Working implementation for HDF5 writer

- Developed a singular interface for IO writers - Wrappers for HDF5 library based on the interface - Defined wavefield format - working implementation for HDF5 format
PrincetonUniversity · Feb 28, 2024 · 304ba07 · 304ba07
1 parent b3def59
commit 304ba07
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diff --git a/include/IO/HDF5/impl/dataset.hpp b/include/IO/HDF5/impl/dataset.hpp
@@ -2,9 +2,8 @@
 #define SPECFEM_IO_HDF5_IMPL_DATASET_HPP
 
 #include "H5Cpp.h"
-#include "file.hpp"
-#include "group.hpp"
 #include "native_type.hpp"
+#include "native_type.tpp"
 #include <memory>
 #include <string>
 
@@ -23,7 +22,7 @@ template <typename ViewType> class Dataset {
 
   const static int rank;
   using value_type = typename ViewType::non_const_value_type;
-  const static H5::PredType native_type;
+  using native_type = typename specfem::IO::impl::HDF5::native_type<value_type>;
   using MemSpace = typename ViewType::memory_space;
 
   Dataset(std::unique_ptr<H5::H5File> &file, const std::string &name,
@@ -37,6 +36,7 @@ template <typename ViewType> class Dataset {
 
 private:
   ViewType data;
+  // native_type datatype;
   std::unique_ptr<H5::DataSet> dataset;
   std::unique_ptr<H5::DataSpace> dataspace;
 };

diff --git a/include/IO/HDF5/impl/dataset.tpp b/include/IO/HDF5/impl/dataset.tpp
@@ -6,11 +6,6 @@
 #include "native_type.hpp"
 #include <string>
 
-template <typename ViewType>
-const H5::PredType specfem::IO::impl::HDF5::Dataset<ViewType>::native_type =
-    specfem::IO::impl::HDF5::native_type<
-        typename ViewType::non_const_value_type>::type;
-
 // check if Kokkos version is < 4.1
 #if KOKKOS_VERSION < 40100
 template <typename ViewType>
@@ -32,10 +27,11 @@ specfem::IO::impl::HDF5::Dataset<ViewType>::Dataset(
                           dims[i] = data.extent(i);
                         }
                         return dims;
-                      }())),
-      dataset(std::make_unique<H5::DataSet>(
-          file->createDataSet(name, native_type, *dataspace))) {
-  ASSERT(data.span_is_contiguous() == true, "ViewType must be contiguous");
+                      }())) {
+
+  this->dataset = std::make_unique<H5::DataSet>(
+      file->createDataSet(name, native_type::type(), *dataspace));
+  ASSERT(data.span_is_contiguous(), "ViewType must be contiguous");
 }
 
 template <typename ViewType>
@@ -50,22 +46,22 @@ specfem::IO::impl::HDF5::Dataset<ViewType>::Dataset(
                           dims[i] = data.extent(i);
                         }
                         return dims;
-                      }())),
-      dataset(std::make_unique<H5::DataSet>(
-          group->createDataSet(name, native_type, *dataspace))) {
+                      }())) {
 
-  ASSERT(data.span_is_contiguous() == true, "ViewType must be contiguous");
+  this->dataset = std::make_unique<H5::DataSet>(
+      group->createDataSet(name, native_type::type(), *dataspace));
+  ASSERT(data.span_is_contiguous(), "ViewType must be contiguous");
 }
 
 template <typename ViewType>
 void specfem::IO::impl::HDF5::Dataset<ViewType>::write() {
   if (std::is_same_v<MemSpace, specfem::kokkos::HostMemSpace>) {
-    dataset->write(data.data(), native_type);
+    dataset->write(data.data(), native_type::type());
     return;
   } else if (std::is_same_v<MemSpace, specfem::kokkos::DevMemSpace>) {
     auto host_data = Kokkos::create_mirror_view(data);
     Kokkos::deep_copy(host_data, data);
-    dataset->write(host_data.data(), native_type);
+    dataset->write(host_data.data(), native_type::type());
     return;
   } else {
     throw std::runtime_error("Unknown memory space");

diff --git a/include/IO/HDF5/impl/file.hpp b/include/IO/HDF5/impl/file.hpp
@@ -3,7 +3,6 @@
 
 #include "H5Cpp.h"
 #include "dataset.hpp"
-#include "dataset.tpp"
 #include "group.hpp"
 #include <memory>
 #include <string>

diff --git a/include/IO/HDF5/impl/group.hpp b/include/IO/HDF5/impl/group.hpp
@@ -3,8 +3,6 @@
 
 #include "H5Cpp.h"
 #include "dataset.hpp"
-#include "dataset.tpp"
-#include "file.hpp"
 #include <memory>
 #include <string>
 

diff --git a/include/IO/HDF5/impl/native_type.hpp b/include/IO/HDF5/impl/native_type.hpp
@@ -8,7 +8,7 @@ namespace IO {
 namespace impl {
 namespace HDF5 {
 
-template <typename T> struct native_type { const static H5::PredType type; };
+template <typename T> struct native_type {};
 } // namespace HDF5
 } // namespace impl
 } // namespace IO

diff --git a/include/IO/HDF5/impl/native_type.tpp b/include/IO/HDF5/impl/native_type.tpp
@@ -0,0 +1,112 @@
+#ifndef SPECFEM_IO_HDF5_IMPL_NATIVE_TYPE_TPP
+#define SPECFEM_IO_HDF5_IMPL_NATIVE_TYPE_TPP
+
+#include "H5Cpp.h"
+#include "native_type.hpp"
+#include <iostream>
+
+template <> struct specfem::IO::impl::HDF5::native_type<int> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_INT);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<float> {
+  static H5::FloatType& type() {
+    static H5::FloatType type(H5::PredType::NATIVE_FLOAT);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<double> {
+  static H5::FloatType& type() {
+    static H5::FloatType type(H5::PredType::NATIVE_DOUBLE);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<long> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_LONG);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<long long> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_LLONG);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<unsigned int> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_UINT);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<unsigned long> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_ULONG);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<unsigned long long> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_ULLONG);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<unsigned char> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_UCHAR);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<char> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_CHAR);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<short> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_SHORT);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<unsigned short> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_USHORT);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+template <> struct specfem::IO::impl::HDF5::native_type<bool> {
+  static H5::IntType& type() {
+    static H5::IntType type(H5::PredType::NATIVE_HBOOL);
+    type.setOrder(H5T_ORDER_LE);
+    return type;
+  }
+};
+
+#endif
diff --git a/src/IO/HDF5/native_type.cpp b/src/IO/HDF5/native_type.cpp
@@ -1,55 +1,31 @@
 #include "IO/HDF5/impl/native_type.hpp"
 #include "H5Cpp.h"
+#include "IO/HDF5/impl/native_type.tpp"
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<float>::type =
-    H5::PredType::NATIVE_FLOAT;
+// Explicit instantiation
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<double>::type =
-    H5::PredType::NATIVE_DOUBLE;
+template struct specfem::IO::impl::HDF5::native_type<float>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<int>::type =
-    H5::PredType::NATIVE_INT;
+template struct specfem::IO::impl::HDF5::native_type<double>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<long>::type =
-    H5::PredType::NATIVE_LONG;
+template struct specfem::IO::impl::HDF5::native_type<int>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<long long>::type =
-    H5::PredType::NATIVE_LLONG;
+template struct specfem::IO::impl::HDF5::native_type<long>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<unsigned int>::type =
-    H5::PredType::NATIVE_UINT;
+template struct specfem::IO::impl::HDF5::native_type<long long>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<unsigned long>::type =
-    H5::PredType::NATIVE_ULONG;
+template struct specfem::IO::impl::HDF5::native_type<unsigned int>;
 
-template <>
-const H5::PredType
-    specfem::IO::impl::HDF5::native_type<unsigned long long>::type =
-        H5::PredType::NATIVE_ULLONG;
+template struct specfem::IO::impl::HDF5::native_type<unsigned long>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<short>::type =
-    H5::PredType::NATIVE_SHORT;
+template struct specfem::IO::impl::HDF5::native_type<unsigned long long>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<unsigned short>::type =
-    H5::PredType::NATIVE_USHORT;
+template struct specfem::IO::impl::HDF5::native_type<short>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<char>::type =
-    H5::PredType::NATIVE_CHAR;
+template struct specfem::IO::impl::HDF5::native_type<unsigned short>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<unsigned char>::type =
-    H5::PredType::NATIVE_UCHAR;
+template struct specfem::IO::impl::HDF5::native_type<char>;
 
-template <>
-const H5::PredType specfem::IO::impl::HDF5::native_type<bool>::type =
-    H5::PredType::NATIVE_HBOOL;
+template struct specfem::IO::impl::HDF5::native_type<unsigned char>;
+
+template struct specfem::IO::impl::HDF5::native_type<bool>;