From 299c7129e98defba256f4be4bada8458664266eb Mon Sep 17 00:00:00 2001
From: Tobias Meisel <tobias.meisel@ufz.de>
Date: Tue, 4 May 2021 09:45:25 +0200
Subject: [PATCH] [MeL/IO] Xdmf: Use hyperslab selector for new hdf5 file
structure
---
MeshLib/IO/XDMF/Xdmf3Writer.cpp | 41 +++++++++++++++++++++----------
MeshLib/IO/XDMF/XdmfData.cpp | 38 +++++++++++++++++++++++-----
MeshLib/IO/XDMF/XdmfHdfWriter.cpp | 2 +-
3 files changed, 61 insertions(+), 20 deletions(-)
diff --git a/MeshLib/IO/XDMF/Xdmf3Writer.cpp b/MeshLib/IO/XDMF/Xdmf3Writer.cpp
index 43fc7eb9cd6..91556c378c9 100644
--- a/MeshLib/IO/XDMF/Xdmf3Writer.cpp
+++ b/MeshLib/IO/XDMF/Xdmf3Writer.cpp
@@ -44,19 +44,27 @@ boost::shared_ptr<const XdmfAttributeCenter> elemTypeOGS2XDMF(
return mesh_item_type_ogs2xdmf.at(elem_type);
}
-static std::string getTimeSection(int const step, std::string const& name)
+static std::string getDataSection(std::string const& name)
{
- return "t_"s + std::to_string(step) + "/"s + name;
+ return "data/"s + name;
+}
+
+static std::vector<XdmfDimType> prependDimension(
+ XdmfDimType const prepend_value, std::vector<XdmfDimType> const& dimensions)
+{
+ std::vector<XdmfDimType> dims = {prepend_value};
+ dims.insert(dims.end(), dimensions.begin(), dimensions.end());
+ return dims;
}
static boost::shared_ptr<XdmfGeometry> getLightGeometry(
- std::string const& hdf5filename, int const step, XdmfData const& geometry)
+ std::string const& hdf5filename, XdmfData const& geometry)
{
auto xdmf_geometry = XdmfGeometry::New();
xdmf_geometry->setType(XdmfGeometryType::XYZ());
boost::shared_ptr<XdmfHDF5Controller> geometry_controller =
XdmfHDF5Controller::New(hdf5filename,
- getTimeSection(step, "geometry"),
+ getDataSection("geometry"),
XdmfArrayType::Float64(),
geometry.starts,
geometry.strides,
@@ -67,13 +75,13 @@ static boost::shared_ptr<XdmfGeometry> getLightGeometry(
}
static boost::shared_ptr<XdmfTopology> getLightTopology(
- std::string const& hdf5filename, int const step, XdmfData const& topology)
+ std::string const& hdf5filename, XdmfData const& topology)
{
auto xdmf_topology = XdmfTopology::New();
xdmf_topology->setType(XdmfTopologyType::Mixed());
auto topology_controller =
XdmfHDF5Controller::New(hdf5filename,
- getTimeSection(step, "topology"),
+ getDataSection("topology"),
XdmfArrayType::Int32(),
topology.starts,
topology.strides,
@@ -86,14 +94,21 @@ static boost::shared_ptr<XdmfTopology> getLightTopology(
static boost::shared_ptr<XdmfAttribute> getLightAttribute(
std::string const& hdf5filename, int const step, XdmfData const& attribute)
{
+ std::vector<XdmfDimType> starts = prependDimension(step, attribute.starts);
+ std::vector<XdmfDimType> strides = prependDimension(1, attribute.strides);
+ std::vector<XdmfDimType> global_block_dims =
+ prependDimension(1, attribute.global_block_dims);
+ std::vector<XdmfDimType> all_global_block_dims =
+ prependDimension(step + 1, attribute.global_block_dims);
+
auto const attribute_controller =
XdmfHDF5Controller::New(hdf5filename,
- getTimeSection(step, attribute.name),
+ getDataSection(attribute.name),
attribute.data_type,
- attribute.starts,
- attribute.strides,
- attribute.global_block_dims,
- attribute.global_block_dims);
+ starts,
+ strides,
+ global_block_dims,
+ all_global_block_dims);
auto const xdmf_attribute = XdmfAttribute::New();
auto const center = elemTypeOGS2XDMF(*(attribute.attribute_center));
@@ -113,8 +128,8 @@ Xdmf3Writer::Xdmf3Writer(XdmfData const& geometry, XdmfData const& topology,
: _variable_attributes(std::move(variable_attributes)),
_hdf5filename(filepath.stem().string() + ".h5")
{
- _initial_geometry = getLightGeometry(_hdf5filename, time_step, geometry);
- _initial_topology = getLightTopology(_hdf5filename, time_step, topology);
+ _initial_geometry = getLightGeometry(_hdf5filename, geometry);
+ _initial_topology = getLightTopology(_hdf5filename, topology);
std::transform(
constant_attributes.begin(), constant_attributes.end(),
diff --git a/MeshLib/IO/XDMF/XdmfData.cpp b/MeshLib/IO/XDMF/XdmfData.cpp
index 5d734997321..a2e0462e48e 100644
--- a/MeshLib/IO/XDMF/XdmfData.cpp
+++ b/MeshLib/IO/XDMF/XdmfData.cpp
@@ -47,13 +47,31 @@ static boost::shared_ptr<XdmfArrayType const> MeshPropertyDataType2XdmfType(
}
}
-XdmfData::XdmfData(std::size_t size_partitioned_dim,
+XdmfData::XdmfData(std::size_t const size_partitioned_dim,
std::size_t const size_tuple,
MeshPropertyDataType const mesh_property_data_type,
std::string const& name,
std::optional<MeshLib::MeshItemType> const attribute_center)
- : starts{0, 0, 0},
- strides{1, 1, 1},
+ : starts([&size_tuple]() {
+ if (size_tuple > 1)
+ {
+ return std::vector<XdmfDimType>{0, 0};
+ }
+ else
+ {
+ return std::vector<XdmfDimType>{0};
+ }
+ }()),
+ strides([&size_tuple]() {
+ if (size_tuple > 1)
+ {
+ return std::vector<XdmfDimType>{1};
+ }
+ else
+ {
+ return std::vector<XdmfDimType>{1, 1};
+ }
+ }()),
name(name),
attribute_center(attribute_center)
{
@@ -64,12 +82,20 @@ XdmfData::XdmfData(std::size_t size_partitioned_dim,
auto const ui_global_components =
static_cast<unsigned int>(partition_info.global_length);
auto const ui_tuple_size = static_cast<unsigned int>(size_tuple);
- global_block_dims = {ui_global_components, ui_tuple_size};
+
+ if (ui_tuple_size == 1)
+ {
+ global_block_dims = {ui_global_components};
+ }
+ else
+ {
+ global_block_dims = {ui_global_components, ui_tuple_size};
+ }
+
data_type = MeshPropertyDataType2XdmfType(mesh_property_data_type);
DBUG(
"XDMF: dataset name: {:s}, offset: {:d} "
"global_blocks: {:d}, tuples: {:d}",
- name, partition_info.local_offset,
- global_block_dims[0], ui_tuple_size);
+ name, partition_info.local_offset, global_block_dims[0], ui_tuple_size);
}
} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
index de17a426143..a33354b118f 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
@@ -21,7 +21,7 @@ XdmfHdfWriter::XdmfHdfWriter(MeshLib::Mesh const& mesh,
std::filesystem::path const& filepath,
int const time_step,
std::set<std::string>
- variable_output_names,
+ variable_output_names,
bool const use_compression)
{
// transform Data into contiguous data and collect meta data
--
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