index 49b06a96..a51c04f2 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,13 +1,16 @@
-LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_IOSTREAMS_LIB) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_THREAD_LIB)
+LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_IOSTREAMS_LIB) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_THREAD_LIB) $(HDF5_LDFLAGS) $(HDF5_LIBS)
noinst_PROGRAMS = io
-io_SOURCES = main.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
-io_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I/usr/local/include
+io_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
+io_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I/usr/local/include $(HDF5_CPPFLAGS)
io_CFLAGS = $(CUDA_CFLAGS)
io_LDADD = $(LINKLIBS)
-nobase_include_HEADERS = CSVWriter/csv_multiarray.hpp CSVWriter/CSVWriter.hpp GraphMLWriter/GraphMLWriter.hpp util.hpp VTKWriter/VTKWriter.hpp VTKWriter/VTKWriter_graph.hpp VTKWriter/VTKWriter_grids.hpp VTKWriter/VTKWriter_grids_st.hpp VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_vector_box.hpp
+nobase_include_HEADERS = CSVWriter/csv_multiarray.hpp CSVWriter/CSVWriter.hpp \
+GraphMLWriter/GraphMLWriter.hpp util.hpp \
+VTKWriter/VTKWriter.hpp VTKWriter/VTKWriter_graph.hpp VTKWriter/VTKWriter_point_set.hpp VTKWriter/VTKWriter_grids.hpp VTKWriter/VTKWriter_grids_st.hpp VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_vector_box.hpp HDF5_XdmfWriter/HDF5_XdmfWriter.hpp HDF5_XdmfWriter/HDF5_XdmfWriter_point_set.hpp HDF5_XdmfWriter/HDF5_XdmfWriter_util.hpp \
+Plot/GoogleChart.hpp Plot/util.hpp
.cu.o :
diff --git a/src/Plot/GoogleChart.hpp b/src/Plot/GoogleChart.hpp
index 105ac735..1bf4a081 100644
--- a/src/Plot/GoogleChart.hpp
+++ b/src/Plot/GoogleChart.hpp
@@ -9,6 +9,7 @@
#define OPENFPM_DATA_SRC_PLOT_GOOGLECHART_HPP_
#include <fstream>
+#include "Vector/map_vector.hpp"
#define GGRAPH_COLUMS 1
#define GGRAPH_POINTS 2
@@ -54,6 +55,9 @@ struct GCoptions
//! Check Google Chart API interval option
std::string intervalext;
+ //! more
+ std::string more;
+
GCoptions & operator=(const GCoptions & opt)
{
title = opt.title;
@@ -66,6 +70,7 @@ struct GCoptions
lineWidth = opt.lineWidth;
intervalsext = opt.intervalsext;
+ more = opt.more;
return *this;
}
@@ -232,6 +237,7 @@ class GoogleChart
str << "seriesType: '" << opt.stype << "',\n";
if (opt.stypeext.size() != 0)
str << "series: " << opt.stypeext << "\n";
+ str << opt.more;
return str.str();
}
@@ -253,6 +259,8 @@ class GoogleChart
if (opt.intervalext.size() != 0)
str << "interval: " << opt.intervalext << "\n";
+ str << opt.more;
+
return str.str();
}
diff --git a/src/Plot/Plot_unit_tests.hpp b/src/Plot/Plot_unit_tests.hpp
index f3df91bb..7c77f192 100644
--- a/src/Plot/Plot_unit_tests.hpp
+++ b/src/Plot/Plot_unit_tests.hpp
@@ -9,6 +9,7 @@
#define OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_
#include "GoogleChart.hpp"
+#include "Plot/util.hpp"
BOOST_AUTO_TEST_SUITE( plot_unit_test )
@@ -382,6 +383,46 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 )
BOOST_REQUIRE_EQUAL(true,test);
}
+//! [Definition of a function]
+
+double f(double x)
+{
+ return x*x;
+}
+
+//! [Definition of a function]
+
+BOOST_AUTO_TEST_CASE( plot_util )
+{
+ //! [fill a vector]
+
+ openfpm::vector<double> x;
+
+ Fill1D(0.0,2.0,5,x);
+
+ BOOST_REQUIRE_EQUAL(x.get(0),0.0);
+ BOOST_REQUIRE_EQUAL(x.get(1),0.5);
+ BOOST_REQUIRE_EQUAL(x.get(2),1.0);
+ BOOST_REQUIRE_EQUAL(x.get(3),1.5);
+ BOOST_REQUIRE_EQUAL(x.get(4),2.0);
+
+ //! [fill a vector]
+
+ x.clear();
+
+ //! [fill a vector with a function]
+
+ Fill1D(0.0,2.0,5,x,f);
+
+ BOOST_REQUIRE_EQUAL(x.get(0),0.0);
+ BOOST_REQUIRE_EQUAL(x.get(1),0.25);
+ BOOST_REQUIRE_EQUAL(x.get(2),1.0);
+ BOOST_REQUIRE_EQUAL(x.get(3),2.25);
+ BOOST_REQUIRE_EQUAL(x.get(4),4.0);
+
+ //! [fill a vector function]
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif /* OPENFPM_DATA_SRC_PLOT_PLOT_UNIT_TESTS_HPP_ */
diff --git a/src/Plot/util.hpp b/src/Plot/util.hpp
new file mode 100644
index 00000000..b9a53c52
--- /dev/null
+++ b/src/Plot/util.hpp
@@ -0,0 +1,45 @@
+/*
+ * util.hpp
+ *
+ * Created on: Feb 23, 2016
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_PLOT_UTIL_HPP_
+#define OPENFPM_IO_SRC_PLOT_UTIL_HPP_
+
+/*! \brief It fill the vector x with function values
+ *
+ * ### Define a function
+ * \snippet Plot_unit_tests.hpp Definition of a function
+ * ### Example vector with points on a specified range
+ * \snippet Plot_unit_tests.hpp fill a vector with a function
+ *
+ */
+template<typename T> static inline void Fill1D(T start, T stop, size_t np, openfpm::vector<T> & x,T f(T x))
+{
+ x.resize(np);
+
+ T spacing = (stop - start) / (np - 1);
+
+ for (size_t i = 0 ; i < np ; i++)
+ x.get(i) = f(start + i*spacing);
+}
+
+/*! \brief It fill the vector x with uniformly distributed set of points
+ *
+ * ### Example vector with points on a specified range
+ * \snippet Plot_unit_tests.hpp fill a vector
+ *
+ */
+template<typename T> static inline void Fill1D(T start, T stop, size_t np, openfpm::vector<T> & x)
+{
+ x.resize(np);
+
+ T spacing = (stop - start) / (np - 1);
+
+ for (size_t i = 0 ; i < np ; i++)
+ x.get(i) = start + i*spacing;
+}
+
+#endif /* OPENFPM_IO_SRC_PLOT_UTIL_HPP_ */
diff --git a/src/VTKWriter/VTKWriter.hpp b/src/VTKWriter/VTKWriter.hpp
index 945dd03d..9567ca75 100644
--- a/src/VTKWriter/VTKWriter.hpp
+++ b/src/VTKWriter/VTKWriter.hpp
@@ -94,13 +94,14 @@ enum file_type
ASCII
};
-#define GRAPH 1
+#define VTK_GRAPH 1
#define VECTOR_BOX 2
#define VECTOR_GRIDS 3
#define VECTOR_ST_GRIDS 4
#define VECTOR_POINTS 5
+#define VTK_WRITER 0x10000
-template <typename Graph, unsigned int imp>
+template <typename Object, unsigned int imp>
class VTKWriter
{
diff --git a/src/VTKWriter/VTKWriter_graph.hpp b/src/VTKWriter/VTKWriter_graph.hpp
index 8d57105e..be7706a5 100644
--- a/src/VTKWriter/VTKWriter_graph.hpp
+++ b/src/VTKWriter/VTKWriter_graph.hpp
@@ -878,7 +878,7 @@ struct prop_out_edge
*/
template<typename Graph>
-class VTKWriter<Graph, GRAPH>
+class VTKWriter<Graph, VTK_GRAPH>
{
const Graph & g;
diff --git a/src/VTKWriter/VTKWriter_unit_tests.hpp b/src/VTKWriter/VTKWriter_unit_tests.hpp
index dd7235e8..09dc9cab 100644
--- a/src/VTKWriter/VTKWriter_unit_tests.hpp
+++ b/src/VTKWriter/VTKWriter_unit_tests.hpp
@@ -200,7 +200,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D )
// Write the VTK file
- VTKWriter<Graph_CSR<vertex2,edge>,GRAPH> vtk(gr);
+ VTKWriter<Graph_CSR<vertex2,edge>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v2.vtk");
// check that match
@@ -278,7 +278,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D_edge )
// Write the VTK file
- VTKWriter<Graph_CSR<vertex2,vertex2>,GRAPH> vtk(gr);
+ VTKWriter<Graph_CSR<vertex2,vertex2>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v4.vtk");
// check that match
@@ -363,7 +363,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph2D )
// Write the VTK file
- VTKWriter<Graph_CSR<vertex3,edge>,GRAPH> vtk(gr);
+ VTKWriter<Graph_CSR<vertex3,edge>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v3.vtk");
// check that match
@@ -443,7 +443,7 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph)
// Write the VTK file
- VTKWriter<Graph_CSR<vertex,edge>,GRAPH> vtk(gr);
+ VTKWriter<Graph_CSR<vertex,edge>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph.vtk");
// check that match
diff --git a/src/main.cpp b/src/main.cpp
index d36a713f..9e6ada39 100755
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -9,4 +9,5 @@
#include "CSVWriter/CSVWriter_unit_tests.hpp"
#include "GraphMLWriter/GraphMLWriter_unit_tests.hpp"
#include "VTKWriter/VTKWriter_unit_tests.hpp"
+#include "HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp"
#include "Plot/Plot_unit_tests.hpp"
--
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