Initial implementation of Attributes with Tests

Refactored IO, Variable class due to common functionality

source/adios2/CMakeLists.txt

@@ -4,6 +4,8 @@
 #------------------------------------------------------------------------------#
   
 add_library(adios2
+  core/Attribute.cpp core/Attribute.tcc
+  core/AttributeBase.cpp
   core/ADIOS.cpp
   core/Engine.cpp
   core/IO.cpp core/IO.tcc

source/adios2/core/Attribute.cpp

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * Attribute.cpp : needed for template separation using Attribute.tcc
+ *
+ *  Created on: Aug 3, 2017
+ *      Author: William F Godoy godoywf@ornl.gov
+ */
+
+#include "Attribute.h"
+#include "Attribute.tcc"
+
+namespace adios2
+{
+
+} // end namespace adios2

source/adios2/core/Attribute.h

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * Attribute.h : template class
+ * Attribute.h : template class that defines typed attributes
  *
  *  Created on: Aug 1, 2017
  *      Author: William F Godoy godoywf@ornl.gov
@@ -45,4 +45,4 @@ public:
 
 } // end namespace adios2
 
-#endif /* SOURCE_ADIOS2_CORE_ATTRIBUTE_H_ */
+#endif /* ADIOS2_CORE_ATTRIBUTE_H_ */

source/adios2/core/Attribute.tcc

@@ -31,7 +31,7 @@ namespace adios2
                                                                                \
     template <>                                                                \
     Attribute<T>::Attribute(const std::string &name, const T &value)           \
-    : AttributeBase(name, GetType<T>(), 1), m_DataValue()                      \
+    : AttributeBase(name, GetType<T>(), 1), m_DataValue(value)                 \
     {                                                                          \
     }
 
@@ -39,3 +39,5 @@ ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(declare_type)
 #undef declare_type
 
 } // end namespace adios2
+
+#endif /* ADIOS2_CORE_ATTRIBUTE_TCC_ */

source/adios2/core/AttributeBase.h

@@ -11,6 +11,13 @@
 #ifndef ADIOS2_CORE_ATTRIBUTEBASE_H_
 #define ADIOS2_CORE_ATTRIBUTEBASE_H_
 
+/// \cond EXCLUDE_FROM_DOXYGEN
+#include <string>
+/// \endcond
+
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOSTypes.h"
+
 namespace adios2
 {
 

source/adios2/core/IO.cpp

@@ -287,11 +287,22 @@ void IO::CheckTransportType(const std::string type) const
 
 // Explicitly instantiate the necessary public template implementations
 #define define_template_instantiation(T)                                       \
-    template Variable<T> &IO::DefineVariable<T>(                               \
-        const std::string &, const Dims, const Dims, const Dims, const bool);  \
+    template Variable<T> &IO::DefineVariable<T>(const std::string &,           \
+                                                const Dims &, const Dims &,    \
+                                                const Dims &, const bool);     \
     template Variable<T> &IO::GetVariable<T>(const std::string &);
 
 ADIOS2_FOREACH_TYPE_1ARG(define_template_instantiation)
 #undef define_template_instatiation
 
+#define declare_template_instantiation(T)                                      \
+    template Attribute<T> &IO::DefineAttribute<T>(const std::string &,         \
+                                                  const T *, const size_t);    \
+    template Attribute<T> &IO::DefineAttribute<T>(const std::string &,         \
+                                                  const T &);                  \
+    template Attribute<T> &IO::GetAttribute(const std::string &);
+
+ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+
 } // end namespace adios

source/adios2/core/IO.h

@@ -118,8 +118,8 @@ public:
      * @return reference to Variable object
      */
     template <class T>
-    Variable<T> &DefineVariable(const std::string &name, const Dims shape = {},
-                                const Dims start = {}, const Dims count = {},
+    Variable<T> &DefineVariable(const std::string &name, const Dims &shape = {},
+                                const Dims &start = {}, const Dims &count = {},
                                 const bool constantShape = false);
 
     /**
@@ -136,13 +136,14 @@ public:
      */
 
     template <class T>
-    VariableCompound &
-    DefineVariableCompound(const std::string &name, const Dims shape = Dims{},
-                           const Dims start = Dims{}, const Dims count = Dims{},
-                           const bool constantShape = false);
+    VariableCompound &DefineVariableCompound(const std::string &name,
+                                             const Dims &shape = Dims{},
+                                             const Dims &start = Dims{},
+                                             const Dims &count = Dims{},
+                                             const bool constantShape = false);
 
     /**
-     * Define attribute from contiguous data array
+     * Define attribute from contiguous data array owned by an application
      * @param name must be unique for the IO object
      * @param array pointer to user data
      * @param elements number of data elements
@@ -153,7 +154,7 @@ public:
                                   const size_t elements);
 
     /**
-     * Define attribute from a single variable
+     * Define attribute from a single variable making a copy
      * @param name must be unique for the IO object
      * @param value single data value
      * @return reference to internal Attribute
@@ -340,8 +341,8 @@ private:
 // Explicit declaration of the public template methods
 #define declare_template_instantiation(T)                                      \
     extern template Variable<T> &IO::DefineVariable<T>(                        \
-        const std::string &name, const Dims, const Dims, const Dims,           \
-        const bool constantShape);                                             \
+        const std::string &, const Dims &, const Dims &, const Dims &,         \
+        const bool);                                                           \
     extern template Variable<T> &IO::GetVariable<T>(const std::string &name);
 
 ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
@@ -349,14 +350,15 @@ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
 
 #define declare_template_instantiation(T)                                      \
     extern template Attribute<T> &IO::DefineAttribute<T>(                      \
-        const std::string &name, const T *array, const size_t elements);       \
-    extern template Attribute<T> &IO::DefineAttribute<T>(                      \
-        const std::string &name, const T &value);
+        const std::string &, const T *, const size_t);                         \
+    extern template Attribute<T> &IO::DefineAttribute<T>(const std::string &,  \
+                                                         const T &);           \
+    extern template Attribute<T> &IO::GetAttribute(const std::string &);
 
 ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(declare_template_instantiation)
 #undef declare_template_instantiation
 
-} // end namespace adios
+} // end namespace adios2
 
 #include "adios2/core/IO.inl"
 

source/adios2/core/IO.inl

@@ -21,10 +21,10 @@ namespace adios2
 {
 
 template <class T>
-VariableCompound &IO::DefineVariableCompound(const std::string &name,
-                                             const Dims shape, const Dims start,
-                                             const Dims count,
-                                             const bool constantShape)
+VariableCompound &
+IO::DefineVariableCompound(const std::string &name, const Dims &shape,
+                           const Dims &start, const Dims &count,
+                           const bool constantShape)
 {
     if (m_DebugMode)
     {

source/adios2/core/IO.tcc

@@ -26,8 +26,8 @@ namespace adios2
 {
 
 template <class T>
-Variable<T> &IO::DefineVariable(const std::string &name, const Dims shape,
-                                const Dims start, const Dims count,
+Variable<T> &IO::DefineVariable(const std::string &name, const Dims &shape,
+                                const Dims &start, const Dims &count,
                                 const bool constantShape)
 {
     if (m_DebugMode)

source/adios2/core/Variable.cpp

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * Variable.cpp  needed for template separation using Variable.tcc
+ * Variable.cpp : needed for template separation using Variable.tcc
  *
  *  Created on: Jun 8, 2017
  *      Author: William F Godoy godoywf@ornl.gov
@@ -14,4 +14,4 @@
 namespace adios2
 {
 
-} // end namespace adios
+} // end namespace adios2

source/adios2/core/Variable.h

@@ -18,8 +18,6 @@
 #include <vector>
 /// \endcond
 
-#include "adios2/ADIOSMacros.h"
-#include "adios2/core/Transform.h"
 #include "adios2/core/VariableBase.h"
 
 namespace adios2
@@ -50,8 +48,8 @@ public:
      * @param constantShape
      * @param debugMode
      */
-    Variable<T>(const std::string &name, const Dims shape, const Dims start,
-                const Dims count, const bool constantShape,
+    Variable<T>(const std::string &name, const Dims &shape, const Dims &start,
+                const Dims &count, const bool constantShape,
                 const bool debugMode);
 
     ~Variable<T>() = default;

source/adios2/core/Variable.tcc

@@ -22,8 +22,8 @@ namespace adios2
 #define declare_type(T)                                                        \
                                                                                \
     template <>                                                                \
-    Variable<T>::Variable(const std::string &name, const Dims shape,           \
-                          const Dims start, const Dims count,                  \
+    Variable<T>::Variable(const std::string &name, const Dims &shape,          \
+                          const Dims &start, const Dims &count,                \
                           const bool constantShape, const bool debugMode)      \
     : VariableBase(name, GetType<T>(), sizeof(T), shape, start, count,         \
                    constantShape, debugMode)                                   \

source/adios2/core/VariableBase.cpp

@@ -21,8 +21,8 @@ namespace adios2
 {
 
 VariableBase::VariableBase(const std::string &name, const std::string type,
-                           const size_t elementSize, const Dims shape,
-                           const Dims start, const Dims count,
+                           const size_t elementSize, const Dims &shape,
+                           const Dims &start, const Dims &count,
                            const bool constantDims, const bool debugMode)
 : m_Name(name), m_Type(type), m_ElementSize(elementSize), m_Shape(shape),
   m_Start(start), m_Count(count), m_ConstantDims(constantDims),
@@ -41,7 +41,7 @@ size_t VariableBase::TotalSize() const noexcept
     return GetTotalSize(m_Count);
 }
 
-void VariableBase::SetSelection(const Dims start, const Dims count)
+void VariableBase::SetSelection(const Dims &start, const Dims &count)
 {
     if (m_DebugMode)
     {

source/adios2/core/VariableBase.h

@@ -63,8 +63,8 @@ public:
     unsigned int m_AvailableSteps = 1;
 
     VariableBase(const std::string &name, const std::string type,
-                 const size_t elementSize, const Dims shape, const Dims start,
-                 const Dims count, const bool constantShape,
+                 const size_t elementSize, const Dims &shape, const Dims &start,
+                 const Dims &count, const bool constantShape,
                  const bool debugMode);
 
     virtual ~VariableBase() = default;
@@ -82,7 +82,7 @@ public:
     size_t TotalSize() const noexcept;
 
     /** Set the local dimension and global offset of the variable */
-    void SetSelection(const Dims start, const Dims count);
+    void SetSelection(const Dims &start, const Dims &count);
 
     /** Overloaded version of SetSelection using a SelectionBoundingBox */
     void SetSelection(const SelectionBoundingBox &selection);

source/adios2/helper/adiosType.inl

@@ -27,6 +27,13 @@ inline std::string GetType<void>() noexcept
 {
     return "unknown";
 }
+
+template <>
+inline std::string GetType<std::string>() noexcept
+{
+    return "string";
+}
+
 template <>
 inline std::string GetType<char>() noexcept
 {

testing/adios2/interface/CMakeLists.txt

@@ -9,5 +9,9 @@ target_link_libraries(TestADIOSInterfaceWrite adios2 gtest gtest_main)
 add_executable(TestADIOSDefineVariable TestADIOSDefineVariable.cpp)
 target_link_libraries(TestADIOSDefineVariable adios2 gtest gtest_main)
 
+add_executable(TestADIOSDefineAttribute TestADIOSDefineAttribute.cpp)
+target_link_libraries(TestADIOSDefineAttribute adios2 gtest gtest_main)
+
 gtest_add_tests(TARGET TestADIOSInterfaceWrite)
-gtest_add_tests(TARGET TestADIOSDefineVariable)
\ No newline at end of file
+gtest_add_tests(TARGET TestADIOSDefineVariable)
+gtest_add_tests(TARGET TestADIOSDefineAttribute)
\ No newline at end of file