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Commit 7d182edb authored by wfg's avatar wfg
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Bug fix for std::vector iterator (or reference) invalidation 

Replaced vectors with map containers for Variables to avoid iterator
invalidation when adding element to a container.
parent b6957815
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1 merge request!8Integrate groupless
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examples/hello/bpWriter/helloBPWriter.cpp
+ 1
− 1
View file @ 7d182edb
......@@ -44,7 +44,7 @@ int main( int argc, char* argv [] )
try
{
//Define variable and local size
auto ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx} );
adios::Variable<double>& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx} );
adios::Variable<float>& ioMyMatrix = adios.DefineVariable<float>( "myMatrix", {rows,columns} );
//Define method for engine creation, it is basically straight-forward parameters
......
examples/hello/bpWriter/helloBPWriter_nompi.cpp
+ 7
− 1
View file @ 7d182edb
......@@ -24,13 +24,18 @@ int main( int argc, char* argv [] )
const std::size_t columns = 3;
std::vector<float> myMatrix = { 1, 2, 3,
4, 5, 6,
7, 8, 9, };
7, 8, 9 };
std::vector<float> myMatrix2 = { -1, -2, -3,
-4, -5, -6,
-7, -8, -9 };
try
{
//Define variable and local size
adios::Variable<double>& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", adios::Dims{Nx} );
adios::Variable<float>& ioMyMatrix = adios.DefineVariable<float>( "myMatrix", adios::Dims{rows,columns} );
adios::Variable<float>& ioMyMatrix2 = adios.DefineVariable<float>( "myMatrix2", adios::Dims{rows,columns} );
//Define method for engine creation, it is basically straight-forward parameters
adios::Method& bpWriterSettings = adios.DeclareMethod( "SinglePOSIXFile" ); //default method type is Writer
......@@ -45,6 +50,7 @@ int main( int argc, char* argv [] )
bpWriter->Write<double>( ioMyDoubles, myDoubles.data() ); // Base class Engine own the Write<T> that will call overloaded Write from Derived
bpWriter->Write<float>( ioMyMatrix, myMatrix.data() ); //2d Example
//bpWriter->Write<float>( ioMyMatrix2, myMatrix2.data() ); //2d Example
bpWriter->Close( );
//
}
......
include/ADIOS.h
+ 101
− 84
View file @ 7d182edb
......@@ -117,9 +117,10 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
const Dims globalOffsets = Dims() )
{
CheckVariableInput( name, dimensions );
m_Compound.emplace_back( name, sizeof(T), dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<T>(), m_Compound.size()-1 ) );
return m_Compound.back();
const unsigned int size = m_Compound.size();
m_Compound.emplace( size, VariableCompound( name, sizeof(T), dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<T>(), size ) );
return m_Compound.at( size );
}
VariableCompound& GetVariableCompound( const std::string name );
......@@ -193,23 +194,23 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
private: //no const to allow default empty and copy constructors
std::vector< Variable<char> > m_Char; ///< Key: variable name, Value: variable of type char
std::vector< Variable<unsigned char> > m_UChar; ///< Key: variable name, Value: variable of type unsigned char
std::vector< Variable<short> > m_Short; ///< Key: variable name, Value: variable of type short
std::vector< Variable<unsigned short> > m_UShort; ///< Key: variable name, Value: variable of type unsigned short
std::vector< Variable<int> > m_Int; ///< Key: variable name, Value: variable of type int
std::vector< Variable<unsigned int> > m_UInt; ///< Key: variable name, Value: variable of type unsigned int
std::vector< Variable<long int> > m_LInt; ///< Key: variable name, Value: variable of type long int
std::vector< Variable<unsigned long int> > m_ULInt; ///< Key: variable name, Value: variable of type unsigned long int
std::vector< Variable<long long int> > m_LLInt; ///< Key: variable name, Value: variable of type long long int
std::vector< Variable<unsigned long long int> > m_ULLInt; ///< Key: variable name, Value: variable of type unsigned long long int
std::vector< Variable<float> > m_Float; ///< Key: variable name, Value: variable of type float
std::vector< Variable<double> > m_Double; ///< Key: variable name, Value: variable of type double
std::vector< Variable<long double> > m_LDouble; ///< Key: variable name, Value: variable of type double
std::vector< Variable<std::complex<float>> > m_CFloat; ///< Key: variable name, Value: variable of type complex<float>
std::vector< Variable<std::complex<double>> > m_CDouble; ///< Key: variable name, Value: variable of type complex<float>
std::vector< Variable<std::complex<long double>> > m_CLDouble; ///< Key: variable name, Value: variable of type complex<float>
std::vector< VariableCompound > m_Compound; ///< Key: variable name, Value: compound type variable
std::map<unsigned int, Variable<char> > m_Char;
std::map<unsigned int, Variable<unsigned char> > m_UChar;
std::map<unsigned int, Variable<short> > m_Short;
std::map<unsigned int, Variable<unsigned short> > m_UShort;
std::map<unsigned int, Variable<int> > m_Int;
std::map<unsigned int, Variable<unsigned int> > m_UInt;
std::map<unsigned int, Variable<long int> > m_LInt;
std::map<unsigned int, Variable<unsigned long int> > m_ULInt;
std::map<unsigned int, Variable<long long int> > m_LLInt;
std::map<unsigned int, Variable<unsigned long long int> > m_ULLInt;
std::map<unsigned int, Variable<float> > m_Float;
std::map<unsigned int, Variable<double> > m_Double;
std::map<unsigned int, Variable<long double> > m_LDouble;
std::map<unsigned int, Variable<std::complex<float>> > m_CFloat;
std::map<unsigned int, Variable<std::complex<double>> > m_CDouble;
std::map<unsigned int, Variable<std::complex<long double>> > m_CLDouble;
std::map<unsigned int, VariableCompound > m_Compound;
std::string m_ConfigFile; ///< XML File to be read containing configuration information
bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code
......@@ -272,9 +273,10 @@ Variable<char>& ADIOS::DefineVariable( const std::string name, const Dims dimens
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_Char.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<char>(), m_Char.size()-1 ) );
return m_Char.back();
const unsigned int size = m_Char.size();
m_Char.emplace( size, Variable<char>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<char>(), size ) );
return m_Char.at( size );
}
......@@ -283,9 +285,10 @@ Variable<unsigned char>& ADIOS::DefineVariable( const std::string name, const Di
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_UChar.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), m_UChar.size()-1 ) );
return m_UChar.back();
const unsigned int size = m_UChar.size();
m_UChar.emplace( size, Variable<unsigned char>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), size ) );
return m_UChar.at( size );
}
......@@ -294,9 +297,10 @@ Variable<short>& ADIOS::DefineVariable( const std::string name, const Dims dimen
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_Short.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), m_Short.size()-1 ) );
return m_Short.back();
const unsigned int size = m_Short.size();
m_Short.emplace( size, Variable<short>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), size ) );
return m_Short.at( size );
}
......@@ -305,9 +309,10 @@ Variable<unsigned short>& ADIOS::DefineVariable( const std::string name, const D
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_UShort.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned short>(), m_UShort.size()-1 ) );
return m_UShort.back();
const unsigned int size = m_UShort.size();
m_UShort.emplace( size, Variable<unsigned short>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned short>(), size ) );
return m_UShort.at( size );
}
......@@ -316,9 +321,10 @@ Variable<int>& ADIOS::DefineVariable( const std::string name, const Dims dimensi
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_Int.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<int>(), m_Int.size()-1 ) );
return m_Int.back();
const unsigned int size = m_Int.size();
m_Int.emplace( size, Variable<int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<int>(), size ) );
return m_Int.at( size );
}
......@@ -327,9 +333,10 @@ Variable<unsigned int>& ADIOS::DefineVariable( const std::string name, const Dim
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_UInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned int>(), m_UInt.size()-1 ) );
return m_UInt.back();
const unsigned int size = m_UInt.size();
m_UInt.emplace( size, Variable<unsigned int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned int>(), size ) );
return m_UInt.at( size );
}
......@@ -338,9 +345,10 @@ Variable<long int>& ADIOS::DefineVariable( const std::string name, const Dims di
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_LInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<long int>(), m_LInt.size()-1 ) );
return m_LInt.back();
const unsigned int size = m_LInt.size();
m_LInt.emplace( size, Variable<long int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<long int>(), size ) );
return m_LInt.at( size );
}
......@@ -349,9 +357,10 @@ Variable<unsigned long int>& ADIOS::DefineVariable( const std::string name, cons
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_ULInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned long int>(), m_ULInt.size()-1 ) );
return m_ULInt.back();
const unsigned int size = m_LInt.size();
m_ULInt.emplace( size, Variable<unsigned long int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned long int>(), size ) );
return m_ULInt.at( size );
}
......@@ -360,9 +369,10 @@ Variable<long long int>& ADIOS::DefineVariable( const std::string name, const Di
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_LLInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<long long int>(), m_LLInt.size()-1 ) );
return m_LLInt.back();
const unsigned int size = m_LLInt.size();
m_LLInt.emplace( size, Variable<long long int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<long long int>(), size ) );
return m_LLInt.at( size );
}
......@@ -371,9 +381,10 @@ Variable<unsigned long long int>& ADIOS::DefineVariable( const std::string name,
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_ULLInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<unsigned long long int>(), m_ULLInt.size()-1 ) );
return m_ULLInt.back();
const unsigned int size = m_ULLInt.size();
m_ULLInt.emplace( size, Variable<unsigned long long int>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<unsigned long long int>(), size ) );
return m_ULLInt.at( size );
}
template<> inline
......@@ -381,9 +392,10 @@ Variable<float>& ADIOS::DefineVariable( const std::string name, const Dims dimen
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_Float.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<float>(), m_Float.size()-1 ) );
return m_Float.back();
const unsigned int size = m_Float.size();
m_Float.emplace( size, Variable<float>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<float>(), size ) );
return m_Float.at( size );
}
......@@ -392,9 +404,10 @@ Variable<double>& ADIOS::DefineVariable( const std::string name, const Dims dime
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_Double.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<double>(), m_Double.size()-1 ) );
return m_Double.back();
const unsigned int size = m_Double.size();
m_Double.emplace( size, Variable<double>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<double>(), size ) );
return m_Double.at( size );
}
......@@ -403,9 +416,10 @@ Variable<long double>& ADIOS::DefineVariable( const std::string name, const Dims
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_LDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<long double>(), m_LDouble.size()-1 ) );
return m_LDouble.back();
const unsigned int size = m_LDouble.size();
m_LDouble.emplace( size, Variable<long double>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<long double>(), size ) );
return m_LDouble.at( size );
}
......@@ -414,9 +428,10 @@ Variable<std::complex<float>>& ADIOS::DefineVariable( const std::string name, co
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_CFloat.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<float>>(), m_CFloat.size()-1 ) );
return m_CFloat.back();
const unsigned int size = m_CFloat.size();
m_CFloat.emplace( size, Variable<std::complex<float>>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<float>>(), size ) );
return m_CFloat.at( size );
}
......@@ -425,9 +440,10 @@ Variable<std::complex<double>>& ADIOS::DefineVariable( const std::string name, c
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_CDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<double>>(), m_CDouble.size()-1 ) );
return m_CDouble.back();
const unsigned int size = m_CDouble.size();
m_CDouble.emplace( size, Variable<std::complex<double>>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<double>>(), size ) );
return m_CDouble.at( size );
}
......@@ -436,76 +452,77 @@ Variable<std::complex<long double>>& ADIOS::DefineVariable( const std::string na
const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_CLDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<double>>(), m_CLDouble.size()-1 ) );
return m_CLDouble.back();
const unsigned int size = m_CLDouble.size();
m_CLDouble.emplace( size, Variable<std::complex<long double>>( name, dimensions, globalDimensions, globalOffsets, m_DebugMode ) );
m_Variables.emplace( name, std::make_pair( GetType<std::complex<long double>>(), size ) );
return m_CLDouble.at( size );
}
//Get template specialization
template<> inline
Variable<char>& ADIOS::GetVariable( const std::string name )
{ return m_Char[ GetVariableIndex<char>(name) ]; }
{ return m_Char.at( GetVariableIndex<char>(name) ); }
template<> inline
Variable<unsigned char>& ADIOS::GetVariable( const std::string name )
{ return m_UChar[ GetVariableIndex<unsigned char>(name) ]; }
{ return m_UChar.at( GetVariableIndex<unsigned char>(name) ); }
template<> inline
Variable<short>& ADIOS::GetVariable( const std::string name )
{ return m_Short[ GetVariableIndex<short>(name) ]; }
{ return m_Short.at( GetVariableIndex<short>(name) ); }
template<> inline
Variable<unsigned short>& ADIOS::GetVariable( const std::string name )
{ return m_UShort[ GetVariableIndex<unsigned short>(name) ]; }
{ return m_UShort.at( GetVariableIndex<unsigned short>(name) ); }
template<> inline
Variable<int>& ADIOS::GetVariable( const std::string name )
{ return m_Int[ GetVariableIndex<int>(name) ]; }
{ return m_Int.at( GetVariableIndex<int>(name) ); }
template<> inline
Variable<unsigned int>& ADIOS::GetVariable( const std::string name )
{ return m_UInt[ GetVariableIndex<unsigned int>(name) ]; }
{ return m_UInt.at( GetVariableIndex<unsigned int>(name) ); }
template<> inline
Variable<long int>& ADIOS::GetVariable( const std::string name )
{ return m_LInt[ GetVariableIndex<unsigned int>(name) ]; }
{ return m_LInt.at( GetVariableIndex<unsigned int>(name) ); }
template<> inline
Variable<unsigned long int>& ADIOS::GetVariable( const std::string name )
{ return m_ULInt[ GetVariableIndex<unsigned long int>(name) ]; }
{ return m_ULInt.at( GetVariableIndex<unsigned long int>(name) ); }
template<> inline
Variable<long long int>& ADIOS::GetVariable( const std::string name )
{ return m_LLInt[ GetVariableIndex<long long int>(name) ]; }
{ return m_LLInt.at( GetVariableIndex<long long int>(name) ); }
template<> inline
Variable<unsigned long long int>& ADIOS::GetVariable( const std::string name )
{ return m_ULLInt[ GetVariableIndex<unsigned long long int>(name) ]; }
{ return m_ULLInt.at( GetVariableIndex<unsigned long long int>(name) ); }
template<> inline
Variable<float>& ADIOS::GetVariable( const std::string name )
{ return m_Float[ GetVariableIndex<float>(name) ]; }
{ return m_Float.at( GetVariableIndex<float>(name) ); }
template<> inline
Variable<double>& ADIOS::GetVariable( const std::string name )
{ return m_Double[ GetVariableIndex<double>(name) ]; }
{ return m_Double.at( GetVariableIndex<double>(name) ); }
template<> inline
Variable<long double>& ADIOS::GetVariable( const std::string name )
{ return m_LDouble[ GetVariableIndex<long double>(name) ]; }
{ return m_LDouble.at( GetVariableIndex<long double>(name) ); }
template<> inline
Variable<std::complex<float>>& ADIOS::GetVariable( const std::string name )
{ return m_CFloat[ GetVariableIndex<std::complex<float>>(name) ]; }
{ return m_CFloat.at( GetVariableIndex<std::complex<float>>(name) ); }
template<> inline
Variable<std::complex<double>>& ADIOS::GetVariable( const std::string name )
{ return m_CDouble[ GetVariableIndex<std::complex<double>>(name) ]; }
{ return m_CDouble.at( GetVariableIndex<std::complex<double>>(name) ); }
template<> inline
Variable<std::complex<long double>>& ADIOS::GetVariable( const std::string name )
{ return m_CLDouble[ GetVariableIndex<std::complex<long double>>(name) ]; }
{ return m_CLDouble.at( GetVariableIndex<std::complex<long double>>(name) ); }
......
src/ADIOS.cpp
+ 3
− 3
View file @ 7d182edb
......@@ -36,7 +36,7 @@ ADIOS::ADIOS( const bool debugMode ):
InitMPI( );
}
#ifdef ADIOS_NOMPI
ADIOS::ADIOS( const std::string configFileName, const bool debugMode ):
m_ConfigFile{ configFileName },
m_DebugMode{ debugMode }
......@@ -44,7 +44,7 @@ ADIOS::ADIOS( const std::string configFileName, const bool debugMode ):
InitMPI( );
// InitXML( m_ConfigFile, m_MPIComm, m_DebugMode, m_Transforms );
}
#endif
ADIOS::ADIOS( const std::string xmlConfigFile, MPI_Comm mpiComm, const bool debugMode ):
......@@ -187,7 +187,7 @@ std::shared_ptr<Engine> ADIOS::Open( const std::string name, const std::string a
VariableCompound& ADIOS::GetVariableCompound( const std::string name )
{
return m_Compound[ GetVariableIndex<void>(name) ];
return m_Compound.at( GetVariableIndex<void>(name) );
}
......
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