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openfpm_io
Commit 6406c98f authored by tonynsyde's avatar tonynsyde
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Merging fixes

parents 1031dd1b e5cdbbf7
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Showing with 5176 additions and 3174 deletions
.gitignore 0 → 100644
View file @ 6406c98f
# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so
# Packages #
############
# it's better to unpack these files and commit the raw source
# git has its own built in compression methods
*.7z
*.dmg
*.gz
*.iso
*.jar
*.rar
*.tar
*.zip
# Logs and databases #
######################
*.log
*.sql
*.sqlite
# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
###### Other
AUTHORS
COPYING
ChangeLog
INSTALL
NEWS
README
Makefile
Makefile.in
config.status
configure
numerics
**/.deps
**/src/config
aclocal.m4
**/autom4te.cache
src/io
csv_out.csv
test_graph.graphml
test_graph2.graphml
*.html
build_io.sh
View file @ 6406c98f
......@@ -11,9 +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
cd "$1/openfpm_data"
git checkout develop
cd ..
git clone git@ppmcore.mpi-cbg.de:incardon/openfpm_vcluster.git openfpm_vcluster
cd "$1/openfpm_io"
......
configure.ac
View file @ 6406c98f
......@@ -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 $host_os in
*cygwin*)
# Do something specific for cygwin
CXXFLAGS+=" --std=gnu++11 "
;;
*)
#Default Case
CXXFLAGS+=" --std=c++11 "
;;
esac
CXXFLAGS+=" -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-unused-parameter "
NVCCFLAGS=" "
INCLUDES_PATH=" "
......@@ -73,6 +84,16 @@ AC_ARG_WITH([pdata],
[pdata_dir="$withval"],
[pdata_dir="../../openfpm_pdata/src"])
####### HDF5
AX_LIB_HDF5([parallel])
if test x"$with_hdf5" = x"no"; then
echo "Cannot detect hdf5, use the --with-hdf5 option if it is not installed in the default location"
exit 207
fi
####### include openfpm_devices include path
INCLUDES_PATH+="-I. -Iconfig -I../../openfpm_data/src -I../../openfpm_devices/src -I../../openfpm_vcluster/src -I$pdata_dir "
......
gc_out2_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2.200000,1.300000,4.500000,0.600000],
['colum2',5.000000,6.100000,1.300000,2.600000],
['colum3',2.100000,1.000000,6.100000,9.300000],
['colum4',1.100000,6.100000,3.000000,2.000000],
['colum5',3.300000,0.300000,0.000000,6.200000],
['colum6',2.000000,1.100000,4.000000,6.100000],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars',
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_out3_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2.200000,1.300000,4.500000,0.600000],
['colum2',5.000000,6.100000,1.300000,2.600000],
['colum3',2.100000,1.000000,6.100000,9.300000],
['colum4',1.100000,6.100000,3.000000,2.000000],
['colum5',3.300000,0.300000,0.000000,6.200000],
['colum6',2.000000,1.100000,4.000000,6.100000],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: '',
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_out4_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['','dataset1','dataset2','dataset3','dataset4'],
['colum1',2.200000,1.300000,4.500000,0.600000],
['colum2',5.000000,6.100000,1.300000,2.600000],
['colum3',2.100000,1.000000,6.100000,9.300000],
['colum4',1.100000,6.100000,3.000000,2.000000],
['colum5',3.300000,0.300000,0.000000,6.200000],
['colum6',2.000000,1.100000,4.000000,6.100000],
]);
var options0= {
title : '',
vAxis: {title: ''},
hAxis: {title: ''},
seriesType: '',
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_out5_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['','','','',''],
['colum1',2.200000,1.300000,4.500000,0.600000],
['colum2',5.000000,6.100000,1.300000,2.600000],
['colum3',2.100000,1.000000,6.100000,9.300000],
['colum4',1.100000,6.100000,3.000000,2.000000],
['colum5',3.300000,0.300000,0.000000,6.200000],
['colum6',2.000000,1.100000,4.000000,6.100000],
]);
var options0= {
title : '',
vAxis: {title: ''},
hAxis: {title: ''},
seriesType: '',
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_out6_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['','','','',''],
['',2.200000,1.300000,4.500000,0.600000],
['',5.000000,6.100000,1.300000,2.600000],
['',2.100000,1.000000,6.100000,9.300000],
['',1.100000,6.100000,3.000000,2.000000],
['',3.300000,0.300000,0.000000,6.200000],
['',2.000000,1.100000,4.000000,6.100000],
]);
var options0= {
title : '',
vAxis: {title: ''},
hAxis: {title: ''},
seriesType: '',
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_out7_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2,3,5,6],
['colum2',5,6,1,6],
['colum3',2,1,6,9],
['colum4',1,6,3,2],
['colum5',3,3,0,6],
['colum6',2,1,4,6],
]);
var data1 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2,3,5,6],
['colum2',5,6,1,6],
['colum3',2,1,6,9],
['colum4',1,6,3,2],
['colum5',3,3,0,6],
['colum6',2,1,4,6],
]);
var data2 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2,3,5,6],
['colum2',5,6,1,6],
['colum3',2,1,6,9],
['colum4',1,6,3,2],
['colum5',3,3,0,6],
['colum6',2,1,4,6],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}
};
var options1= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}
};
var options2= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));chart.draw(data1, options1);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));chart.draw(data2, options2);
}</script>
</head>
<body>
<h2>Before first graph</h2><div id="chart_div0" style="width: 900px; height: 500px;"></div>
<h2>Before second graph</h2><div id="chart_div1" style="width: 900px; height: 500px;"></div>
<h2>Before third graph</h2><div id="chart_div2" style="width: 900px; height: 500px;"></div>
<h2>At the end</h2></body>
</html>
gc_out_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = google.visualization.arrayToDataTable([
['X Axis','dataset1','dataset2','dataset3','dataset4'],
['colum1',2,3,5,6],
['colum2',5,6,1,6],
['colum3',2,1,6,9],
['colum4',1,6,3,2],
['colum5',3,3,0,6],
['colum6',2,1,4,6],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_plot2_out_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = new google.visualization.DataTable();
data0.addColumn('string','X Axis');
data0.addColumn('number','line0');
data0.addColumn('number','line1');
data0.addColumn('number','line2');
data0.addColumn('number','line3');
data0.addColumn('number','line4');
data0.addColumn('number','line5');
data0.addColumn('number','line6');
data0.addColumn('number','line7');
data0.addColumn('number','line8');
data0.addRows([
['colum1',0.1,0.2,0.19,0.22,0.195,0.215,0.35,0.34,0.36],
['colum2',0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37],
['colum3',0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36],
['colum4',0.15,0.25,0.2,0.26,0.22,0.255,0.36,0.35,0.37],
['colum5',0.09,0.29,0.25,0.3,0.26,0.295,0.35,0.34,0.36],
['colum6',0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
curveType: 'function',
lineWidth: 1,
intervals: { 'style':'area' },
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
gc_plot_out_test.html 0 → 100644
View file @ 6406c98f
<html>
<head>
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript">
google.charts.load('current', {'packages':['corechart']});
google.charts.setOnLoadCallback(drawVisualization);
function drawVisualization() {
var data0 = new google.visualization.DataTable();
data0.addColumn('string','X Axis');
data0.addColumn('number','line1');
data0.addColumn('number','line2');
data0.addColumn({id:'i0', type:'number', role:'interval'});
data0.addColumn({id:'i0', type:'number', role:'interval'});
data0.addColumn({id:'i1', type:'number', role:'interval'});
data0.addColumn({id:'i1', type:'number', role:'interval'});
data0.addColumn('number','line3');
data0.addColumn({id:'i2', type:'number', role:'interval'});
data0.addColumn({id:'i2', type:'number', role:'interval'});
data0.addRows([
['colum1',0.1,0.2,0.19,0.22,0.195,0.215,0.35,0.34,0.36],
['colum2',0.11,0.21,0.18,0.22,0.19,0.215,0.36,0.35,0.37],
['colum3',0.12,0.22,0.21,0.23,0.215,0.225,0.35,0.34,0.36],
['colum4',0.15,0.25,0.2,0.26,0.22,0.255,0.36,0.35,0.37],
['colum5',0.09,0.29,0.25,0.3,0.26,0.295,0.35,0.34,0.36],
['colum6',0.08,0.28,0.27,0.29,0.275,0.285,0.36,0.35,0.37],
]);
var options0= {
title : 'Example',
vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
curveType: 'function',
lineWidth: 1,
intervals: { 'style':'area' },
interval: {'i2': { 'color': '#4374E0', 'style':'bars', 'lineWidth':4, 'fillOpacity':1 } }
};
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
}</script>
</head>
<body>
<div id="chart_div0" style="width: 900px; height: 500px;"></div>
</body>
</html>
src/CSVWriter.hpp → src/CSVWriter/CSVWriter.hpp
View file @ 6406c98f
......@@ -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.
......@@ -54,7 +56,7 @@ struct csv_prp
void operator()(T& t)
{
// This is the type of the csv column
typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
typedef decltype(obj.template get<T::value>()) col_type;
// Remove the reference from the column type
typedef typename boost::remove_reference<col_type>::type col_rtype;
......@@ -87,7 +89,7 @@ struct csv_col
void operator()(T& t)
{
// This is the type of the csv column
typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
typedef decltype(std::declval<Tobj>.template get<T::value>()) col_type;
// Remove the reference from the column type
typedef typename boost::remove_reference<col_type>::type col_rtype;
......@@ -181,9 +183,10 @@ class CSVWriter
*
* \param v_pos vector that contain the positional information
* \param v_prp vector that contain the property information
* \param offset from where to start
*
*/
std::string get_csv_data(v_pos & vp, v_prp & vpr)
std::string get_csv_data(v_pos & vp, v_prp & vpr, size_t offset)
{
std::stringstream str;
......@@ -195,7 +198,7 @@ class CSVWriter
}
// Write the data
for (size_t i = 0 ; i < vp.size() ; i++)
for (size_t i = offset ; i < vp.size() ; i++)
{
for (size_t j = 0 ; j < v_pos::value_type::dims ; j++)
{
......@@ -206,9 +209,9 @@ class CSVWriter
}
// Object to write
typename v_prp::value_type obj = vpr.get(i);
auto obj = vpr.get(i);
csv_prp<typename v_prp::value_type> c_prp(str,obj);
csv_prp<decltype(obj)> c_prp(str,obj);
// write the properties to the stream string
boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
......@@ -228,10 +231,11 @@ public:
* \param file path where to write
* \param v_pos positional vector
* \param v_prp properties vector
* \param offset from where to start to write
*
*/
bool write(std::string file, v_pos & v , v_prp & prp)
bool write(std::string file, v_pos & v , v_prp & prp, size_t offset=0)
{
// Header for csv (colums name)
std::string csv_header;
......@@ -242,7 +246,7 @@ public:
csv_header = get_csv_colums();
// For each property in the vertex type produce a point data
point_data = get_csv_data(v,prp);
point_data = get_csv_data(v,prp,offset);
// write the file
std::ofstream ofs(file);
......
src/GraphMLWriter.hpp → src/GraphMLWriter/GraphMLWriter.hpp
View file @ 6406c98f
......@@ -208,6 +208,11 @@ struct vertex_node
create_prop<typename G::V_type>(attributes_names);
};
inline ~vertex_node()
{
delete [] attributes_names;
}
#ifdef DEBUG
/*! \brief Constructor
*
......@@ -558,7 +563,7 @@ class GraphMLWriter
vn.new_node(nc);
// Iterate through all the vertex and create the vertex list
boost::mpl::for_each< boost::mpl::range_c<int,0,Graph::V_type::max_prop> >(vn);
boost::mpl::for_each_ref< boost::mpl::range_c<int,0,Graph::V_type::max_prop> >(vn);
// end node
vn.end_node();
......
src/GraphMLWriter_unit_tests.hpp → src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
View file @ 6406c98f
......@@ -11,7 +11,6 @@
#define GS_SIZE 8
#include "GraphMLWriter.hpp"
#include "VTKWriter.hpp"
#include "Graph/CartesianGraphFactory.hpp"
#include "util.hpp"
......@@ -94,14 +93,22 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
n1.get_i() = 6.0;
n1.get_str() = std::string("test");
g_csr2.addVertex(n1);
n1.get_str() = std::string("tes2");
g_csr2.addVertex(n1);
n1.get_str() = std::string("test3");
g_csr2.addVertex(n1);
n1.get_str() = std::string("test4");
g_csr2.addVertex(n1);
n1.get_str() = std::string("test5");
g_csr2.addEdge(0,1,n1);
n1.get_str() = std::string("test6");
g_csr2.addEdge(2,1,n1);
n1.get_str() = std::string("test7");
g_csr2.addEdge(3,1,n1);
n1.get_str() = std::string("test8");
g_csr2.addEdge(2,0,n1);
n1.get_str() = std::string("test9");
g_csr2.addEdge(3,2,n1);
// Create a graph ML
......@@ -123,7 +130,10 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
// Box
Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
Graph_CSR<ne_cp,ne_cp> g_csr = g_factory.construct<5,float,2,ne_cp::x,ne_cp::y,ne_cp::z>(sz,box);
// Boundary conditions, non periodic
size_t bc[] = {NON_PERIODIC,NON_PERIODIC,NON_PERIODIC};
Graph_CSR<ne_cp,ne_cp> g_csr = g_factory.construct<5,NO_VERTEX_ID,float,2,ne_cp::x,ne_cp::y,ne_cp::z>(sz,box,bc);
// Create a graph ML
GraphMLWriter<Graph_CSR<ne_cp,ne_cp>> gw(g_csr);
......
src/HDF5_XdmfWriter/HDF5_XdmfWriter.hpp 0 → 100644
View file @ 6406c98f
/*
* 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_