diff --git a/Makefile b/Makefile
index 1c1e3ef4c7e35cd64e9dc2ec99fd60de7af55b76..4398777cb5e321d78e07fde97440f0e7c931d790 100644
--- a/Makefile
+++ b/Makefile
@@ -13,7 +13,7 @@ AR:=$(SYS_BIN)/ar
MPICC:=$(SYS_BIN)/mpic++
LIBS:= -L$(SYS_LIB) -L$(LOCAL_LIB)
-CFLAGS:=-c -Wall -O0 -g -Wpedantic -Woverloaded-virtual -std=c++11
+CFLAGS:=-c -Wall -O0 -g -Wpedantic -Woverloaded-virtual -std=c++14
ARFLAGS:=rcs
#ADIOS
@@ -54,4 +54,4 @@ nompi: $(HFiles) $(OBJNoMPI)
$(CC) $(CFLAGS) $(INC) -o $@ $<
clean:
- rm ./bin/mpi/*.o ./lib/libadios.a ./bin/nompi/*.o ./lib/libadios_nompi.a
\ No newline at end of file
+ rm ./bin/mpi/*.o ./lib/libadios.a ./bin/nompi/*.o ./lib/libadios_nompi.a
diff --git a/include/core/CGroup.h b/include/core/CGroup.h
index c363f90ef183748acc83db74002f3309a0068de1..4cb83d8a38eefecb80c4415a6ae889121583d3f2 100644
--- a/include/core/CGroup.h
+++ b/include/core/CGroup.h
@@ -23,7 +23,7 @@
#endif
-#include "core/CVariableBase.h"
+#include "core/CVariable.h"
#include "core/SAttribute.h"
#include "core/CTransport.h"
@@ -83,29 +83,26 @@ public:
/**
- * @brief Sets a variable in current Group, name must be unique
- * @param name variable name
- * @param isGlobal
- * @param type supported type
- * @param dimensionsCSV comma separated dimensions, default 1D = {1}
- * @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9 . If no level is defined then library default is taken
+ * Sets a new variable in the group object
+ * @param name variable name, must be unique. If name exists it removes the current variable. In debug mode program will exit.
+ * @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
+ * @param dimensionsCSV comma separated variable local dimensions (e.g. "Nx,Ny,Nz")
+ * @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9
+ * @param globalDimensionsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
+ * @param globalOffsetsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
*/
- void CreateLocalVariable( const std::string name, const std::string type,
- const std::string dimensionsCSV, const std::string transform );
-
- void CreateGlobalVariable( const std::string name, const std::string type,
- const std::string dimensionsCSV, const std::string transform,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV );
+ void SetVariable( const std::string name, const std::string type,
+ const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV );
/**
- * @brief Sets a variable in current Group
- * @param name passed to Name
+ * @brief Sets a new attribute in current Group
+ * @param name attribute name, must be unique. If name exists it removes the current variable. In debug mode program will exit.
* @param isGlobal
* @param type
- * @param path
* @param value
*/
- void CreateAttribute( const std::string name, const bool isGlobal, const std::string type, const std::string path, const std::string value );
+ void SetAttribute( const std::string name, const bool isGlobal, const std::string type, const std::string value );
/**
@@ -115,8 +112,8 @@ public:
* @param iteration iterations between writes of a group to gauge how quickly this data should be evacuated from the compute node
* @param mpiComm MPI communicator from User->ADIOS->Group
*/
- void CreateTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
- const MPI_Comm mpiComm );
+ void SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
+ const MPI_Comm mpiComm );
/**
@@ -139,7 +136,9 @@ private:
* Value: Polymorphic value is always unique child defined in SVariableTemplate.h, allow different variable types
* </pre>
*/
- std::map< std::string, std::shared_ptr<CVariableBase> > m_Variables;
+ std::map< std::string, CVariable > m_Variables;
+ std::vector< std::string > m_VariableTransforms; ///< if a variable has a transform it fills this container, the variable hold an index
+
/**
* @brief Contains all group attributes from SAttribute.h
@@ -150,14 +149,12 @@ private:
*/
std::map< std::string, SAttribute > m_Attributes;
- std::vector<std::string> m_GlobalDimensions; ///< from global-bounds in XML File, data in global space
- std::vector<std::string> m_GlobalOffsets; ///< from global-bounds in XML File, data in global space
+ std::vector< std::pair< std::string, std::string > > m_GlobalBounds; ///< if a variable or an attribute is global it fills this container, from global-bounds in XML File, data in global space, pair.first = global dimensions, pair.second = global bounds
- std::shared_ptr<CTransport> m_Transport; ///< transport method defined in XML File, using shared_ptr as CGroup is put in a map copy constructor deleted
- std::string m_ActiveTransport;
+ std::string m_CurrentTransport; ///< current transport method associated with this group
+ std::string m_OutputName; ///< associated output (file, stream, buffer, etc.) if the Group is opened.
- std::string m_FileName; ///< associated fileName is the Group is opened.
- std::string m_AcessMode; ///< file access mode "r"->read, "w"->write, "a"->append
+ unsigned long int m_SerialSize; ///< size used for potential serialization of metadata into a std::vector<char>. Counts sizes from m_Variables, m_Attributes, m_GlobalBounds
/**
* Called from XML constructor
diff --git a/include/core/CTransform.h b/include/core/CTransform.h
index d4b08284e9e55e1f3482c56d5f408d1f6c2225e7..97c899e0fa17378a09d35128efdab840795dc3b0 100644
--- a/include/core/CTransform.h
+++ b/include/core/CTransform.h
@@ -10,10 +10,10 @@
/// \cond EXCLUDE_FROM_DOXYGEN
+#include <core/CVariable.h>
#include <string>
/// \endcond
-#include "core/CVariableBase.h"
namespace adios
diff --git a/include/core/CTransport.h b/include/core/CTransport.h
index 13f83a0f688943e52922018442e9ae79b9f9dab6..c68219cafdf5a28491f870e3789c9c5aade616ab 100644
--- a/include/core/CTransport.h
+++ b/include/core/CTransport.h
@@ -18,7 +18,7 @@
#include "public/mpidummy.h"
#endif
-#include "core/CVariableBase.h"
+#include <core/CVariable.h>
namespace adios
diff --git a/include/core/CVariable.h b/include/core/CVariable.h
index 2a3961661301f049cedefb1dcc2012aaddf5acf5..82e575b019fd37acc06a1b3b84cf7e723b7a34b0 100644
--- a/include/core/CVariable.h
+++ b/include/core/CVariable.h
@@ -1,67 +1,55 @@
/*
- * CVariableType.h
+ * CVariable.h
*
- * Created on: Oct 18, 2016
+ * Created on: Oct 6, 2016
* Author: wfg
*/
#ifndef CVARIABLE_H_
#define CVARIABLE_H_
-
-#include "core/CVariableBase.h"
+/// \cond EXCLUDE_FROM_DOXYGEN
+#include <string>
+#include <vector>
+#include <typeinfo> // for typeid
+#include <sstream>
+/// \endcond
namespace adios
{
-
/**
- * Derived template class of CVariableBase. Will hold a pointer of the right type to the void* passed from user app in ADIOS.
+ * @param Base (parent) class for template derived (child) class CVariable. Required to put CVariable objects in STL containers.
*/
-template<class T>
-class CVariable : public CVariableBase
+class CVariable
{
public:
/**
- * Template constructor class required for putting CVariable objects as value in a STL map container
- * @param isGlobal
- * @param type
- * @param dimensionsCSV
- * @param transform
+ * Unique constructor for local and global variables
+ * @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
+ * @param dimensionsCSV comma separated variable local dimensions (e.g. "Nx,Ny,Nz")
+ * @param transformIndex
+ * @param globalIndex
*/
- CVariable( const std::string type, const std::string dimensionsCSV, const std::string transform ):
- CVariableBase( type, dimensionsCSV, transform )
- { }
+ CVariable( const std::string type, const std::string dimensionsCSV,
+ const int globalIndex, const int transformIndex );
- CVariable( const std::string type, const std::string dimensionsCSV, const std::string transform,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ):
- CVariableBase( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV )
- { }
+ virtual ~CVariable( );
- ~CVariable( )
- { }
+ void* m_Values;
- const T* m_Value = nullptr; // pointer or no pointer?
- const T* Get() const { return m_Value; }
+protected:
- void Set( const void* values ){ m_Value = static_cast<const T*>( values ); }
+ const std::string m_Type; ///< mandatory, double, float, unsigned integer, integer, etc.
+ const std::string m_DimensionsCSV; ///< comma separated list for variables to search for local dimensions
};
-template<class T> const T* CVariableBase::Get( ) const
-{
- return dynamic_cast< const CVariable<T>& >(*this).Get( );
-}
-
-template<class T> void CVariableBase::Set( const void* values )
-{
- return dynamic_cast< CVariable<T>& >( *this ).Set( values );
-}
+} //end namespace
-} //end namespace
#endif /* CVARIABLE_H_ */
diff --git a/include/core/CVariableBase.h b/include/core/CVariableBase.h
deleted file mode 100644
index 9dab28e0a082785548b46e2b3cb3c16e79b0caf2..0000000000000000000000000000000000000000
--- a/include/core/CVariableBase.h
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * CVariable.h
- *
- * Created on: Oct 6, 2016
- * Author: wfg
- */
-
-#ifndef CVARIABLEBASE_H_
-#define CVARIABLEBASE_H_
-
-/// \cond EXCLUDE_FROM_DOXYGEN
-#include <string>
-#include <vector>
-#include <typeinfo> // for typeid
-#include <sstream>
-/// \endcond
-
-
-namespace adios
-{
-/**
- * @param Base (parent) class for template derived (child) class CVariable. Required to put CVariable objects in STL containers.
- */
-class CVariableBase
-{
-
-public:
-
- CVariableBase( const std::string type, const std::string dimensionsCSV, const std::string transform );
-
- CVariableBase( const std::string type, const std::string dimensionsCSV, const std::string transform,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV );
-
-
- virtual ~CVariableBase( );
-
- template<class T> const T* Get( ) const;
- template<class T> void Set( const void* values );
-
-
-protected:
-
- const std::string m_Type; ///< mandatory, double, float, unsigned integer, integer, etc.
- const std::string m_DimensionsCSV; ///< comma separated list for variables to search for local dimensions
- const std::string m_Transform; ///< data transform: zlib:1, bzip2:4, szip:9 which level of compression
- const std::string m_GlobalDimensionsCSV; ///< comma separated list for variables to search for global dimensions
- const std::string m_GlobalOffsetsCSV; ///< comma separated list for variables to search for global offsets
- const bool m_IsGlobal = false; ///< boolean flag that identifies is a variable is global or not
-
-};
-
-
-} //end namespace
-
-
-
-#endif /* CVARIABLEBASE_H_ */
diff --git a/include/core/SAttribute.h b/include/core/SAttribute.h
index 04ce885e456e52b9bfc9bea7657f1705fbefdd80..b2f8c4564c130d92f2e4a8eeee26ccd9e9163391 100644
--- a/include/core/SAttribute.h
+++ b/include/core/SAttribute.h
@@ -20,9 +20,9 @@ namespace adios
*/
struct SAttribute
{
- const bool IsGlobal; ///< true: static, defined in XML Config file, false: dynamic, defined in non-XML API
const std::string Type; ///< string or numeric type
const std::string Value; ///< information about the attribute
+ const int GlobalIndex; ///< if -1, local, else corresponding index to m_GlobalBounds in CGroup
};
diff --git a/include/functions/GroupFunctions.h b/include/functions/GroupFunctions.h
index 7b4a39f6430a41db4e93f90bf0077c7a7eb53474..81d3c669731f1faa17c8d5702f6461a09d6a9a4f 100644
--- a/include/functions/GroupFunctions.h
+++ b/include/functions/GroupFunctions.h
@@ -1,5 +1,5 @@
/*
- * GroupFunctions.h helper functions for class CGroup
+ri * GroupFunctions.h helper functions for class CGroup
*
* Created on: Oct 27, 2016
* Author: wfg
@@ -20,69 +20,31 @@
#include "public/mpidummy.h"
#endif
-#include "core/CVariableBase.h"
+#include <core/CVariable.h>
#include "core/CTransport.h"
+
namespace adios
{
/**
* Create a language (C++, C, Fortran, etc.) supported type variable and add it to variables map
- * @param hostLanguage must be in SSupport::HostLanguages in public/SSupport.h
- * @param name name of variable, key in variables map
- * @param isGlobal true: global variable defined in XML Config
+ * @param name key in variables map
* @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
- * @param dimensionsCSV dimensionsCSV comma separated variable dimensions
+ * @param dimensionsCSV comma separated variable local dimensions (e.g. "Nx,Ny,Nz")
* @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9
+ * @param globalDimensionsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
+ * @param globalOffsetsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
* @param variables map belonging to class CGroup
*/
-void CreateVariableLanguage( const std::string hostLanguage, const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
+void CreateVariableLanguage( const std::string name, const std::string type,
+ const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV,
std::map<std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
-/**
- * Create a C++ supported variable, including STL vector types
- * @param name name of variable, key in variables map
- * @param isGlobal true: global variable defined in XML Config
- * @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
- * @param dimensionsCSV dimensionsCSV comma separated variable dimensions
- * @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9
- * @param variables map belonging to class CGroup
- */
-void CreateVariableCpp( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
-
-/**
- * Create a C supported variable, including STL vector types
- * @param name name of variable, key in variables map
- * @param isGlobal true: global variable defined in XML Config
- * @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
- * @param dimensionsCSV dimensionsCSV comma separated variable dimensions
- * @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9
- * @param variables map belonging to class CGroup
- */
-void CreateVariableC( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
-
-/**
- * Create a Fortran supported variable, including STL vector types
- * @param name name of variable, key in variables map
- * @param isGlobal true: global variable defined in XML Config
- * @param type variable type, must be in SSupport::Datatypes[hostLanguage] in public/SSupport.h
- * @param dimensionsCSV dimensionsCSV comma separated variable dimensions
- * @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9
- * @param variables map belonging to class CGroup
- */
-void CreateVariableFortran( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
-
/**
* Looks up the variable type and cast the appropriate values type to m_Value in CVariable
- * Maybe it produces exceptions? Must double-check
* @param variables always a derived CVariable object from CVariableBase
* @param values to be casted to the right type
*/
diff --git a/include/public/SSupport.h b/include/public/SSupport.h
index 49d2ea990f0ef70d7b693bb012be767f30c71b69..6584f145ed557701a9e7da3df324f64956df7833 100644
--- a/include/public/SSupport.h
+++ b/include/public/SSupport.h
@@ -12,6 +12,7 @@
#include <set>
#include <string>
#include <map>
+#include <array>
/// \endcond
namespace adios
@@ -24,6 +25,7 @@ struct SSupport
static const std::set<std::string> Transports; ///< supported transport methods
static const std::set<std::string> Transforms; ///< supported data transform methods
static const std::map<std::string, std::set<std::string> > Datatypes; ///< supported data types
+
};
diff --git a/src/core/CGroup.cpp b/src/core/CGroup.cpp
index dcb5e8b356d1ddb758e43952deb4bf176b1055fa..a178628e4015ef5543171183873a19eb360619cc 100644
--- a/src/core/CGroup.cpp
+++ b/src/core/CGroup.cpp
@@ -20,13 +20,15 @@ namespace adios
CGroup::CGroup( const std::string& hostLanguage, const bool debugMode ):
m_HostLanguage{ hostLanguage },
- m_DebugMode{ debugMode }
+ m_DebugMode{ debugMode },
+ m_SerialSize{ 0 }
{ }
CGroup::CGroup( const std::string& hostLanguage, const std::string& xmlGroup, const bool debugMode ):
m_HostLanguage{ hostLanguage },
- m_DebugMode{ debugMode }
+ m_DebugMode{ debugMode },
+ m_SerialSize{ 0 }
{
ParseXMLGroup( xmlGroup );
}
@@ -39,12 +41,12 @@ CGroup::~CGroup( )
void CGroup::Open( const std::string fileName, const std::string accessMode )
{
m_IsOpen = true;
- m_Transport->Open( fileName, accessMode );
}
-void CGroup::SetVariable( const std::string name, const bool isGlobal, const std::string type, const std::string dimensionsCSV,
- const std::string transform )
+void CGroup::SetVariable( const std::string name, const std::string type,
+ const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV )
{
if( m_DebugMode == true )
{
@@ -52,18 +54,18 @@ void CGroup::SetVariable( const std::string name, const bool isGlobal, const std
throw std::invalid_argument( "ERROR: type " + type + " for variable " + name + " is not supported.\n" );
if( m_Variables.count( name ) == 0 ) //variable doesn't exists
- CreateVariableLanguage( m_HostLanguage, name, isGlobal, type, dimensionsCSV, transform, m_Variables );
+ CreateVariableLanguage( name, type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV, m_Variables );
else //name is found
throw std::invalid_argument( "ERROR: variable " + name + " exists more than once.\n" );
}
else
{
- CreateVariableLanguage( m_HostLanguage, name, isGlobal, type, dimensionsCSV, transform, m_Variables );
+ CreateVariableLanguage( name, type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV, m_Variables );
}
}
-void CGroup::SetAttribute( const std::string name, const bool isGlobal, const std::string type, const std::string path,
+void CGroup::SetAttribute( const std::string name, const bool isGlobal, const std::string type,
const std::string value )
{
if( m_DebugMode == true )
@@ -80,29 +82,6 @@ void CGroup::SetAttribute( const std::string name, const bool isGlobal, const st
}
-void CGroup::SetGlobalBounds( const std::string dimensionsCSV, const std::string offsetsCSV )
-{
- auto lf_SetGlobalMember = []( const std::string inputCSV, std::vector<std::string>& output )
- {
- if( inputCSV.empty() ) return;
- std::istringstream inputSS( inputCSV );
- std::string element;
-
- while( std::getline( inputSS, element, ',' ) ) //might have to check for "comma" existence
- output.push_back( element );
- };
-
- if( m_DebugMode == true )
- {
- if( m_GlobalDimensions.empty() == false ) throw std::invalid_argument("ERROR: global dimensions already set\n" );
- if( m_GlobalOffsets.empty() == false ) throw std::invalid_argument("ERROR: global offsets already set\n" );
- }
-
- lf_SetGlobalMember( dimensionsCSV, m_GlobalDimensions );
- lf_SetGlobalMember( offsetsCSV, m_GlobalOffsets );
-}
-
-
void CGroup::SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
const MPI_Comm mpiComm )
{
@@ -167,15 +146,23 @@ void CGroup::Monitor( std::ostream& logStream ) const
void CGroup::ParseXMLGroup( const std::string& xmlGroup )
{
std::string::size_type currentPosition( 0 );
- bool isGlobal = false;
+ bool isGlobal = false; //used to set attributes
+ std::string globalDimensionsCSV; //used to set variables
+ std::string globalOffsetsCSV; //used to set variables
while( currentPosition != std::string::npos )
{
//Get tag
std::string tag;
GetSubString( "<", ">", xmlGroup, tag, currentPosition );
- if( tag == "</adios-group>" ) break;
- if( tag == "</global-bounds>" ) isGlobal = false;
+ if( tag == "</adios-group>" ) break; //end of current group
+
+ if( tag == "</global-bounds>" )
+ {
+ isGlobal = false; //used for attributes
+ globalDimensionsCSV.clear(); //used for variables
+ globalOffsetsCSV.clear(); //used for variables
+ }
if( m_DebugMode == true )
{
@@ -202,7 +189,7 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup )
else if( pair.first == "dimensions" ) dimensionsCSV = pair.second;
else if( pair.first == "transform" ) transform = pair.second;
}
- SetVariable( name, isGlobal, type, dimensionsCSV, transform );
+ SetVariable( name, type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
}
else if( tagName == "attribute" )
{
@@ -210,22 +197,31 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup )
for( auto& pair : pairs ) //loop through all pairs
{
if( pair.first == "name" ) name = pair.second;
- else if( pair.first == "path" ) path = pair.second;
else if( pair.first == "value" ) value = pair.second;
else if( pair.first == "type" ) type = pair.second;
}
- SetAttribute( name, isGlobal, type, path, value );
+ SetAttribute( name, isGlobal, type, value );
}
else if( tagName == "global-bounds" )
{
- isGlobal = true;
- std::string dimensionsCSV, offsetsCSV;
for( auto& pair : pairs ) //loop through all pairs
{
- if( pair.first == "dimensions" ) dimensionsCSV = pair.second;
- else if( pair.first == "offsets" ) offsetsCSV = pair.second;
+ if( pair.first == "dimensions" )
+ globalDimensionsCSV = pair.second;
+ else if( pair.first == "offsets" )
+ globalOffsetsCSV = pair.second;
+ }
+
+ if( m_DebugMode == true )
+ {
+ if( globalDimensionsCSV.empty() )
+ throw std::invalid_argument( "ERROR: dimensions missing in global-bounds tag\n");
+
+ if( globalDimensionsCSV.empty() )
+ throw std::invalid_argument( "ERROR: offsets missing in global-bounds tag\n");
}
- SetGlobalBounds( dimensionsCSV, offsetsCSV );
+
+ isGlobal = true;
}
} //end while loop
}
diff --git a/src/core/CVariable.cpp b/src/core/CVariable.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..eec3520ee564abee07c62ee7b6343a51948706b8
--- /dev/null
+++ b/src/core/CVariable.cpp
@@ -0,0 +1,33 @@
+/*
+ * CVariable.cpp
+ *
+ * Created on: Oct 18, 2016
+ * Author: wfg
+ */
+
+
+#include "core/CVariable.h"
+
+namespace adios
+{
+
+CVariable::CVariable( const std::string type, const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ):
+ m_Type{ type },
+ m_DimensionsCSV{ dimensionsCSV },
+ m_Transform{ transform },
+ m_GlobalDimensionsCSV{ globalDimensionsCSV },
+ m_GlobalOffsetsCSV{ globalOffsetsCSV }
+{
+ if( m_GlobalDimensionsCSV.empty() || m_GlobalOffsetsCSV.empty() )
+ m_IsGlobal = false;
+ else
+ m_IsGlobal = true;
+}
+
+
+CVariable::~CVariable()
+{ }
+
+
+} //end namespace
diff --git a/src/core/CVariableBase.cpp b/src/core/CVariableBase.cpp
deleted file mode 100644
index 6f71277605be21da734eedab4ccd45cefcf370dc..0000000000000000000000000000000000000000
--- a/src/core/CVariableBase.cpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * CVariable.cpp
- *
- * Created on: Oct 18, 2016
- * Author: wfg
- */
-
-
-#include "core/CVariableBase.h"
-
-namespace adios
-{
-
-
-CVariableBase::CVariableBase( const std::string type, const std::string dimensionsCSV, const std::string transform ):
- m_Type{ type },
- m_DimensionsCSV{ dimensionsCSV },
- m_Transform{ transform },
- m_IsGlobal{ false }
-{ }
-
-CVariableBase::CVariableBase( const std::string type, const std::string dimensionsCSV, const std::string transform,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ):
- m_Type{ type },
- m_DimensionsCSV{ dimensionsCSV },
- m_Transform{ transform },
- m_GlobalDimensionsCSV{ globalDimensionsCSV },
- m_GlobalOffsetsCSV{ globalOffsetsCSV },
- m_IsGlobal{ true }
-{ }
-
-
-CVariableBase::~CVariableBase()
-{ }
-
-
-
-} //end namespace
diff --git a/src/functions/GroupFunctions.cpp b/src/functions/GroupFunctions.cpp
index 07a13eb4ed6a0b290bf3074f57814b5d5ed1988f..dafe410d561e11fabf900cd667742f5f8d2569bb 100644
--- a/src/functions/GroupFunctions.cpp
+++ b/src/functions/GroupFunctions.cpp
@@ -18,134 +18,184 @@ namespace adios
{
-void CreateVariableLanguage( const std::string hostLanguage, const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
+void CreateVariableLanguage( const std::string name, const std::string type,
+ const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV,
std::map<std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
{
- if( hostLanguage == "C++" )
- CreateVariableCpp( name, isGlobal, type, dimensionsCSV, transform, variables );
+ std::shared_ptr<CVariableBase> variable;
+ //Common Primitive types to most languages
+ if( type == "char" || type == "character" )
+ variable = std::make_shared< CVariable<char> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( hostLanguage == "C" )
- CreateVariableC( name, isGlobal, type, dimensionsCSV, transform, variables );
+ else if( type == "unsigned char" )
+ variable = std::make_shared< CVariable<unsigned char> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( hostLanguage == "Fortran" )
- CreateVariableFortran( name, isGlobal, type, dimensionsCSV, transform, variables );
-}
-
-
-void CreateVariableCpp( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
-{
- //Primitive types
- if( type == "char")
- variables.emplace( name, std::make_shared< CVariable<char> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "short" || type == "integer*2" )
+ variables = std::make_shared< CVariable<short> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "unsigned char")
- variables.emplace( name, std::make_shared< CVariable<unsigned char> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "unsigned short" )
+ variables = std::make_shared< CVariable<unsigned short> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "int" || type == "integer" )
- variables.emplace( name, std::make_shared< CVariable<int> >( isGlobal, type, dimensionsCSV, transform ) );
+ variables = std::make_shared< CVariable<int> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
+
+ else if( type == "unsigned int" || type == "unsigned integer" )
+ variable = std::make_shared< CVariable<unsigned int> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "unsigned int" )
- variables.emplace( name, std::make_shared< CVariable<unsigned int> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "long int" || type == "long" || type == "long integer" )
+ variable = std::make_shared< CVariable<long int> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "long int" || type == "long" )
- variables.emplace( name, std::make_shared< CVariable<long int> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "long long int" || type == "long long" || type == "long long integer" )
+ variable = std::make_shared< CVariable<long long int> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "long long int" || type == "long long" )
- variables.emplace( name, std::make_shared< CVariable<long long int> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "float" || type == "real" || type == "real*4" )
+ variable = std::make_shared< CVariable<float> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "float" )
- variables.emplace( name, std::make_shared< CVariable<float> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "double" || type == "double precision" || type == "real*8" )
+ variable = std::make_shared< CVariable<double> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "double")
- variables.emplace( name, std::make_shared< CVariable<double> >( isGlobal, type, dimensionsCSV, transform ) );
+ else if( type == "long double" || type == "real*16" )
+ variable = std::make_shared< CVariable<long double> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- else if( type == "long double")
- variables.emplace( name, std::make_shared< CVariable<long double> >( isGlobal, type, dimensionsCSV, transform ) );
+ //C++
+ else if( type == "std::string" || type == "string" )
+ variable = std::make_shared< CVariable<std::string> >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
- //STL types
else if( type == "std::vector<char>" || type == "vector<char>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<char> > >( isGlobal, type, dimensionsCSV, transform ) );
+ variable = std::make_shared< CVariable< std::vector<char> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<int>" || type == "vector<int>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<int> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector<int> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<unsigned int>" || type == "vector<unsigned int>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<unsigned int> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector<unsigned int> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<long int>" || type == "std::vector<long>" ||
- type == "vector<long int>" || type == "vector<long>" )
- variables.emplace( name, std::make_shared< CVariable<std::vector<long int> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ type == "vector<long int>" || type == "vector<long>" )
+ variable = std::make_shared< CVariable<std::vector<long int> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<long long int>" || type == "std::vector<long long>" ||
- type == "vector<long long int>" || type == "vector<long long>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<long long int> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ type == "vector<long long int>" || type == "vector<long long>" )
+ variable = std::make_shared< CVariable< std::vector<long long int> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<float>" || type == "vector<float>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<float> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector<float> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<double>" || type == "vector<double>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<double> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector<double> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<long double>" || type == "vector<long double>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector<long double> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector<long double> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
//STL Complex types
else if( type == "std::complex<float>" || type == "complex<float>" )
- variables.emplace( name, std::make_shared< CVariable< std::complex<float> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::complex<float> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::complex<double>" || type == "complex<double>" )
- variables.emplace( name, std::make_shared< CVariable< std::complex<double> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::complex<double> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::complex<long double>" || type == "complex<long double>" )
- variables.emplace( name, std::make_shared< CVariable< std::complex<long double> > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::complex<long double> > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<std::complex<float>>" || type == "vector<complex<float>>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector< std::complex<float> > > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector< std::complex<float> > > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<std::complex<double>>" || type == "vector<complex<double>>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector< std::complex<double> > > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector< std::complex<double> > > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
else if( type == "std::vector<std::complex<long double>>" || type == "vector<complex<long double>>" )
- variables.emplace( name, std::make_shared< CVariable< std::vector< std::complex<long double> > > >( isGlobal, type, dimensionsCSV, transform ) ) ;
+ variable = std::make_shared< CVariable< std::vector< std::complex<long double> > > >( type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
+
+ variables[name] = variable;
}
-void CreateVariableC( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
+void SetVariableValues( CVariableBase& variable, const void* values ) noexcept
{
+ const std::string type( variable.m_Type );
-}
+ if( type == "char" || type == "character" )
+ variable.Set<char>( values );
+ else if( type == "unsigned char" )
+ variable.Set<unsigned char>( values );
-void CreateVariableFortran( const std::string name, const bool isGlobal,
- const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
-{
+ else if( type == "short" || type == "integer*2" )
+ variable.Set<short>( values );
-}
+ else if( type == "unsigned short" )
+ variable.Set<unsigned short>( values );
+ else if( type == "int" || type == "integer" )
+ variable.Set<int>( values );
-void SetVariableValues( CVariableBase& variable, const void* values ) noexcept
-{
- const std::string type = variable.m_Type;
+ else if( type == "unsigned int" || type == "unsigned integer" )
+ variable.Set<unsigned int>( values );
+
+ else if( type == "long int" || type == "long" || type == "long integer" )
+ variable.Set<long int>( values );
- //Set variable values, add more support
- if( type == "double" )
+ else if( type == "long long int" || type == "long long" || type == "long long integer" )
+ variable.Set<long long int>( values );
+
+ else if( type == "float" || type == "real" || type == "real*4" )
+ variable.Set<float>( values );
+
+ else if( type == "double" || type == "double precision" || type == "real*8" )
variable.Set<double>( values );
- else if( type == "int" || type == "integer" )
- variable.Set<int>( values );
+ else if( type == "long double" || type == "real*16" )
+ variable.Set<long double>( values );
+
+ //C++
+ else if( type == "std::string" || type == "string" )
+ variable.Set<std::string>( values );
- else if( type == "std::vector<int>" || type == "vector<int>" )
+ else if( type == "std::vector<char>" || type == "vector<char>" )
+ variable.Set< std::vector<char> >( values );
+
+ else if( type == "std::vector<int>" || type == "vector<int>" )
variable.Set< std::vector<int> >( values );
- else if( type == "std::vector<double>" || type == "vector<double>" )
+ else if( type == "std::vector<unsigned int>" || type == "vector<unsigned int>" )
+ variable.Set< std::vector<unsigned int> >( values );
+
+ else if( type == "std::vector<long int>" || type == "std::vector<long>" ||
+ type == "vector<long int>" || type == "vector<long>" )
+ variable.Set<std::vector<long int> >( values );
+
+ else if( type == "std::vector<long long int>" || type == "std::vector<long long>" ||
+ type == "vector<long long int>" || type == "vector<long long>" )
+ variable.Set< std::vector<long long int> >( values );
+
+ else if( type == "std::vector<float>" || type == "vector<float>" )
+ variable.Set< std::vector<float> >( values );
+
+ else if( type == "std::vector<double>" || type == "vector<double>" )
variable.Set< std::vector<double> >( values );
+ else if( type == "std::vector<long double>" || type == "vector<long double>" )
+ variable.Set< std::vector<long double> >( values );
+
+ //STL Complex types
+ else if( type == "std::complex<float>" || type == "complex<float>" )
+ variable.Set< std::complex<float> >( values );
+
+ else if( type == "std::complex<double>" || type == "complex<double>" )
+ variable.Set< std::complex<double> >( values );
+
+ else if( type == "std::complex<long double>" || type == "complex<long double>" )
+ variable.Set< std::complex<long double> >( values );
+
+ else if( type == "std::vector<std::complex<float>>" || type == "vector<complex<float>>" )
+ variable.Set< std::vector< std::complex<float> > >( values );
+
+ else if( type == "std::vector<std::complex<double>>" || type == "vector<complex<double>>" )
+ variable.Set< std::vector< std::complex<double> > >( values );
+
+ else if( type == "std::vector<std::complex<long double>>" || type == "vector<complex<long double>>" )
+ variable.Set< std::vector< std::complex<long double> > >( values );
}
diff --git a/src/public/SSupport.cpp b/src/public/SSupport.cpp
index 2942c9fec7b572aea1ccfca0a40c8a0509134ec1..94dae63fefb0d60d27d04a919bc5d2fdeb81b362 100644
--- a/src/public/SSupport.cpp
+++ b/src/public/SSupport.cpp
@@ -31,6 +31,8 @@ const std::set<std::string> SSupport::Transforms{
};
+
+
const std::map<std::string, std::set<std::string> > SSupport::Datatypes
{
{ "C++",
@@ -58,12 +60,12 @@ const std::map<std::string, std::set<std::string> > SSupport::Datatypes
"unsigned char",
"short",
"unsigned short",
- "int",
- "unsigned int",
- "long int", "long",
- "unsigned long int", "unsigned long",
- "long long int", "long long"
- "unsigned long long int", "unsigned long long",
+ "int", "integer"
+ "unsigned int", "unsigned integer",
+ "long int", "long", "long integer",
+ "unsigned long int", "unsigned long", "unsigned long integer",
+ "long long int", "long long", "long long integer",
+ "unsigned long long int", "unsigned long long", "unsigned long long integer",
"float",
"float complex"
"double",
@@ -74,10 +76,11 @@ const std::map<std::string, std::set<std::string> > SSupport::Datatypes
{ "Fortran",
{
"character",
+ "integer*2",
"integer",
- "real",
+ "real", "real*4",
+ "double precision", "real*8",
"complex",
- "double precision",
"double complex"
}
}
diff --git a/src/transport/CFStream.cpp b/src/transport/CFStream.cpp
index e3eb90773e0abc2bb630fa71045c83bab397daa4..ea14fa2f8f9312dc7ad0256ee2b30da28dc500bd 100644
--- a/src/transport/CFStream.cpp
+++ b/src/transport/CFStream.cpp
@@ -6,6 +6,7 @@
*/
/// \cond EXCLUDED_FROM_DOXYGEN
+#include <core/CVariable.h>
#include <iostream>
#include <sstream>
#include <cmath>
@@ -15,7 +16,8 @@
#include "transport/CFStream.h"
#include "core/CVariable.h"
-
+#include "functions/GroupFunctions.h"
+#include "functions/Templates.h"
namespace adios
{
@@ -55,65 +57,69 @@ void CFStream::Open( const std::string fileName, const std::string accessMode )
}
-void CFStream::Write( const CVariableBase& variable )
+void CFStream::Write( const CVariable& variable )
{
//local buffer, to be send over MPI
std::vector<char> buffer;
-
- if( variable.m_Type.find( "vector" ) ) //is a vector
- {
- //find total size first
- auto values = variable.Get< std::vector<int> >();
- unsigned int sizeSum = 0;
- for( auto element : *values )
- sizeSum += (int) std::log10( (double) std::abs( element ) ) + 1;
-
- buffer.reserve( 2*sizeSum );
-
- for( auto element : *values )
- {
- const char* elementChar = std::to_string( element ).c_str();
- buffer.insert( buffer.end(), elementChar, elementChar + strlen( elementChar ) );
- buffer.push_back(' ');
- }
-
- if( m_RankMPI == 0 )
- {
- std::cout << "Writing to file " << m_StreamName << "\n";
-
- m_FStream << "Hello from rank " << m_RankMPI << " : ";
- m_FStream.write( &buffer[0], buffer.size() );
- m_FStream << "\n";
-
- MPI_Status* status = NULL;
-
- for( int r = 1; r < m_SizeMPI; ++r )
- {
- int bufferSize;
- MPI_Recv( &bufferSize, 1, MPI_INT, r, 0, m_MPIComm, status ); //receive from r the buffer size
- std::cout << "Getting from rank: " << r << " buffer size "<< bufferSize << "\n";
-
- buffer.resize( bufferSize );
- MPI_Recv( &buffer[0], bufferSize, MPI_CHAR, r, 1, m_MPIComm, status ); //receive from r the buffer
-
- m_FStream << "Hello from rank " << r << " : ";
- m_FStream.write( &buffer[0], bufferSize );
- m_FStream << "\n";
- }
- }
- else
- {
- int bufferSize = (int)buffer.size();
- MPI_Send( &bufferSize, 1, MPI_INT, 0, 0, m_MPIComm ); //send to rank=0 the buffer size
-
- std::cout << "Hello from rank: " << m_RankMPI << "\n";
- std::cout << "Buffer size: " << bufferSize << "\n";
-
- MPI_Send( &buffer[0], bufferSize, MPI_CHAR, 0, 1, m_MPIComm ); //send to rank=0 the buffer
- }
-
- MPI_Barrier( m_MPIComm );
- }
+ const std::string type( variable.m_Type );
+ auto var = GetVariableValues( variable );
+
+// if( type.find( "vector" ) ) //is a vector
+// {
+// //find total size first
+// //auto values = variable.Get< std::vector<int> >();
+// auto values = GetVariableValues( variable );
+// //auto values = GetVariableValues( variable );
+// unsigned int sizeSum = 0;
+// for( auto element : *values )
+// sizeSum += (int) std::log10( (double) std::abs( element ) ) + 1;
+//
+// buffer.reserve( 2*sizeSum );
+//
+// for( auto element : *values )
+// {
+// const char* elementChar = std::to_string( element ).c_str();
+// buffer.insert( buffer.end(), elementChar, elementChar + strlen( elementChar ) );
+// buffer.push_back(' ');
+// }
+//
+// if( m_RankMPI == 0 )
+// {
+// std::cout << "Writing to file " << m_StreamName << "\n";
+//
+// m_FStream << "Hello from rank " << m_RankMPI << " : ";
+// m_FStream.write( &buffer[0], buffer.size() );
+// m_FStream << "\n";
+//
+// MPI_Status* status = NULL;
+//
+// for( int r = 1; r < m_SizeMPI; ++r )
+// {
+// int bufferSize;
+// MPI_Recv( &bufferSize, 1, MPI_INT, r, 0, m_MPIComm, status ); //receive from r the buffer size
+// std::cout << "Getting from rank: " << r << " buffer size "<< bufferSize << "\n";
+//
+// buffer.resize( bufferSize );
+// MPI_Recv( &buffer[0], bufferSize, MPI_CHAR, r, 1, m_MPIComm, status ); //receive from r the buffer
+//
+// m_FStream << "Hello from rank " << r << " : ";
+// m_FStream.write( &buffer[0], bufferSize );
+// m_FStream << "\n";
+// }
+// }
+// else
+// {
+// int bufferSize = (int)buffer.size();
+// MPI_Send( &bufferSize, 1, MPI_INT, 0, 0, m_MPIComm ); //send to rank=0 the buffer size
+//
+// std::cout << "Hello from rank: " << m_RankMPI << "\n";
+// std::cout << "Buffer size: " << bufferSize << "\n";
+//
+// MPI_Send( &buffer[0], bufferSize, MPI_CHAR, 0, 1, m_MPIComm ); //send to rank=0 the buffer
+// }
+//
+// MPI_Barrier( m_MPIComm );
+// }
}
void CFStream::Close( )