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Commit b37d1f14 authored by Stéphane Del Pino's avatar Stéphane Del Pino
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Change VTKWriter to produce binary data 

This generally does not reduces the file sizes, but it reduces the
writing and reading times (no encoding/decoding is required)
parent ca70212f
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1 merge request!80Feature/writers improvement
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CMakeLists.txt
+ 10
− 0
View file @ b37d1f14
......@@ -113,6 +113,16 @@ if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
endif()
endif()
#------------------------------------------------------
include (TestBigEndian)
TEST_BIG_ENDIAN(IS_BIG_ENDIAN)
if(IS_BIG_ENDIAN)
set(PUGS_LITTLE_ENDIAN FALSE)
else()
set(PUGS_LITTLE_ENDIAN TRUE)
endif()
#------------------------------------------------------
# defaults use of MPI
set(PUGS_ENABLE_MPI AUTO CACHE STRING
......
src/output/VTKWriter.cpp
+ 163
− 80
View file @ b37d1f14
......@@ -6,6 +6,7 @@
#include <mesh/MeshDataManager.hpp>
#include <utils/Messenger.hpp>
#include <utils/RevisionInfo.hpp>
#include <utils/pugs_config.hpp>
#include <ctime>
#include <fstream>
......@@ -13,6 +14,99 @@
#include <sstream>
#include <unordered_map>
class ICharArrayEmbedder
{
public:
ICharArrayEmbedder() = default;
ICharArrayEmbedder(const ICharArrayEmbedder&) = default;
ICharArrayEmbedder(ICharArrayEmbedder&&) = default;
virtual size_t size() const = 0;
virtual void write(std::ostream&) const = 0;
virtual ~ICharArrayEmbedder() = default;
};
template <typename InputDataT>
class CharArrayEmbedder : public ICharArrayEmbedder
{
CastArray<InputDataT, char> m_char_cast_array;
public:
size_t
size() const final
{
return m_char_cast_array.size();
}
void
write(std::ostream& os) const final
{
os.write(&(m_char_cast_array[0]), m_char_cast_array.size());
}
CharArrayEmbedder(Array<InputDataT> array) : m_char_cast_array{array} {}
CharArrayEmbedder() = default;
CharArrayEmbedder(const CharArrayEmbedder&) = default;
CharArrayEmbedder(CharArrayEmbedder&&) = default;
~CharArrayEmbedder() = default;
};
class VTKWriter::SerializedDataList
{
private:
std::vector<std::shared_ptr<ICharArrayEmbedder>> m_serialized_data_list;
size_t m_offset = 0;
public:
size_t
offset() const
{
return m_offset;
}
template <typename DataT>
void
add(Array<DataT> array)
{
auto array_data = std::make_shared<CharArrayEmbedder<DataT>>(array);
auto size_data = std::make_shared<CharArrayEmbedder<int>>([&] {
Array<int> size_array(1);
size_array[0] = array_data->size();
return size_array;
}());
m_serialized_data_list.push_back(size_data);
m_serialized_data_list.push_back(array_data);
m_offset += size_data->size() + array_data->size();
}
template <typename DataT, ItemType item_type, typename ConnectivityT>
void
add(const ItemValue<DataT, item_type, ConnectivityT>& item_value)
{
Array<std::remove_const_t<DataT>> array(item_value.numberOfItems());
parallel_for(
item_value.numberOfItems(), PUGS_LAMBDA(ItemIdT<item_type> item_id) { array[item_id] = item_value[item_id]; });
this->add(array);
}
void
write(std::ostream& os) const
{
for (auto serialized_data : m_serialized_data_list) {
serialized_data->write(os);
}
}
SerializedDataList() = default;
~SerializedDataList() = default;
};
std::string
VTKWriter::_getFilenamePVTU() const
{
......@@ -134,141 +228,114 @@ struct VTKWriter::VTKType
template <typename DataType>
void
VTKWriter::_write_array(std::ofstream& os, const std::string& name, const Array<DataType>& item_value) const
VTKWriter::_write_array(std::ofstream& os,
const std::string& name,
const Array<DataType>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\">\n";
for (typename Array<DataType>::index_type i = 0; i < item_value.size(); ++i) {
// The following '+' enforces integer output for char types
os << +item_value[i] << ' ';
}
os << "\n</DataArray>\n";
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" offset=\""
<< serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <size_t N, typename DataType>
void
VTKWriter::_write_array(std::ofstream& os,
const std::string& name,
const Array<TinyVector<N, DataType>>& item_value) const
const Array<TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" NumberOfComponents=\"" << N
<< "\">\n";
for (typename Array<DataType>::index_type i = 0; i < item_value.size(); ++i) {
for (size_t j = 0; j < N; ++j) {
// The following '+' enforces integer output for char types
os << +item_value[i][j] << ' ';
}
}
os << "\n</DataArray>\n";
<< "\" offset=\"" << serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <typename DataType>
void
VTKWriter::_write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const DataType>& item_value) const
const NodeValue<const DataType>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\">\n";
for (NodeId i = 0; i < item_value.size(); ++i) {
// The following '+' enforces integer output for char types
os << +item_value[i] << ' ';
}
os << "\n</DataArray>\n";
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" offset=\""
<< serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <size_t N, typename DataType>
void
VTKWriter::_write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const TinyVector<N, DataType>>& item_value) const
const NodeValue<const TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" NumberOfComponents=\"" << N
<< "\">\n";
for (NodeId i = 0; i < item_value.size(); ++i) {
for (size_t j = 0; j < N; ++j) {
// The following '+' enforces integer output for char types
os << +item_value[i][j] << ' ';
}
}
os << "\n</DataArray>\n";
<< "\" offset=\"" << serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <size_t N, typename DataType>
void
VTKWriter::_write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const TinyMatrix<N, DataType>>& item_value) const
const NodeValue<const TinyMatrix<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" NumberOfComponents=\"" << N * N
<< "\">\n";
for (NodeId i = 0; i < item_value.size(); ++i) {
for (size_t j = 0; j < N; ++j) {
for (size_t k = 0; k < N; ++k) {
// The following '+' enforces integer output for char types
os << +item_value[i](j, k) << ' ';
}
}
}
os << "\n</DataArray>\n";
<< "\" offset=\"" << serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <typename DataType>
void
VTKWriter::_write_node_value(std::ofstream&, const std::string&, const CellValue<const DataType>&) const
VTKWriter::_write_node_value(std::ofstream&,
const std::string&,
const CellValue<const DataType>&,
SerializedDataList&) const
{}
template <typename DataType>
void
VTKWriter::_write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const DataType>& item_value) const
const CellValue<const DataType>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\">\n";
for (CellId i = 0; i < item_value.size(); ++i) {
// The following '+' enforces integer output for char types
os << +item_value[i] << ' ';
}
os << "\n</DataArray>\n";
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" offset=\""
<< serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <size_t N, typename DataType>
void
VTKWriter::_write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const TinyVector<N, DataType>>& item_value) const
const CellValue<const TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" NumberOfComponents=\"" << N
<< "\">\n";
for (CellId i = 0; i < item_value.size(); ++i) {
for (size_t j = 0; j < N; ++j) {
// The following '+' enforces integer output for char types
os << +item_value[i][j] << ' ';
}
}
os << "\n</DataArray>\n";
<< "\" offset=\"" << serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <size_t N, typename DataType>
void
VTKWriter::_write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const TinyMatrix<N, DataType>>& item_value) const
const CellValue<const TinyMatrix<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const
{
os << "<DataArray type=\"" << VTKType<DataType>::name << "\" Name=\"" << name << "\" NumberOfComponents=\"" << N * N
<< "\">\n";
for (CellId i = 0; i < item_value.size(); ++i) {
for (size_t j = 0; j < N; ++j) {
for (size_t k = 0; k < N; ++k) {
// The following '+' enforces integer output for char types
os << +item_value[i](j, k) << ' ';
}
}
}
os << "\n</DataArray>\n";
<< "\" offset=\"" << serialized_data_list.offset() << "\" format=\"appended\"/>\n";
serialized_data_list.add(item_value);
}
template <typename DataType>
void
VTKWriter::_write_cell_value(std::ofstream&, const std::string&, const NodeValue<const DataType>&) const
VTKWriter::_write_cell_value(std::ofstream&,
const std::string&,
const NodeValue<const DataType>&,
SerializedDataList&) const
{}
template <typename MeshType>
......@@ -329,23 +396,34 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
fout << "</VTKFile>\n";
}
{ // write VTK files
{
SerializedDataList serialize_data_list;
// write VTK files
std::ofstream fout(_getFilenameVTU(parallel::rank()));
fout << "<?xml version=\"1.0\"?>\n";
fout << _getDateAndVersionComment();
fout << "<VTKFile type=\"UnstructuredGrid\">\n";
fout << "<VTKFile type=\"UnstructuredGrid\"";
#if defined(PUGS_LITTLE_ENDIAN)
fout << " byte_order=\"LittleEndian\"";
#else
fout << " byte_order=\"BigEndian\"";
#endif
fout << ">\n";
fout << "<UnstructuredGrid>\n";
fout << "<Piece NumberOfPoints=\"" << mesh->numberOfNodes() << "\" NumberOfCells=\"" << mesh->numberOfCells()
<< "\">\n";
fout << "<CellData>\n";
for (const auto& [name, item_value_variant] : output_named_item_value_set) {
std::visit([&, name = name](auto&& item_value) { return this->_write_cell_value(fout, name, item_value); },
std::visit([&, name = name](
auto&& item_value) { return this->_write_cell_value(fout, name, item_value, serialize_data_list); },
item_value_variant);
}
fout << "</CellData>\n";
fout << "<PointData>\n";
for (const auto& [name, item_value_variant] : output_named_item_value_set) {
std::visit([&, name = name](auto&& item_value) { return this->_write_node_value(fout, name, item_value); },
std::visit([&, name = name](
auto&& item_value) { return this->_write_node_value(fout, name, item_value, serialize_data_list); },
item_value_variant);
}
fout << "</PointData>\n";
......@@ -363,7 +441,7 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
positions[r][i] = 0;
}
});
_write_array(fout, "Positions", positions);
_write_array(fout, "Positions", positions, serialize_data_list);
}
fout << "</Points>\n";
......@@ -371,7 +449,7 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
{
const auto& cell_to_node_matrix = mesh->connectivity().cellToNodeMatrix();
_write_array(fout, "connectivity", cell_to_node_matrix.entries());
_write_array(fout, "connectivity", cell_to_node_matrix.entries(), serialize_data_list);
}
{
......@@ -383,7 +461,7 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
offset += cell_nodes.size();
offsets[j] = offset;
}
_write_array(fout, "offsets", offsets);
_write_array(fout, "offsets", offsets, serialize_data_list);
}
{
......@@ -437,7 +515,7 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
}
}
});
_write_array(fout, "types", types);
_write_array(fout, "types", types, serialize_data_list);
if constexpr (MeshType::Dimension == 3) {
const bool has_general_polyhedron = [&] {
for (size_t i = 0; i < types.size(); ++i) {
......@@ -507,6 +585,11 @@ VTKWriter::_write(const std::shared_ptr<const MeshType>& mesh,
fout << "</Cells>\n";
fout << "</Piece>\n";
fout << "</UnstructuredGrid>\n";
fout << "<AppendedData encoding=\"raw\">\n";
fout << "_";
serialize_data_list.write(fout);
fout << '\n';
fout << "</AppendedData>\n";
fout << "</VTKFile>\n";
}
......
src/output/VTKWriter.hpp
+ 34
− 10
View file @ b37d1f14
......@@ -14,6 +14,8 @@ class IMesh;
class VTKWriter : public WriterBase
{
private:
class SerializedDataList;
std::string _getDateAndVersionComment() const;
std::string _getFilenamePVTU() const;
......@@ -56,42 +58,64 @@ class VTKWriter : public WriterBase
struct VTKType;
template <typename DataType>
void _write_array(std::ofstream& os, const std::string& name, const Array<DataType>& item_value) const;
void _write_array(std::ofstream& os,
const std::string& name,
const Array<DataType>& item_value,
SerializedDataList& serialized_data_list) const;
template <size_t N, typename DataType>
void _write_array(std::ofstream& os, const std::string& name, const Array<TinyVector<N, DataType>>& item_value) const;
void _write_array(std::ofstream& os,
const std::string& name,
const Array<TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const;
template <typename DataType>
void _write_node_value(std::ofstream& os, const std::string& name, const NodeValue<const DataType>& item_value) const;
void _write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const DataType>& item_value,
SerializedDataList& serialized_data_list) const;
template <size_t N, typename DataType>
void _write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const TinyVector<N, DataType>>& item_value) const;
const NodeValue<const TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const;
template <size_t N, typename DataType>
void _write_node_value(std::ofstream& os,
const std::string& name,
const NodeValue<const TinyMatrix<N, DataType>>& item_value) const;
const NodeValue<const TinyMatrix<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const;
template <typename DataType>
void _write_node_value(std::ofstream&, const std::string&, const CellValue<const DataType>&) const;
void _write_node_value(std::ofstream&,
const std::string&,
const CellValue<const DataType>&,
SerializedDataList&) const;
template <typename DataType>
void _write_cell_value(std::ofstream& os, const std::string& name, const CellValue<const DataType>& item_value) const;
void _write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const DataType>& item_value,
SerializedDataList& serialized_data_list) const;
template <size_t N, typename DataType>
void _write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const TinyVector<N, DataType>>& item_value) const;
const CellValue<const TinyVector<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const;
template <size_t N, typename DataType>
void _write_cell_value(std::ofstream& os,
const std::string& name,
const CellValue<const TinyMatrix<N, DataType>>& item_value) const;
const CellValue<const TinyMatrix<N, DataType>>& item_value,
SerializedDataList& serialized_data_list) const;
template <typename DataType>
void _write_cell_value(std::ofstream&, const std::string&, const NodeValue<const DataType>&) const;
void _write_cell_value(std::ofstream&,
const std::string&,
const NodeValue<const DataType>&,
SerializedDataList&) const;
template <typename MeshType>
void _write(const std::shared_ptr<const MeshType>& mesh,
......
src/utils/pugs_config.hpp.in
+ 2
− 0
View file @ b37d1f14
......@@ -9,6 +9,8 @@
#cmakedefine SYSTEM_IS_DARWIN
#cmakedefine SYSTEM_IS_WINDOWS
#cmakedefine PUGS_LITTLE_ENDIAN
#define PUGS_BUILD_TYPE "@CMAKE_BUILD_TYPE@"
#define PUGS_BINARY_DIR "@PUGS_BINARY_DIR@"
......
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