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Commit 08df6993 authored by Pietro Incardona's avatar Pietro Incardona
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VTKWriter for point set

parents 575fbc37 3308edce
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build.sh
+ 14
− 0
View file @ 08df6993
......@@ -17,6 +17,20 @@ git clone git@git.mpi-cbg.de:openfpm/openfpm_data.git openfpm_data
git clone git@git.mpi-cbg.de:openfpm/openfpm_pdata.git openfpm_pdata
git clone git@git.mpi-cbg.de:openfpm/openfpm_vcluster.git openfpm_vcluster
# Go in the right branch
cd openfpm_pdata
git checkout Release_0.9.0
cd ..
cd openfpm_data
git checkout Release_0.9.0
cd ..
cd openfpm_vcluster
git checkout Release_0.9.0
cd ..
cd "$1/openfpm_io"
echo "Compiling on $2"
......
configure.ac
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......@@ -34,6 +34,11 @@ CXXFLAGS+=" -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-
NVCCFLAGS=" "
INCLUDES_PATH=" "
AC_LANG_PUSH([C++])
AC_CHECK_HEADER(mpi.h,[],[echo "mpi.h not found"
exit 200])
AC_LANG_POP([C++])
# set default prefix
if test "$prefix" = "NONE"; then
prefix="/usr/local"
......
gc_out2_test.html
+ 2
− 1
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......@@ -38,7 +38,8 @@ vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: 'bars'};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_out3_test.html
+ 2
− 1
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......@@ -38,7 +38,8 @@ vAxis: {title: 'Y Axis'},
hAxis: {title: 'X Axis'},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_out4_test.html
+ 2
− 1
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......@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_out5_test.html
+ 2
− 1
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......@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_out6_test.html
+ 2
− 1
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......@@ -38,7 +38,8 @@ vAxis: {title: ''},
hAxis: {title: ''},
seriesType: ''};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_out7_test.html
+ 6
− 3
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......@@ -79,11 +79,14 @@ hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
$("#export_svg1").on("click", function (event) {exportToSVG.apply(this,[1]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));chart.draw(data1, options1);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div1'));
chart.draw(data1, options1);
$("#export_svg2").on("click", function (event) {exportToSVG.apply(this,[2]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));chart.draw(data2, options2);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div2'));
chart.draw(data2, options2);
}</script>
</head>
<body>
......
gc_out_test.html
+ 2
− 1
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......@@ -39,7 +39,8 @@ hAxis: {title: 'X Axis'},
seriesType: 'bars',
series: {3: {type: 'line'}}};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_plot2_out_test.html
+ 2
− 1
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......@@ -45,7 +45,8 @@ curveType: 'function',
lineWidth: 1,
intervals: { 'style':'area' }};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
gc_plot_out_test.html
+ 2
− 1
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......@@ -47,7 +47,8 @@ intervals: { 'style':'area' },
interval: {'i2': { 'color': '#4374E0', 'style':'bars', 'lineWidth':4, 'fillOpacity':1 } }
};
$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
chart.draw(data0, options0);
}</script>
</head>
<body>
......
m4/acx_mpi.m4 100755 → 100644
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File mode changed from 100755 to 100644
src/CSVWriter/CSVWriter.hpp
+ 1
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......@@ -16,7 +16,7 @@
#include <boost/mpl/range_c.hpp>
#include <boost/mpl/for_each.hpp>
#include "csv_multiarray.hpp"
#include "util.hpp"
#include "util/util.hpp"
#include "is_csv_writable.hpp"
#define CSV_WRITER 0x30000
......
src/CSVWriter/CSVWriter_unit_tests.hpp
+ 7
− 2
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......@@ -9,6 +9,11 @@ BOOST_AUTO_TEST_SUITE( csv_writer_test )
BOOST_AUTO_TEST_CASE( csv_writer_particles )
{
Vcluster & v_cl = create_vcluster();
if (v_cl.getProcessUnitID() != 0)
return;
{
// Allocate a property vector
auto v_prp = allocate_openfpm_prp(16);
......@@ -29,7 +34,7 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles )
// Write the CSV
csv_writer.write("csv_out.csv",v_pos,v_prp);
bool test = compare("csv_out.csv","csv_out_test.csv");
bool test = compare("csv_out.csv","test_data/csv_out_test.csv");
BOOST_REQUIRE_EQUAL(true,test);
}
......@@ -53,7 +58,7 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles )
// Write the CSV
csv_writer.write("csv_out_unk.csv",v_pos,v_prp);
bool test = compare("csv_out_unk.csv","csv_out_unk_test.csv");
bool test = compare("csv_out_unk.csv","test_data/csv_out_unk_test.csv");
BOOST_REQUIRE_EQUAL(true,test);
}
......
src/CSVWriter/is_csv_writable.hpp
+ 24
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......@@ -9,111 +9,132 @@
#define OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_
//! Indicate if the property T is writable in CSV
template<typename T>
struct is_csv_writable
{
//! as default if not recognized is not writable
enum
{
value = false
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<float>
{
//! float is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<double>
{
//! double is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<char>
{
//! char is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned char>
{
//! unsigned char is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<short>
{
//! short is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned short>
{
//! unsigned is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<int>
{
//! int is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned int>
{
//! unsigned int is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<long int>
{
//! long int is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<unsigned long int>
{
//! unsigned long int is writable
enum
{
value = true
};
};
//! Indicate if the property T is writable in CSV
template<>
struct is_csv_writable<bool>
{
//! bool is writable
enum
{
value = true
......
src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
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......@@ -12,7 +12,7 @@
#include "GraphMLWriter.hpp"
#include "Graph/CartesianGraphFactory.hpp"
#include "util.hpp"
#include "util/util.hpp"
BOOST_AUTO_TEST_SUITE( graphml_writer_test )
......@@ -77,6 +77,11 @@ const std::string ne_cp::attributes::name[] = {"x","y","z","double_num","long_nu
BOOST_AUTO_TEST_CASE( graphml_writer_use)
{
Vcluster & v_cl = create_vcluster();
if (v_cl.getProcessUnitID() != 0)
return;
Graph_CSR<ne_cp,ne_cp> g_csr2;
// Add 4 vertex and connect
......@@ -114,7 +119,7 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
// check that match
bool test = compare("test_graph2.graphml","test_graph2_test.graphml");
bool test = compare("test_graph2.graphml","test_data/test_graph2_test.graphml");
BOOST_REQUIRE_EQUAL(true,test);
//! Create a graph
......@@ -138,7 +143,7 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
// check that match
test = compare("test_graph.graphml","test_graph_test.graphml");
test = compare("test_graph.graphml","test_data/test_graph_test.graphml");
BOOST_REQUIRE_EQUAL(true,test);
}
......
src/HDF5_wr/HDF5_reader.hpp 0 → 100644
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/*
* HDF5_loader.hpp
*
* Created on: May 1, 2017
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
#include "VCluster/VCluster.hpp"
template <unsigned int type>
class HDF5_reader
{
void load()
{
std::cerr << __FILE__ << ":" << __LINE__ << " Error: we do not know how to write this type of data" << std::endl;
}
};
#include "HDF5_reader_vd.hpp"
#include "HDF5_reader_gd.hpp"
#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_ */
src/HDF5_wr/HDF5_reader_gd.hpp 0 → 100644
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/*
* HDF5_reader_gr.hpp
*
* Created on: May 2, 2017
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
#include "Packer_Unpacker/Pack_selector.hpp"
#include "Packer_Unpacker/Packer.hpp"
#include "Packer_Unpacker/Unpacker.hpp"
#include "util/GBoxes.hpp"
template <>
class HDF5_reader<GRID_DIST>
{
template<typename device_grid> void load_block(long int bid,
hssize_t mpi_size_old,
int * metadata_out,
openfpm::vector<size_t> & metadata_accum,
hid_t plist_id,
hid_t dataset_2,
openfpm::vector<device_grid> & loc_grid_old,
openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
{
hsize_t offset[1];
hsize_t block[1];
if (bid < mpi_size_old && bid != -1)
{
offset[0] = metadata_accum.get(bid);
block[0] = metadata_out[bid];
}
else
{
offset[0] = 0;
block[0] = 0;
}
hsize_t count[1] = {1};
//Select file dataspace
hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
hsize_t mdim_2[1] = {block[0]};
//Create data space in memory
hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
// allocate the memory
HeapMemory pmem;
//pmem.allocate(req);
ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
mem.incRef();
// Read the dataset.
H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
mem.allocate(pmem.size());
Unpack_stat ps;
openfpm::vector<device_grid> loc_grid_old_unp;
openfpm::vector<GBoxes<device_grid::dims>> gdb_ext_old_unp;
Unpacker<typename std::remove_reference<decltype(loc_grid_old)>::type,HeapMemory>::unpack(mem,loc_grid_old_unp,ps,1);
Unpacker<typename std::remove_reference<decltype(gdb_ext_old)>::type,HeapMemory>::unpack(mem,gdb_ext_old_unp,ps,1);
for (size_t i = 0; i < loc_grid_old_unp.size(); i++)
loc_grid_old.add(loc_grid_old_unp.get(i));
for (size_t i = 0; i < gdb_ext_old_unp.size(); i++)
gdb_ext_old.add(gdb_ext_old_unp.get(i));
mem.decRef();
delete &mem;
}
public:
template<typename device_grid> inline void load(const std::string & filename,
openfpm::vector<device_grid> & loc_grid_old,
openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
{
Vcluster & v_cl = create_vcluster();
MPI_Comm comm = v_cl.getMPIComm();
MPI_Info info = MPI_INFO_NULL;
int mpi_rank = v_cl.getProcessUnitID();
//int mpi_size = v_cl.getProcessingUnits();
// Set up file access property list with parallel I/O access
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
//Open a file
hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
H5Pclose(plist_id);
//Open dataset
hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
//Create property list for collective dataset read
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//Select file dataspace
hid_t file_dataspace_id = H5Dget_space(dataset);
hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
//if (mpi_rank == 0)
//printf ("\nOld MPI size: %llu\n", mpi_size_old);
//Where to read metadata
int metadata_out[mpi_size_old];
for (int i = 0; i < mpi_size_old; i++)
{
metadata_out[i] = 0;
}
//Size for data space in memory
hsize_t mdim[1] = {(size_t)mpi_size_old};
//Create data space in memory
hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
/*
if (mpi_rank == 0)
{
hssize_t size;
size = H5Sget_select_npoints (mem_dataspace_id);
printf ("\nmemspace_id size: %llu\n", size);
size = H5Sget_select_npoints (file_dataspace_id);
printf ("dataspace_id size: %llu\n", size);
}
*/
// Read the dataset.
H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
/*
if (mpi_rank == 0)
{
std::cout << "Metadata_out[]: ";
for (int i = 0; i < mpi_size_old; i++)
{
std::cout << metadata_out[i] << " ";
}
std::cout << " " << std::endl;
}
*/
openfpm::vector<size_t> metadata_accum;
metadata_accum.resize(mpi_size_old);
metadata_accum.get(0) = 0;
for (int i = 1 ; i < mpi_size_old ; i++)
metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
//Open dataset
hid_t dataset_2 = H5Dopen (file, "grid_dist", H5P_DEFAULT);
//Create property list for collective dataset read
plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
/////////////////////////////////////
openfpm::vector<size_t> n_block;
n_block.resize(v_cl.getProcessingUnits());
for(size_t i = 0 ; i < n_block.size() ; i++)
n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
// std::cout << "MPI size old: " << mpi_size_old << std::endl;
//std::cout << "MPI size: " << v_cl.getProcessingUnits() << std::endl;
// std::cout << "Rest block: " << rest_block << std::endl;
size_t max_block;
if (rest_block != 0)
max_block = n_block.get(0) + 1;
else
max_block = n_block.get(0);
//for(size_t i = 0 ; i < n_block.size() ; i++)
for(size_t i = 0 ; i < rest_block ; i++)
n_block.get(i) += 1;
//for(size_t i = 0 ; i < n_block.size() ; i++)
//std::cout << "n_block.get(i): " << n_block.get(i) << std::endl;
size_t start_block = 0;
size_t stop_block = 0;
if (v_cl.getProcessUnitID() != 0)
{
for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
start_block += n_block.get(i);
}
stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
// std::cout << "ID: " << v_cl.getProcessUnitID() << "; Start block: " << start_block << "; " << "Stop block: " << stop_block << std::endl;
if (mpi_rank >= mpi_size_old)
load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
else
{
size_t n_bl = 0;
size_t lb = start_block;
for ( ; lb < stop_block ; lb++, n_bl++)
load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
if (n_bl < max_block)
load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
}
////////////////////////////////////
//std::cout << "LOAD: sum: " << sum << std::endl;
// Close the dataset.
H5Dclose(dataset);
H5Dclose(dataset_2);
// Close the file.
H5Fclose(file);
H5Pclose(plist_id);
}
};
#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_ */
src/HDF5_wr/HDF5_reader_vd.hpp 0 → 100644
+ 244
− 0
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/*
* HDF5_reader_vd.hpp
*
* Created on: May 1, 2017
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
template <>
class HDF5_reader<VECTOR_DIST>
{
private:
template<unsigned int dim, typename St,typename prp>
bool load_block(long int bid,
hssize_t mpi_size_old,
int * metadata_out,
openfpm::vector<size_t> metadata_accum,
hid_t plist_id,
hid_t dataset_2,
size_t & g_m,
openfpm::vector<Point<dim,St>> & v_pos,
openfpm::vector<prp> & v_prp)
{
hsize_t offset[1];
hsize_t block[1];
if (bid < mpi_size_old && bid != -1)
{
offset[0] = metadata_accum.get(bid);
block[0] = metadata_out[bid];
}
else
{
offset[0] = 0;
block[0] = 0;
}
hsize_t count[1] = {1};
//Select file dataspace
hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
if (file_dataspace_id_2 < 0) {return false;}
herr_t err = H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
if (err < 0) {return false;}
hsize_t mdim_2[1] = {block[0]};
//Create data space in memory
hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
if (mem_dataspace_id_2 < 0) {return false;}
size_t sum = 0;
for (int i = 0; i < mpi_size_old; i++)
sum += metadata_out[i];
// allocate the memory
HeapMemory pmem;
ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
mem.incRef();
// Read the dataset.
err = H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
if (err < 0) {return false;}
mem.allocate(pmem.size());
Unpack_stat ps;
openfpm::vector<Point<dim, St>> v_pos_unp;
openfpm::vector<prp> v_prp_unp;
Unpacker<decltype(v_pos_unp),HeapMemory>::unpack(mem,v_pos_unp,ps,1);
Unpacker<decltype(v_prp_unp),HeapMemory>::unpack(mem,v_prp_unp,ps,1);
mem.decRef();
delete &mem;
for (size_t i = 0; i < v_pos_unp.size(); i++)
v_pos.add(v_pos_unp.get(i));
for (size_t i = 0; i < v_prp_unp.size(); i++)
v_prp.add(v_prp_unp.get(i));
g_m = v_pos.size();
H5Sclose(file_dataspace_id_2);
H5Sclose(mem_dataspace_id_2);
return true;
}
public:
template<unsigned int dim, typename St, typename prp> inline bool load(const std::string & filename,
openfpm::vector<Point<dim,St>> & v_pos,
openfpm::vector<prp> & v_prp,
size_t & g_m)
{
Vcluster & v_cl = create_vcluster();
v_pos.clear();
v_prp.clear();
g_m = 0;
MPI_Comm comm = v_cl.getMPIComm();
MPI_Info info = MPI_INFO_NULL;
int mpi_rank = v_cl.getProcessUnitID();
// Set up file access property list with parallel I/O access
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
if (plist_id == -1) {return false;}
herr_t err = H5Pset_fapl_mpio(plist_id, comm, info);
if (err < 0)
return false;
//Open a file
hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
if (file < 0) {return false;}
H5Pclose(plist_id);
//Open dataset
hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
if (dataset < 0) {return false;}
//Create property list for collective dataset read
plist_id = H5Pcreate(H5P_DATASET_XFER);
if (plist_id == -1) {return false;}
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
//Select file dataspace
hid_t file_dataspace_id = H5Dget_space(dataset);
if (file_dataspace_id < 0) {return false;}
hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
if (mpi_size_old < 0) {return false;}
//Where to read metadata
int metadata_out[mpi_size_old];
for (int i = 0; i < mpi_size_old; i++)
{metadata_out[i] = 0;}
//Size for data space in memory
hsize_t mdim[1] = {(size_t)mpi_size_old};
//Create data space in memory
hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
if (mem_dataspace_id < 0) {return false;}
// Read the dataset.
err = H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
if (err < 0) {return false;}
openfpm::vector<size_t> metadata_accum;
metadata_accum.resize(mpi_size_old);
metadata_accum.get(0) = 0;
for (int i = 1 ; i < mpi_size_old ; i++)
metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
//Open dataset
hid_t dataset_2 = H5Dopen (file, "vector_dist", H5P_DEFAULT);
if (dataset_2 < 0) {return false;}
//Create property list for collective dataset read
plist_id = H5Pcreate(H5P_DATASET_XFER);
if (plist_id == -1) {return false;}
err = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
if (err < 0) {return false;}
openfpm::vector<size_t> n_block;
n_block.resize(v_cl.getProcessingUnits());
for(size_t i = 0 ; i < n_block.size() ; i++)
n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
size_t max_block;
if (rest_block != 0)
max_block = n_block.get(0) + 1;
else
max_block = n_block.get(0);
//for(size_t i = 0 ; i < n_block.size() ; i++)
for(size_t i = 0 ; i < rest_block ; i++)
n_block.get(i) += 1;
size_t start_block = 0;
size_t stop_block = 0;
if (v_cl.getProcessUnitID() != 0)
{
for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
start_block += n_block.get(i);
}
stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
if (mpi_rank >= mpi_size_old)
load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
else
{
size_t n_bl = 0;
size_t lb = start_block;
for ( ; lb < stop_block ; lb++, n_bl++)
load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
if (n_bl < max_block)
load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
}
// Close open object
H5Sclose(mem_dataspace_id);
H5Sclose(file_dataspace_id);
// Close the dataset.
H5Dclose(dataset);
H5Dclose(dataset_2);
// Close the file.
H5Fclose(file);
H5Pclose(plist_id);
return true;
}
};
#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_ */
src/HDF5_wr/HDF5_wr.hpp 0 → 100644
+ 19
− 0
View file @ 08df6993
/*
* HDF5_wr.hpp
*
* Created on: May 1, 2017
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
#define VECTOR_DIST 1
#define GRID_DIST 2
#include "HDF5_writer.hpp"
#include "HDF5_reader.hpp"
#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_ */
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