diff --git a/include/core/CCapsule.h b/include/core/CCapsule.h
index dbc1ab59728cbaa14abfd46c8313f168c8d1abcc..a8c7d2a8b15ed4f96faa9bc55d14c67507406ebe 100644
--- a/include/core/CCapsule.h
+++ b/include/core/CCapsule.h
@@ -66,7 +66,7 @@ public:
~CCapsule( );
/**
- *
+ * Add a transport to a stream
* @param streamName
* @param accessMode
* @param isDefault
diff --git a/include/core/CGroup.h b/include/core/CGroup.h
index 15420bedbf08459ad596f3621846df93d601d5db..6a6d83ec634d8740e188a43aa932a9fdccf8b2db 100644
--- a/include/core/CGroup.h
+++ b/include/core/CGroup.h
@@ -60,23 +60,33 @@ public:
~CGroup( ); ///< Using STL containers, no deallocation
/**
- * Creates a new variable in the group object
+ * Define a new variable in the group object
* @param name variable name, must be unique in the group. 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 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 DefineVariable( const std::string name, const std::string type,
+ void DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV,
const std::string globalDimensionsCSV, const std::string globalOffsetsCSV );
+
+ /**
+ * Sets a variable transform contained in ADIOS.m_Transforms (single container for all groups and variables)
+ * @param variableName variable to be assigned a transformation
+ * @param transformIndex index in
+ * @param compressionLevel from 0 to 9
+ */
+ void SetTransform( const std::string variableName, const unsigned int transformIndex, const unsigned int compressionLevel );
+
+
/**
- *
- * @param name attribute name, must be unique. If name exists it removes the current variable. In debug mode program will exit.
+ * Define a new attribute
+ * @param attributeName attribute name, must be unique. If name exists it removes the current variable. In debug mode program will exit.
* @param type attribute type string or numeric type
* @param value information about the attribute
*/
- void DefineAttribute( const std::string name, const std::string type, const std::string value );
+ void DefineAttribute( const std::string attributeName, const std::string type, const std::string value );
/**
* @brief Dumps groups information to a file stream or standard output.
diff --git a/include/core/SVariable.h b/include/core/SVariable.h
index 74b21893a381fd4b75e1339d26cdc54e4f2d42dc..c4aedf6849c7a1d681fc5042374ac1f21b44acf5 100644
--- a/include/core/SVariable.h
+++ b/include/core/SVariable.h
@@ -23,10 +23,11 @@ namespace adios
template< class T >
struct SVariable
{
- const std::string m_DimensionsCSV; ///< comma separated list for variables to search for local dimensions
- const T* m_Values; ///< pointer to values passed from ADIOS Write
- const short m_GlobalBoundsIndex; ///< if global > 0, index corresponds to global-bounds in m_GlobalBounds in CGroup, if local then = -1
- short m_TransformIndex; ///< if global > 0, index corresponds to , if local then = -1
+ const std::string DimensionsCSV; ///< comma separated list for variables to search for local dimensions
+ const T* Values; ///< pointer to values passed from ADIOS Write
+ const short GlobalBoundsIndex; ///< if global > 0, index corresponds to global-bounds in m_GlobalBounds in CGroup, if local then = -1
+ short TransformIndex = -1; ///< if no transformation then = -1, otherwise index to m_Transforms container in ADIOS
+ unsigned short CompressionLevel = 0; ///< if 0, then use default, values from 1 to 9 indicate compression level
};
diff --git a/include/public/ADIOS.h b/include/public/ADIOS.h
index fb9a99634c6f5c49db5c56391cc1632406274a84..3fa2eaafc8c0391fa05d1e3f30e1857766726198 100644
--- a/include/public/ADIOS.h
+++ b/include/public/ADIOS.h
@@ -197,7 +197,6 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param variableName corresponding variable name
* @param type variable type
* @param dimensionsCSV comma separated (no space) dimensions "Nx,Ny,Nz" defined by other variables
- * @param transform transformation method applied to current variable
* @param globalDimensionsCSV comma separated (no space) global dimensions "gNx,gNy,gNz" defined by other variables
* @param globalOffsetsCSV comma separated (no space) global offsets "oNx,oNy,oNz" defined by other variables
*/
diff --git a/src/core/CCapsule.cpp b/src/core/CCapsule.cpp
index 83488cae2668f267d153cb2b1a93dfc9e539543f..620fb9cebc572b3f859d3e7c5c67ab42d0a8434c 100644
--- a/src/core/CCapsule.cpp
+++ b/src/core/CCapsule.cpp
@@ -62,6 +62,11 @@ int CCapsule::AddTransport( const std::string streamName, const std::string acce
else if( transport == "DataMan" )
m_Transports.push_back( std::make_shared<CDataMan>( m_MPIComm, m_DebugMode, arguments ) );
+
+ int transportIndex = static_cast<int>( m_Transports.size() - 1 );
+ m_Transports[ transportIndex ]->Open( name, accessMode );
+
+ return transportIndex;
}
@@ -99,36 +104,11 @@ std::string CCapsule::GetName( const std::vector<std::string>& arguments ) const
if( m_DebugMode == true )
{
if( name.empty() || isNameFound == false )
- std::invalid_argument("ERROR: argument to name= is empty in call to AddTransport" );
+ std::invalid_argument( "ERROR: argument to name= is empty or not found in call to AddTransport" );
}
return name;
}
-
-//void CCapsule::CreateTransform( const std::string transform )
-//{
-// std::string method( transform );
-// auto colonPosition = transform.find(":");
-//
-// if( colonPosition != transform.npos )
-// {
-// method = transform.substr( 0, colonPosition );
-// }
-//
-// if( m_Transforms.find( method ) != m_Transforms.end() ) //transform method already exists, do nothing
-// return;
-//
-// if( method == "bzip2" ) //here must add debug mode exception
-// {
-// #ifdef HAVE_BZIP2
-// m_Transforms["bzip2"] = std::make_shared<CBZIP2>( );
-// #endif
-// }
-//}
-
-
-
-
} //end namespace
diff --git a/src/core/CGroup.cpp b/src/core/CGroup.cpp
index 70f5804c999bf90c13e723635380d029f2ccde89..015271e483e99e5bb2555198a26e6ee604b086b0 100644
--- a/src/core/CGroup.cpp
+++ b/src/core/CGroup.cpp
@@ -38,82 +38,165 @@ CGroup::~CGroup( )
{ }
-void CGroup::DefineVariable( const std::string name, const std::string type,
+void CGroup::DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV,
const std::string globalDimensionsCSV, const std::string globalOffsetsCSV )
{
if( m_DebugMode == true )
{
if( SSupport::Datatypes.at( m_HostLanguage ).count( type ) == 0 )
- throw std::invalid_argument( "ERROR: type " + type + " for variable " + name + " is not supported.\n" );
- if( m_Variables.count( name ) == 0 ) //variable doesn't exists
- m_Variables[name] = std::make_pair( type, CurrentTypeIndex( type ) );
+ throw std::invalid_argument( "ERROR: type " + type + " for variable " + variableName + " is not supported.\n" );
+ if( m_Variables.count( variableName ) == 0 ) //variable doesn't exists
+ m_Variables[variableName] = std::make_pair( type, CurrentTypeIndex( type ) );
else //name is found
- throw std::invalid_argument( "ERROR: variable " + name + " exists more than once.\n" );
+ throw std::invalid_argument( "ERROR: variable " + variableName + " exists more than once.\n" );
}
else
{
- m_Variables[name] = std::make_pair( type, CurrentTypeIndex( type ) );
+ m_Variables[variableName] = std::make_pair( type, CurrentTypeIndex( type ) );
}
- int transformIndex = SetTransforms( transform );
int globalBoundsIndex = SetGlobalBounds( globalDimensionsCSV, globalOffsetsCSV );
if( type == "char" || type == "character" )
- m_Char.push_back( SVariable<char>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_Char.push_back( SVariable<char>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "unsigned char" )
- m_UChar.push_back( SVariable<unsigned char>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_UChar.push_back( SVariable<unsigned char>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "short" || type == "integer*2" )
- m_Short.push_back( SVariable<short>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_Short.push_back( SVariable<short>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "unsigned short" )
- m_UShort.push_back( SVariable<unsigned short>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_UShort.push_back( SVariable<unsigned short>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "int" || type == "integer" )
- m_Int.push_back( SVariable<int>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_Int.push_back( SVariable<int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "unsigned int" || type == "unsigned integer" )
- m_UInt.push_back( SVariable<unsigned int>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_UInt.push_back( SVariable<unsigned int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "long int" || type == "long" || type == "long integer" )
- m_LInt.push_back( SVariable<long int>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_LInt.push_back( SVariable<long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
+
+ else if( type == "unsigned long int" || type == "unsigned long" || type == "unsigned long integer" )
+ m_ULInt.push_back( SVariable<unsigned long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "long long int" || type == "long long" || type == "long long integer" )
- m_LLInt.push_back( SVariable<long long int>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_LLInt.push_back( SVariable<long long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "unsigned long long int" || type == "unsigned long long" || type == "unsigned long long integer" )
- m_ULLInt.push_back( SVariable<unsigned long long int>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_ULLInt.push_back( SVariable<unsigned long long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "float" || type == "real" || type == "real*4" )
- m_Float.push_back( SVariable<float>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_Float.push_back( SVariable<float>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "double" || type == "double precision" || type == "real*8" )
- m_Double.push_back( SVariable<double>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_Double.push_back( SVariable<double>{ dimensionsCSV, nullptr, globalBoundsIndex } );
else if( type == "long double" || type == "real*16" )
- m_LDouble.push_back( SVariable<long double>{ dimensionsCSV, nullptr, transformIndex, globalBoundsIndex } );
+ m_LDouble.push_back( SVariable<long double>{ dimensionsCSV, nullptr, globalBoundsIndex } );
+
+ m_SerialSize += variableName.size() + type.size() + dimensionsCSV.size() + 4 * sizeof( char ); //4, adding one more for globalBoundsIndex
+}
+
+
+void CGroup::SetTransform( const std::string variableName, const unsigned int transformIndex, const unsigned int compressionLevel )
+{
+ auto itVariable = m_Variables.find( variableName );
+
+ if( m_DebugMode == true )
+ {
+ if( itVariable == m_Variables.end() ) //variable doesn't exists
+ throw std::invalid_argument( "ERROR: variable " + variableName + " doesn't exist, in call to SetTransform.\n" );
+ }
+
+ const std::string type( itVariable->second.first );
+ const unsigned int index = itVariable->second.second;
- m_SerialSize += name.size() + type.size() + dimensionsCSV.size() + transform.size() + 5 * sizeof(char); //5, adding one more for globalBoundsIndex
+ if( type == "char" || type == "character" )
+ {
+ m_Char[index].TransformIndex = transformIndex;
+ m_Char[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "unsigned char" )
+ {
+ m_UChar[index].TransformIndex = transformIndex;
+ m_UChar[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "short" || type == "integer*2" )
+ {
+ m_Short[index].TransformIndex = transformIndex;
+ m_Short[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "unsigned short" )
+ {
+ m_UShort[index].TransformIndex = transformIndex;
+ m_UShort[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "int" || type == "integer" )
+ {
+ m_Int[index].TransformIndex = transformIndex;
+ m_Int[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "unsigned int" || type == "unsigned integer" )
+ {
+ m_UInt[index].TransformIndex = transformIndex;
+ m_UInt[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "long int" || type == "long" || type == "long integer" )
+ {
+ m_LInt[index].TransformIndex = transformIndex;
+ m_LInt[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "unsigned long int" || type == "unsigned long" || type == "unsigned long integer" )
+ {
+ m_ULInt[index].TransformIndex = transformIndex;
+ m_ULInt[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "long long int" || type == "long long" || type == "long long integer" )
+ {
+ m_ULInt[index].TransformIndex = transformIndex;
+ m_ULInt[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "unsigned long long int" || type == "unsigned long long" || type == "unsigned long long integer" )
+ {
+ m_ULLInt[index].TransformIndex = transformIndex;
+ m_ULLInt[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "float" || type == "real" || type == "real*4" )
+ {
+ m_Float[index].TransformIndex = transformIndex;
+ m_Float[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "double" || type == "double precision" || type == "real*8" )
+ {
+ m_Double[index].TransformIndex = transformIndex;
+ m_Double[index].CompressionLevel = compressionLevel;
+ }
+ else if( type == "long double" || type == "real*16" )
+ {
+ m_LDouble[index].TransformIndex = transformIndex;
+ m_LDouble[index].CompressionLevel = compressionLevel;
+ }
}
-void CGroup::CreateAttribute( const std::string name, const std::string type, const std::string value )
+void CGroup::DefineAttribute( const std::string attributeName, const std::string type, const std::string value )
{
if( m_DebugMode == true )
{
- if( m_Attributes.count( name ) == 0 ) //variable doesn't exists
- m_Attributes.emplace( name, SAttribute{ type, value } );
+ if( m_Attributes.count( attributeName ) == 0 ) //attribute doesn't exists
+ m_Attributes.emplace( attributeName, SAttribute{ type, value } );
else //name is found
- throw std::invalid_argument( "ERROR: attribute " + name + " exists, NOT setting a new variable\n" );
+ throw std::invalid_argument( "ERROR: attribute " + attributeName + " exists, NOT setting a new variable\n" );
}
else
{
- m_Attributes.emplace( name, SAttribute{ type, value } );
+ m_Attributes.emplace( attributeName, SAttribute{ type, value } );
}
- m_SerialSize += name.size() + type.size() + value.size() + 3; //3 is one byte storing the size as a char
+ m_SerialSize += attributeName.size() + type.size() + value.size() + 3 * sizeof( char ); //3 is one byte storing the size as a char
}
@@ -130,28 +213,28 @@ const unsigned long long int CGroup::GetIntVariableValue( const std::string vari
const unsigned long long int value = 0;
if( type == "short" )
- value = *( m_Short[index].m_Values );
+ value = *( m_Short[index].Values );
else if( type == "unsigned short" )
- value = *( m_UShort[index].m_Values );
+ value = *( m_UShort[index].Values );
else if( type == "int" )
- value = *( m_Int[index].m_Values );
+ value = *( m_Int[index].Values );
else if( type == "unsigned int" )
- value = *( m_UInt[index].m_Values );
+ value = *( m_UInt[index].Values );
else if( type == "long int" )
- value = *( m_LInt[index].m_Values );
+ value = *( m_LInt[index].Values );
else if( type == "unsigned long int" )
- value = *( m_ULInt[index].m_Values );
+ value = *( m_ULInt[index].Values );
else if( type == "long long int" )
- value = *( m_LLInt[index].m_Values );
+ value = *( m_LLInt[index].Values );
else if( type == "unsigned long long int" )
- value = *( m_ULLInt[index].m_Values );
+ value = *( m_ULLInt[index].Values );
else
throw std::invalid_argument( "ERROR: variable " + variableName + " must be of short, int or associated type (long int, unsigned long int, etc.)\n" );
@@ -245,18 +328,18 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup )
else if( pair.first == "dimensions" ) dimensionsCSV = pair.second;
else if( pair.first == "transform" ) transform = pair.second;
}
- CreateVariable( name, type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
+ DefineVariable( name, type, dimensionsCSV, globalDimensionsCSV, globalOffsetsCSV );
}
else if( tagName == "attribute" )
{
- std::string name, path, value, type;
+ std::string name, value, type;
for( auto& pair : pairs ) //loop through all pairs
{
if( pair.first == "name" ) name = pair.second;
else if( pair.first == "value" ) value = pair.second;
else if( pair.first == "type" ) type = pair.second;
}
- CreateAttribute( name, type, value, globalDimensionsCSV, globalOffsetsCSV );
+ DefineAttribute( name, type, value );
}
else if( tagName == "global-bounds" )
{
@@ -351,25 +434,5 @@ const int CGroup::SetGlobalBounds( const std::string globalDimensionsCSV, const
}
-const int CGroup::SetTransforms( const std::string transform ) noexcept
-{
- if( transform.empty() )
- return -1;
-
- int transformIndex = -1;
- auto itTransform = std::find( m_Transforms.begin(), m_Transforms.end(), transform );
- if( itTransform != m_Transforms.end() )
- {
- transformIndex = std::distance( m_Transforms.begin(), itTransform );
- }
- else
- {
- m_Transforms.push_back( transform );
- transformIndex = m_Transforms.size();
- }
-
- return transformIndex;
-}
-
} //end namespace
diff --git a/src/public/ADIOS.cpp b/src/public/ADIOS.cpp
index 71b66771074a47ccdd5d3d225db9c2777d49d438..961d1d8e213ef8587cd27b0e7efde3a1b1faa790 100644
--- a/src/public/ADIOS.cpp
+++ b/src/public/ADIOS.cpp
@@ -117,9 +117,32 @@ void ADIOS::DefineVariable( const std::string groupName, const std::string varia
void ADIOS::SetTransform( const std::string groupName, const std::string variableName, const std::string transform )
{
auto itGroup = m_Groups.find( groupName );
- if( m_DebugMode == true )
+ if( m_DebugMode == true ) //check group and transform
+ {
CheckGroup( itGroup, groupName, " from call to SetTransform \n" );
+ if( SSupport::Transforms.count( transform ) == 0 )
+ throw std::invalid_argument( "ERROR: transform method " + transform + " not supported, in call to SetTransform\n" );
+ }
+
+ //get method:compressionLevel from transform
+ std::string method( transform );
+ int compressionLevel = 0;
+
+ auto colonPosition = transform.find( ":" );
+
+ if( colonPosition != transform.npos )
+ {
+ if( m_DebugMode == true )
+ {
+ if( colonPosition == transform.size() - 1 )
+ throw std::invalid_argument( "ERROR: wrong format for transform " + transform + ", in call to SetTransform\n" );
+ }
+
+ method = transform.substr( 0, colonPosition );
+ compressionLevel = std::stoi( transform.substr( colonPosition+1 ) );
+ }
+
int transformIndex = -1;
for( unsigned int i = 0; i < m_Transforms.size(); ++i )
{
@@ -129,7 +152,16 @@ void ADIOS::SetTransform( const std::string groupName, const std::string variabl
break;
}
}
- //itGroup->second.SetTransform( variableName, transform );
+
+ if( transformIndex == -1 ) //not found, then create a new transform
+ {
+ if( transform == "bzip2" )
+ {
+ m_Transforms.push_back( std::make_shared<CBZIP2>( ) );
+ }
+ }
+
+ itGroup->second.SetTransform( variableName, transformIndex, compressionLevel );
}
diff --git a/src/public/SSupport.cpp b/src/public/SSupport.cpp
index eeafd7c177e2a6d639a8f8614e923b917bbc53cc..b0a2d38084a14dab88f4cc032d35138df8e41097 100644
--- a/src/public/SSupport.cpp
+++ b/src/public/SSupport.cpp
@@ -27,7 +27,7 @@ const std::set<std::string> SSupport::Transports{
const std::set<std::string> SSupport::Transforms{
- { "none", "identity", "bzip2", "isobar" }
+ { "none", "identity", "bzip2", "isobar", "szip" , "zlib" }
};