From 7ee45d4224b1ae003447ad7468c01b68c23d5bc0 Mon Sep 17 00:00:00 2001
From: Tobias Meisel <tobias.meisel@ufz.de>
Date: Tue, 15 Dec 2020 13:02:21 +0100
Subject: [PATCH] [MeL/IO] Introduce data structure for handling meta data for
hdf writing algorithm
---
MeshLib/IO/XDMF/HdfData.cpp | 49 +++++++++++++++++++++++++
MeshLib/IO/XDMF/HdfData.h | 36 +++++++++++++++++++
MeshLib/IO/XDMF/XdmfData.cpp | 68 +++++++++++++++++++++++++++++++++++
MeshLib/IO/XDMF/XdmfData.h | 65 +++++++++++++++++++--------------
MeshLib/IO/XDMF/XdmfHdfData.h | 44 +++++++++++++++++++++++
5 files changed, 235 insertions(+), 27 deletions(-)
create mode 100644 MeshLib/IO/XDMF/HdfData.cpp
create mode 100644 MeshLib/IO/XDMF/HdfData.h
create mode 100644 MeshLib/IO/XDMF/XdmfData.cpp
create mode 100644 MeshLib/IO/XDMF/XdmfHdfData.h
diff --git a/MeshLib/IO/XDMF/HdfData.cpp b/MeshLib/IO/XDMF/HdfData.cpp
new file mode 100644
index 00000000000..54e3c15b48d
--- /dev/null
+++ b/MeshLib/IO/XDMF/HdfData.cpp
@@ -0,0 +1,49 @@
+#include "HdfData.h"
+
+#include <hdf5.h>
+
+#include <map>
+
+#include "BaseLib/Error.h"
+#include "BaseLib/Logging.h"
+#include "partition.h"
+
+namespace MeshLib::IO
+{
+static hid_t meshPropertyType2HdfType(MeshPropertyDataType const ogs_data_type)
+{
+ std::map<MeshPropertyDataType const, hid_t> ogs_to_hdf_type = {
+ {MeshPropertyDataType::float64, H5T_IEEE_F64LE},
+ {MeshPropertyDataType::float32, H5T_IEEE_F32LE},
+ {MeshPropertyDataType::int32, H5T_STD_I32LE},
+ {MeshPropertyDataType::int64, H5T_STD_I64LE},
+ {MeshPropertyDataType::uint32, H5T_STD_U32LE},
+ {MeshPropertyDataType::uint64, H5T_STD_U64LE},
+ {MeshPropertyDataType::int8, H5T_STD_I8LE},
+ {MeshPropertyDataType::uint8, H5T_STD_U8LE}};
+ try
+ {
+ return ogs_to_hdf_type.at(ogs_data_type);
+ }
+ catch (std::exception const& e)
+ {
+ OGS_FATAL("No known HDF5 type for OGS type. {:s}", e.what());
+ }
+}
+
+HdfData::HdfData(void const* data_start, std::size_t const size_partitioned_dim,
+ std::size_t const size_tuple, std::string const& name,
+ MeshPropertyDataType const mesh_property_data_type)
+ : data_start(data_start),
+ data_space{size_partitioned_dim, size_tuple},
+ name(name)
+{
+ auto const& partition_info = getPartitionInfo(size_partitioned_dim);
+ DBUG("HdfData: The partition of dataset {:s} has dimension {:d} and offset {:d}.",
+ name, size_partitioned_dim, partition_info.first);
+ auto const& offset_partitioned_dim = partition_info.first;
+ offsets = {offset_partitioned_dim, 0};
+ file_space = {partition_info.second, size_tuple};
+ data_type = meshPropertyType2HdfType(mesh_property_data_type);
+}
+} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/HdfData.h b/MeshLib/IO/XDMF/HdfData.h
new file mode 100644
index 00000000000..e31bb62c90b
--- /dev/null
+++ b/MeshLib/IO/XDMF/HdfData.h
@@ -0,0 +1,36 @@
+/**
+ * \file
+ * \author Tobias Meisel
+ * \date 2020-12-08
+ * \brief Collects and holds all metadata for writing HDF5 file
+ * \copyright Copyright (c) 2012-2020, OpenGeoSys Community
+ * (http://www.opengeosys.org) Distributed under a Modified BSD License. See
+ * accompanying file LICENSE.txt or http://www.opengeosys.org/project/license
+ */
+
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include "MeshPropertyDataType.h"
+
+namespace MeshLib::IO
+{
+using Hdf5DimType = unsigned long long;
+
+struct HdfData
+{
+ HdfData(void const* data_start, std::size_t size_partitioned_dim,
+ std::size_t size_tuple, std::string const& name,
+ MeshPropertyDataType mesh_property_data_type);
+ void const* data_start;
+ std::vector<Hdf5DimType> const data_space;
+ std::vector<Hdf5DimType> offsets;
+ std::vector<Hdf5DimType> file_space;
+ std::string const name;
+ int64_t data_type;
+};
+
+} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/XdmfData.cpp b/MeshLib/IO/XDMF/XdmfData.cpp
new file mode 100644
index 00000000000..cdee513cad8
--- /dev/null
+++ b/MeshLib/IO/XDMF/XdmfData.cpp
@@ -0,0 +1,68 @@
+#include "XdmfData.h"
+
+#include <XdmfArrayType.hpp>
+#include <XdmfAttributeCenter.hpp>
+#include <XdmfTopologyType.hpp>
+#include <cassert>
+#include <map>
+
+#include "BaseLib/Error.h"
+#include "MeshLib/Location.h"
+#include "partition.h"
+
+namespace MeshLib::IO
+
+{
+static boost::shared_ptr<XdmfArrayType const> MeshPropertyDataType2XdmfType(
+ MeshPropertyDataType const ogs_data_type)
+{
+ std::map<MeshPropertyDataType, boost::shared_ptr<XdmfArrayType const>> const
+ ogs_to_xdmf_type = {
+ {MeshPropertyDataType::float64, XdmfArrayType::Float64()},
+ {MeshPropertyDataType::float32, XdmfArrayType::Float32()},
+ {MeshPropertyDataType::int32, XdmfArrayType::Int32()},
+ // TODO (tm) XdmfLib does not support 64 bit data types so far
+ //{MeshPropertyDataType::int64, XdmfArrayType::Int64()},
+ {MeshPropertyDataType::uint32, XdmfArrayType::UInt32()},
+ // TODO (tm) XdmfLib does not support 64 bit data types so far
+ //{MeshPropertyDataType::uint64, XdmfArrayType::UInt64},
+ {MeshPropertyDataType::int8, XdmfArrayType::Int8()},
+ {MeshPropertyDataType::uint8, XdmfArrayType::UInt8()}};
+ try
+ {
+ return ogs_to_xdmf_type.at(ogs_data_type);
+ }
+ catch (const std::exception& e)
+ {
+ OGS_FATAL("No known HDF5 type for XDMF type. {:s}", e.what());
+ }
+}
+
+XdmfData::XdmfData(std::size_t 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},
+ name(name),
+ attribute_center(attribute_center)
+{
+ auto partition_info = getPartitionInfo(size_partitioned_dim);
+ DBUG(
+ "XdmfData: The partition of dataset {:s} has dimension {:d} and offset "
+ "{:d}.",
+ name, size_partitioned_dim, partition_info.first);
+ // TODO (tm) XdmfLib does not support 64 bit data types so far
+ assert(partition_info.second < std::numeric_limits<unsigned int>::max());
+ auto const ui_global_components =
+ static_cast<unsigned int>(partition_info.second);
+ auto const ui_tuple_size = static_cast<unsigned int>(size_tuple);
+
+ piece_dims = {ui_global_components, ui_tuple_size};
+ block_dims = {static_cast<XdmfDimType>(size_partitioned_dim),
+ ui_tuple_size};
+
+ data_type = MeshPropertyDataType2XdmfType(mesh_property_data_type);
+}
+} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/XdmfData.h b/MeshLib/IO/XDMF/XdmfData.h
index 2a8ad7d90d5..6bb86b6aa09 100644
--- a/MeshLib/IO/XDMF/XdmfData.h
+++ b/MeshLib/IO/XDMF/XdmfData.h
@@ -2,7 +2,7 @@
* \file
* \author Tobias Meisel
* \date 2020-11-13
- * \brief Definition of the data layer for writing Meshes
+ * \brief Collects and holds all metadata for writing XDMF file
* \copyright
* Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
* Distributed under a Modified BSD License.
@@ -13,43 +13,54 @@
#pragma once
#include <boost/shared_ptr.hpp>
+#include <optional>
#include <string>
#include <vector>
-class XdmfAttributeCenter;
+#include "MeshLib/Location.h"
+#include "MeshPropertyDataType.h"
+
class XdmfArrayType;
namespace MeshLib::IO
{
using XdmfDimType = unsigned int;
-using Hdf5DimType = unsigned long long;
-struct Geometry final
-{
- std::vector<double> flattend_values;
- std::vector<XdmfDimType> const starts;
- std::vector<XdmfDimType> const strides;
- std::vector<XdmfDimType> const vdims;
- std::vector<Hdf5DimType> const vldims;
-};
-struct Topology final
+struct XdmfData
{
- std::vector<int> flattend_values;
+ /**
+ * \brief XdmfData contains meta data to be passed to the XdmfWriter - it
+ * does not contain the actual values!!
+ * @param size_partitioned_dim The first dimension (index 0) is assumed to
+ * be the dimension that is partitioned. This first dimension expresses the
+ * length, usually the number of nodes or the number of cells. These values
+ * give the length of the local partition.
+ * @param size_tuple We assume there is at most a rank of 2 of data
+ * (properties). The size of tuple gives the length of the second dimension
+ * (index 1).
+ * @param name The name of the attribute. It assumed to be unique.
+ * @param attribute_center XdmfData is used for topology, geometry and
+ * attributes. Geometry and topology have never a attribute_center.
+ * Attributes have always an attribute_center
+ * @return vector of meta data
+ */
+ XdmfData(std::size_t size_partitioned_dim, std::size_t size_tuple,
+ MeshPropertyDataType mesh_property_data_type,
+ std::string const& name,
+ std::optional<MeshLib::MeshItemType> attribute_center);
+ // a hyperslab is defined by starts and strides see
+ // https://www.xdmf.org/index.php/XDMF_Model_and_Format#HyperSlab
std::vector<XdmfDimType> const starts;
std::vector<XdmfDimType> const strides;
- std::vector<XdmfDimType> const vdims;
- std::vector<Hdf5DimType> const vldims;
-};
-
-struct AttributeMeta final
-{
- const void* data_start;
- std::string name;
- boost::shared_ptr<const XdmfAttributeCenter> attribute_center;
+ // piece and block nomenclature taken from
+ // https://www.paraview.org/Wiki/VTK/Tutorials/Composite_Datasets in XDMF it
+ // refers to spatial grid collection composed from subsets
+ // https://www.xdmf.org/index.php/XDMF_Model_and_Format#Grid
+ std::vector<XdmfDimType> piece_dims;
+ std::vector<XdmfDimType> block_dims;
boost::shared_ptr<const XdmfArrayType> data_type;
- std::vector<XdmfDimType> starts;
- std::vector<XdmfDimType> strides;
- std::vector<XdmfDimType> vdims;
- std::vector<Hdf5DimType> vldims;
+ std::string const name;
+ std::optional<MeshLib::MeshItemType> const attribute_center;
};
-} // namespace MeshLib::IO
\ No newline at end of file
+
+} // namespace MeshLib::IO
diff --git a/MeshLib/IO/XDMF/XdmfHdfData.h b/MeshLib/IO/XDMF/XdmfHdfData.h
new file mode 100644
index 00000000000..1b049e40f2b
--- /dev/null
+++ b/MeshLib/IO/XDMF/XdmfHdfData.h
@@ -0,0 +1,44 @@
+/**
+ * \file
+ * \author Tobias Meisel
+ * \date 2020-11-13
+ * \brief Holds all data for the combined writing of xdmf and hdf5 file
+ * \copyright
+ * Copyright (c) 2012-2020, OpenGeoSys Community (http://www.opengeosys.org)
+ * Distributed under a Modified BSD License.
+ * See accompanying file LICENSE.txt or
+ * http://www.opengeosys.org/project/license
+ */
+
+#pragma once
+
+#include <boost/shared_ptr.hpp>
+#include <vector>
+
+#include "HdfData.h"
+#include "XdmfData.h"
+
+// TODO (tm) This structs are the result of transformData.cpp. This structures
+// can be eliminated.
+namespace MeshLib::IO
+{
+struct Geometry final
+{
+ std::vector<double> flattened_values;
+ HdfData hdf;
+ XdmfData xdmf;
+};
+
+struct Topology final
+{
+ std::vector<int> flattened_values;
+ HdfData hdf;
+ XdmfData xdmf;
+};
+
+struct AttributeMeta final
+{
+ HdfData hdf;
+ XdmfData xdmf;
+};
+} // namespace MeshLib::IO
\ No newline at end of file
--
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