From 857cdfc4c547b5d6020d28ee111ac4501a842777 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Tue, 1 Aug 2017 17:49:52 -0400
Subject: [PATCH] Started adding support for Attributes
---
source/adios2/ADIOSMacros.h | 20 ++++
source/adios2/core/Attribute.h | 48 +++++++++
source/adios2/core/Attribute.tcc | 41 ++++++++
source/adios2/core/AttributeBase.cpp | 22 +++++
source/adios2/core/AttributeBase.h | 39 ++++++++
source/adios2/core/IO.cpp | 40 +++++---
source/adios2/core/IO.h | 104 +++++++++++++++++---
source/adios2/core/IO.inl | 17 ++--
source/adios2/core/IO.tcc | 141 ++++++++++++++++++++++++++-
source/adios2/core/Variable.h | 2 +-
source/adios2/core/Variable.tcc | 2 +-
11 files changed, 437 insertions(+), 39 deletions(-)
create mode 100644 source/adios2/core/Attribute.h
create mode 100644 source/adios2/core/Attribute.tcc
create mode 100644 source/adios2/core/AttributeBase.cpp
create mode 100644 source/adios2/core/AttributeBase.h
diff --git a/source/adios2/ADIOSMacros.h b/source/adios2/ADIOSMacros.h
index f3043732b..f15756cac 100644
--- a/source/adios2/ADIOSMacros.h
+++ b/source/adios2/ADIOSMacros.h
@@ -8,6 +8,8 @@
#ifndef ADIOS2_ADIOSMACROS_H
#define ADIOS2_ADIOSMACROS_H
+#include <string>
+
#include "adios2/ADIOSTypes.h"
// The ADIOS_FOREACH_TYPE_1ARG macro assumes the given argument is a macro which
// takes a single argument that is a type and then inserts the given MACRO for
@@ -49,6 +51,8 @@
MACRO(unsigned int) \
MACRO(long int) \
MACRO(unsigned long int) \
+ MACRO(long long int) \
+ MACRO(unsigned long long int) \
MACRO(float) \
MACRO(double)
@@ -62,4 +66,20 @@
MACRO(float) \
MACRO(double)
+#define ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(MACRO) \
+ MACRO(std::string) \
+ MACRO(char) \
+ MACRO(unsigned char) \
+ MACRO(short) \
+ MACRO(unsigned short) \
+ MACRO(int) \
+ MACRO(unsigned int) \
+ MACRO(long int) \
+ MACRO(unsigned long int) \
+ MACRO(long long int) \
+ MACRO(unsigned long long int) \
+ MACRO(float) \
+ MACRO(double) \
+ MACRO(long double)
+
#endif /* ADIOS2_ADIOSMACROS_H */
diff --git a/source/adios2/core/Attribute.h b/source/adios2/core/Attribute.h
new file mode 100644
index 000000000..7ed3cc779
--- /dev/null
+++ b/source/adios2/core/Attribute.h
@@ -0,0 +1,48 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * Attribute.h : template class
+ *
+ * Created on: Aug 1, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#ifndef ADIOS2_CORE_ATTRIBUTE_H_
+#define ADIOS2_CORE_ATTRIBUTE_H_
+
+#include "adios2/core/AttributeBase.h"
+
+namespace adios2
+{
+/** @brief Attributes provide complementary information to IO Variables*/
+template <class T>
+class Attribute : public AttributeBase
+{
+
+public:
+ const T *m_DataArray = nullptr;
+ T m_DataValue;
+
+ /**
+ * Data array constructor
+ * @param name
+ * @param data
+ * @param elements
+ */
+ Attribute<T>(const std::string &name, const T *data, const size_t elements);
+
+ /**
+ * Single value constructor
+ * @param name
+ * @param data
+ * @param elements
+ */
+ Attribute<T>(const std::string &name, const T &data);
+
+ ~Attribute<T>() = default;
+};
+
+} // end namespace adios2
+
+#endif /* SOURCE_ADIOS2_CORE_ATTRIBUTE_H_ */
diff --git a/source/adios2/core/Attribute.tcc b/source/adios2/core/Attribute.tcc
new file mode 100644
index 000000000..47343256f
--- /dev/null
+++ b/source/adios2/core/Attribute.tcc
@@ -0,0 +1,41 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * Attribute.tcc
+ *
+ * Created on: Aug 1, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#ifndef ADIOS2_CORE_ATTRIBUTE_TCC_
+#define ADIOS2_CORE_ATTRIBUTE_TCC_
+
+#include "Attribute.h"
+
+#include "adios2/ADIOSMacros.h"
+#include "adios2/helper/adiosFunctions.h" //GetType<T>
+
+namespace adios2
+{
+
+#define declare_type(T) \
+ \
+ template <> \
+ Attribute<T>::Attribute(const std::string &name, const T *array, \
+ const size_t elements) \
+ : AttributeBase(name, GetType<T>(), elements), m_DataArray(array), \
+ m_DataValue() \
+ { \
+ } \
+ \
+ template <> \
+ Attribute<T>::Attribute(const std::string &name, const T &value) \
+ : AttributeBase(name, GetType<T>(), 1), m_DataValue() \
+ { \
+ }
+
+ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(declare_type)
+#undef declare_type
+
+} // end namespace adios2
diff --git a/source/adios2/core/AttributeBase.cpp b/source/adios2/core/AttributeBase.cpp
new file mode 100644
index 000000000..498e7fbfc
--- /dev/null
+++ b/source/adios2/core/AttributeBase.cpp
@@ -0,0 +1,22 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * AttributeBase.cpp
+ *
+ * Created on: Aug 1, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#include "AttributeBase.h"
+
+namespace adios2
+{
+
+AttributeBase::AttributeBase(const std::string &name, const std::string type,
+ const size_t elements)
+: m_Name(name), m_Type(type), m_Elements(elements)
+{
+}
+
+} // end namespace adios2
diff --git a/source/adios2/core/AttributeBase.h b/source/adios2/core/AttributeBase.h
new file mode 100644
index 000000000..cf09b54f3
--- /dev/null
+++ b/source/adios2/core/AttributeBase.h
@@ -0,0 +1,39 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * AttributeBase.h : base class for Attribute<T> class, allows RTTI at read time
+ *
+ * Created on: Aug 1, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#ifndef ADIOS2_CORE_ATTRIBUTEBASE_H_
+#define ADIOS2_CORE_ATTRIBUTEBASE_H_
+
+namespace adios2
+{
+
+class AttributeBase
+{
+
+public:
+ const std::string m_Name;
+ const std::string m_Type;
+ const size_t m_Elements;
+
+ /**
+ * Unique constructor used by Attribute<T> derived class
+ * @param name
+ * @param type
+ * @param elements
+ */
+ AttributeBase(const std::string &name, const std::string type,
+ const size_t elements);
+
+ virtual ~AttributeBase() = default;
+};
+
+} // end namespace adios2
+
+#endif /* ADIOS2_CORE_ATTRIBUTEBASE_H_ */
diff --git a/source/adios2/core/IO.cpp b/source/adios2/core/IO.cpp
index fe70d534e..4fd7b69fc 100644
--- a/source/adios2/core/IO.cpp
+++ b/source/adios2/core/IO.cpp
@@ -62,7 +62,7 @@ unsigned int IO::AddTransport(const std::string type, const Params ¶meters)
VariableCompound &IO::GetVariableCompound(const std::string &name)
{
- return m_Compound.at(GetVariableIndex(name));
+ return m_Compound.at(GetMapIndex(name, m_Variables, "VariableCompound"));
}
std::string IO::GetVariableType(const std::string &name) const
@@ -235,30 +235,42 @@ std::shared_ptr<Engine> IO::Open(const std::string &name,
}
// PRIVATE Functions
-unsigned int IO::GetVariableIndex(const std::string &name) const
+unsigned int IO::GetMapIndex(const std::string &name, const DataMap &dataMap,
+ const std::string hint) const
{
+ auto itDataMap = dataMap.find(name);
+
if (m_DebugMode)
{
- if (!VariableExists(name))
+ if (IsEnd(itDataMap, dataMap))
{
- throw std::invalid_argument(
- "ERROR: variable " + m_Name +
- " wasn't created with DefineVariable, in call to IO object " +
- m_Name + " GetVariable\n");
+ throw std::invalid_argument("ERROR: " + hint + " " + m_Name +
+ " wasn't created with Define " + hint +
+ ", in call to IO object " + m_Name +
+ " Get" + hint + "\n");
}
}
- auto itVariable = m_Variables.find(name);
- return itVariable->second.second;
+ return itDataMap->second.second;
+}
+
+void IO::CheckAttributeCommon(const std::string &name) const
+{
+ auto itAttribute = m_Attributes.find(name);
+ if (!IsEnd(itAttribute, m_Attributes))
+ {
+ throw std::invalid_argument("ERROR: attribute " + name +
+ " exists in IO object " + m_Name +
+ ", in call to DefineAttribute\n");
+ }
}
-bool IO::VariableExists(const std::string &name) const
+bool IO::IsEnd(DataMap::const_iterator itDataMap, const DataMap &dataMap) const
{
- bool exists = false;
- if (m_Variables.count(name) == 1)
+ if (itDataMap == dataMap.end())
{
- exists = true;
+ return true;
}
- return exists;
+ return false;
}
void IO::CheckTransportType(const std::string type) const
diff --git a/source/adios2/core/IO.h b/source/adios2/core/IO.h
index 59fc9f6c7..a738fd7bc 100644
--- a/source/adios2/core/IO.h
+++ b/source/adios2/core/IO.h
@@ -24,12 +24,16 @@
#include "adios2/ADIOSMPICommOnly.h"
#include "adios2/ADIOSMacros.h"
#include "adios2/ADIOSTypes.h"
+#include "adios2/core/Attribute.h"
#include "adios2/core/Variable.h"
#include "adios2/core/VariableCompound.h"
namespace adios2
{
+/** used for Variables and Attributes */
+using DataMap = std::map<std::string, std::pair<std::string, unsigned int>>;
+
// forward declaration needed as IO is passed to Engine derived
// classes
class Engine;
@@ -137,6 +141,26 @@ public:
const Dims start = Dims{}, const Dims count = Dims{},
const bool constantShape = false);
+ /**
+ * Define attribute from contiguous data array
+ * @param name must be unique for the IO object
+ * @param array pointer to user data
+ * @param elements number of data elements
+ * @return reference to internal Attribute
+ */
+ template <class T>
+ Attribute<T> &DefineAttribute(const std::string &name, const T *array,
+ const size_t elements);
+
+ /**
+ * Define attribute from a single variable
+ * @param name must be unique for the IO object
+ * @param value single data value
+ * @return reference to internal Attribute
+ */
+ template <class T>
+ Attribute<T> &DefineAttribute(const std::string &name, const T &value);
+
/**
* Removes an existing Variable previously created with DefineVariable or
* DefineVariableCompound
@@ -163,6 +187,15 @@ public:
*/
VariableCompound &GetVariableCompound(const std::string &name);
+ /**
+ * Gets an existing attribute of primitive type by name
+ * @param name of attribute to be retrieved
+ * @return reference to an existing attribute created with DefineAttribute
+ * throws an exception if Attribute is not found
+ */
+ template <class T>
+ Attribute<T> &GetAttribute(const std::string &name);
+
/**
* Get the type if variable (by name id) exists
* @param name input id
@@ -222,7 +255,7 @@ private:
* pair.second = index in fixed size map (e.g. m_Int8, m_Double)
* </pre>
*/
- std::map<std::string, std::pair<std::string, unsigned int>> m_Variables;
+ DataMap m_Variables;
/** Variable containers based on fixed-size type */
std::map<unsigned int, Variable<char>> m_Char;
@@ -243,25 +276,63 @@ private:
std::map<unsigned int, Variable<cldouble>> m_CLDouble;
std::map<unsigned int, VariableCompound> m_Compound;
- std::map<std::string, std::string> m_AttributesString;
- std::map<std::string, double> m_AttributesNumeric;
-
- std::set<std::string> m_EngineNames;
-
/** Gets the internal reference to a variable map for type T
* This function is specialized in IO.tcc */
template <class T>
std::map<unsigned int, Variable<T>> &GetVariableMap();
- /** Gets the internal index in variable map for an existing variable */
- unsigned int GetVariableIndex(const std::string &name) const;
+ /**
+ * Map holding attribute identifiers
+ * <pre>
+ * key: unique attribute name,
+ * value: pair.first = type as string GetType<T> from
+ * helper/adiosTemplates.h
+ * pair.second = index in fixed size map (e.g. m_Int8, m_Double)
+ * </pre>
+ */
+ DataMap m_Attributes;
+
+ std::map<unsigned int, Attribute<std::string>> m_StringA;
+ std::map<unsigned int, Attribute<char>> m_CharA;
+ std::map<unsigned int, Attribute<unsigned char>> m_UCharA;
+ std::map<unsigned int, Attribute<short>> m_ShortA;
+ std::map<unsigned int, Attribute<unsigned short>> m_UShortA;
+ std::map<unsigned int, Attribute<int>> m_IntA;
+ std::map<unsigned int, Attribute<unsigned int>> m_UIntA;
+ std::map<unsigned int, Attribute<long int>> m_LIntA;
+ std::map<unsigned int, Attribute<unsigned long int>> m_ULIntA;
+ std::map<unsigned int, Attribute<long long int>> m_LLIntA;
+ std::map<unsigned int, Attribute<unsigned long long int>> m_ULLIntA;
+ std::map<unsigned int, Attribute<float>> m_FloatA;
+ std::map<unsigned int, Attribute<double>> m_DoubleA;
+ std::map<unsigned int, Attribute<long double>> m_LDoubleA;
+
+ template <class T>
+ std::map<unsigned int, Attribute<T>> &GetAttributeMap();
/**
- * Checks if variable exists by checking its name
- * @param name unique variable name to be checked against existing variables
- * @return true: variable name exists, false: variable name doesn't exist
+ * Gets map index for Variables or Attributes
+ * @param name
+ * @param dataMap m_Variables or m_Attributes
+ * @param hint "Variable", "Attribute", or "VariableCompound"
+ * @return index in type map
*/
- bool VariableExists(const std::string &name) const;
+ unsigned int GetMapIndex(const std::string &name, const DataMap &dataMap,
+ const std::string hint) const;
+
+ /** Checks if attribute exists, called from DefineAttribute different
+ * signatures */
+ void CheckAttributeCommon(const std::string &name) const;
+
+ std::set<std::string> m_EngineNames;
+
+ /**
+ * Checks if iterator points to end. Used for Variables and Attributes.
+ * @param itDataMap iterator to be tested
+ * @param dataMap map
+ * @return true: itDataMap == dataMap.end(), false otherwise
+ */
+ bool IsEnd(DataMap::const_iterator itDataMap, const DataMap &dataMap) const;
void CheckTransportType(const std::string type) const;
};
@@ -276,6 +347,15 @@ private:
ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
#undef 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);
+
+ADIOS2_FOREACH_ATTRIBUTE_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+
} // end namespace adios
#include "adios2/core/IO.inl"
diff --git a/source/adios2/core/IO.inl b/source/adios2/core/IO.inl
index 6ef9299c0..9dd0f53f2 100644
--- a/source/adios2/core/IO.inl
+++ b/source/adios2/core/IO.inl
@@ -2,7 +2,8 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * IO.inl inline template functions implementation of IO class
+ * IO.inl inline template functions implementation of IO class. VariableCompound
+ * can take any type so must be inlined as type is not known a priori.
*
* Created on: May 15, 2017
* Author: William F Godoy godoywf@ornl.gov
@@ -27,14 +28,16 @@ VariableCompound &IO::DefineVariableCompound(const std::string &name,
{
if (m_DebugMode)
{
- if (VariableExists(name))
+ auto itVariable = m_Variables.find(name);
+ if (!IsEnd(itVariable, m_Variables))
{
- throw std::invalid_argument("ERROR: variable " + name +
- " exists in IO object " + m_Name +
- ", in call to DefineVariable\n");
+ throw std::invalid_argument(
+ "ERROR: compound variable " + name + " exists in IO object " +
+ m_Name + ", in call to DefineVariableCompound\n");
}
}
- const unsigned int size = m_Compound.size();
+ const unsigned int size =
+ static_cast<const unsigned int>(m_Compound.size());
auto itVariableCompound = m_Compound.emplace(
size, VariableCompound(name, sizeof(T), shape, start, count,
constantShape, m_DebugMode));
@@ -42,6 +45,6 @@ VariableCompound &IO::DefineVariableCompound(const std::string &name,
return itVariableCompound.first->second;
}
-} // end namespace adios
+} // end namespace adios2
#endif /* ADIOS2_CORE_IO_INL_ */
diff --git a/source/adios2/core/IO.tcc b/source/adios2/core/IO.tcc
index dddb31678..572fa53bf 100644
--- a/source/adios2/core/IO.tcc
+++ b/source/adios2/core/IO.tcc
@@ -32,7 +32,8 @@ Variable<T> &IO::DefineVariable(const std::string &name, const Dims shape,
{
if (m_DebugMode)
{
- if (VariableExists(name))
+ auto itVariable = m_Variables.find(name);
+ if (!IsEnd(itVariable, m_Variables))
{
throw std::invalid_argument("ERROR: variable " + name +
" exists in IO object " + m_Name +
@@ -41,7 +42,8 @@ Variable<T> &IO::DefineVariable(const std::string &name, const Dims shape,
}
auto &variableMap = GetVariableMap<T>();
- const unsigned int size = variableMap.size();
+ const unsigned int size =
+ static_cast<const unsigned int>(variableMap.size());
auto itVariablePair =
variableMap.emplace(size, Variable<T>(name, shape, start, count,
constantShape, m_DebugMode));
@@ -53,7 +55,53 @@ Variable<T> &IO::DefineVariable(const std::string &name, const Dims shape,
template <class T>
Variable<T> &IO::GetVariable(const std::string &name)
{
- return GetVariableMap<T>().at(GetVariableIndex(name));
+ return GetVariableMap<T>().at(GetMapIndex(name, m_Variables, "Variable"));
+}
+
+template <class T>
+Attribute<T> &IO::DefineAttribute(const std::string &name, const T &value)
+{
+ if (m_DebugMode)
+ {
+ CheckAttributeCommon(name);
+ }
+
+ auto &attributeMap = GetAttributeMap<T>();
+ const unsigned int size =
+ static_cast<const unsigned int>(attributeMap.size());
+
+ auto itAttributePair =
+ attributeMap.emplace(size, Attribute<T>(name, value));
+ m_Attributes.emplace(name, std::make_pair(GetType<T>(), size));
+
+ return itAttributePair.first->second;
+}
+
+template <class T>
+Attribute<T> &IO::DefineAttribute(const std::string &name, const T *array,
+ const size_t elements)
+{
+ if (m_DebugMode)
+ {
+ CheckAttributeCommon(name);
+ }
+
+ auto &attributeMap = GetAttributeMap<T>();
+ const unsigned int size =
+ static_cast<const unsigned int>(attributeMap.size());
+
+ auto itAttributePair =
+ attributeMap.emplace(size, Attribute<T>(name, array, elements));
+ m_Attributes.emplace(name, std::make_pair(GetType<T>(), size));
+
+ return itAttributePair.first->second;
+}
+
+template <class T>
+Attribute<T> &IO::GetAttribute(const std::string &name)
+{
+ return GetAttributeMap<T>().at(
+ GetMapIndex(name, m_Attributes, "Attribute"));
}
// PRIVATE
@@ -153,6 +201,91 @@ std::map<unsigned int, Variable<cldouble>> &IO::GetVariableMap()
return m_CLDouble;
}
-} // end namespace adios
+// attributes
+template <>
+std::map<unsigned int, Attribute<std::string>> &IO::GetAttributeMap()
+{
+ return m_StringA;
+}
+
+template <>
+std::map<unsigned int, Attribute<char>> &IO::GetAttributeMap()
+{
+ return m_CharA;
+}
+
+template <>
+std::map<unsigned int, Attribute<unsigned char>> &IO::GetAttributeMap()
+{
+ return m_UCharA;
+}
+
+template <>
+std::map<unsigned int, Attribute<short>> &IO::GetAttributeMap()
+{
+ return m_ShortA;
+}
+
+template <>
+std::map<unsigned int, Attribute<unsigned short>> &IO::GetAttributeMap()
+{
+ return m_UShortA;
+}
+
+template <>
+std::map<unsigned int, Attribute<int>> &IO::GetAttributeMap()
+{
+ return m_IntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<unsigned int>> &IO::GetAttributeMap()
+{
+ return m_UIntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<long int>> &IO::GetAttributeMap()
+{
+ return m_LIntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<unsigned long int>> &IO::GetAttributeMap()
+{
+ return m_ULIntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<long long int>> &IO::GetAttributeMap()
+{
+ return m_LLIntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<unsigned long long int>> &IO::GetAttributeMap()
+{
+ return m_ULLIntA;
+}
+
+template <>
+std::map<unsigned int, Attribute<float>> &IO::GetAttributeMap()
+{
+ return m_FloatA;
+}
+
+template <>
+std::map<unsigned int, Attribute<double>> &IO::GetAttributeMap()
+{
+ return m_DoubleA;
+}
+
+template <>
+std::map<unsigned int, Attribute<long double>> &IO::GetAttributeMap()
+{
+ return m_LDoubleA;
+}
+
+} // end namespace adios2
#endif /* ADIOS2_CORE_IO_TCC_ */
diff --git a/source/adios2/core/Variable.h b/source/adios2/core/Variable.h
index 9ed428735..8f5482857 100644
--- a/source/adios2/core/Variable.h
+++ b/source/adios2/core/Variable.h
@@ -54,7 +54,7 @@ public:
const Dims count, const bool constantShape,
const bool debugMode);
- virtual ~Variable<T>() = default;
+ ~Variable<T>() = default;
void ApplyTransforms() final;
};
diff --git a/source/adios2/core/Variable.tcc b/source/adios2/core/Variable.tcc
index e5a241109..603b9300d 100644
--- a/source/adios2/core/Variable.tcc
+++ b/source/adios2/core/Variable.tcc
@@ -14,7 +14,7 @@
#include "Variable.h"
#include "adios2/ADIOSMacros.h"
-#include "adios2/helper/adiosFunctions.h" //GetType
+#include "adios2/helper/adiosFunctions.h" //GetType<T>
namespace adios2
{
--
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