diff --git a/README.md b/README.md
index aa096b1f69069241721dfae3419f8eca72a7943e..adf4da6d499f5f164830a9bdaa5ab4ec51526f7b 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,15 @@
# ADIOSPP
-Next generation ADIOS in C++ for exascale computations
-Read ./doc/CodingGuidelines first if you are a developer
-
-Create ./lib and ./bin libraries before compiling
-make -> build ./lib/libadios.a with truly MPI code (from mpi.h)
-make mpi -> build ./lib/libadios.a with truly MPI code (from mpi.h)
-make nompi -> build ./lib/libadios_nompi.a with serial (dummy MPI) code only calling ./public/mpiduumy.h
-
-
+Next generation ADIOS in C++11/14 for exascale computations.
+Read ./doc/CodingGuidelines first if you are a developer.
+Doxygen documentation can be generated running doxygen under ./doc, a ./doc/html directory will be created
+
+Requirements:
+1) C++11 compiler (e.g. gnu gcc 4.8.x and above) in PATH, default is g++
+2) MPI compiler (e.g. openmpi, mpich2 ) in PATH, default is mpic++
+
+make -> build ./lib/libadios.a and ./lib/libadios_nompi.a
+make mpi -> build ./lib/libadios.a with truly MPI code (from mpi.h) using mpic++
+make nompi -> build ./lib/libadios_nompi.a with serial (dummy MPI) code only calling mpiduumy.h using g++ (C++11)
+
+For examples, start with examples/hello/writer/helloWriter_OOP.cpp, build as above after ADIOS library is built
\ No newline at end of file
diff --git a/examples/hello/dataman/Makefile b/examples/hello/dataman/Makefile
index 88896bd67f4553c5e1e5210179485ba1765fb072..16893cb71bd92822c1036dd0603502f8ef9e4d7a 100644
--- a/examples/hello/dataman/Makefile
+++ b/examples/hello/dataman/Makefile
@@ -7,9 +7,8 @@ BASE_NAME=helloDataMan_OOP
TOOL_DIR=/usr/bin
-CC=$(TOOL_DIR)/g++ # Compiling with mpicc for now
-MPICC=$(TOOL_DIR)/mpic++
-AR=$(TOOL_DIR)/ar
+CC=g++ # Compiling with mpicc for now
+MPICC=mpic++
#ADIOS LOCATION
ADIOS_DIR=../../..
diff --git a/examples/hello/dataman/helloDataMan_OOP.cpp b/examples/hello/dataman/helloDataMan_OOP.cpp
index 2be3296e767cd15b244f84a65c3b6275a9caea63..da29cf6c6d81cdbd26f176a0781b6ed07f0d231a 100644
--- a/examples/hello/dataman/helloDataMan_OOP.cpp
+++ b/examples/hello/dataman/helloDataMan_OOP.cpp
@@ -27,30 +27,29 @@ int main( int argc, char* argv [] )
int rank;
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
const bool adiosDebug = true;
+ adios::ADIOS adios( MPI_COMM_WORLD, adiosDebug );
//Application variable
- std::vector<double> myInts = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
- int myIntsSize = static_cast<int>( myInts.size() );
+ std::vector<double> myNumbers = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ int myNX = static_cast<int>( myNumbers.size() );
try
{
//Define group and variables
- adios::Group group( adiosDebug );
- group.DefineVariable( "myIntsSize", "int" ); //define size as scalar
- group.DefineVariable( "myInts", "double", "myIntsSize" ); //define variable with associate size
-
- //Define method
- adios::Method method( "DataMan", adiosDebug );
- method.AddCapsule( "Heap" );
- method.AddTransport( "POSIX", "have_metadata_file=0" ); //option to save to file
- method.AddTransport( "TCP_IP", "fname=myfile.tcp" ); //here you can add as many options as you want in the format "parameter=value"
-
- //Create engine and Write
- adios::engine::DataMan dataMan( "myMessage", "w", MPI_COMM_WORLD, method, adiosDebug );
- dataMan.SetDefaultGroup( group );
- dataMan.Write( "myIntsSize", &myIntsSize ); //issue hello
- dataMan.Write( "myInts", &myInts.front() ); //issue hello
- dataMan.Close( );
+ adios::Group& wanGroup = adios.DeclareGroup( "WAN_Group" );
+ adios::Var ioNX = wanGroup.DefineVariable<int>( "myNX" );
+ adios::Dims ioDim1D = wanGroup.SetDimensions( {ioNX} ); //can be extended to many dimensions {ioNx, ioNy}
+ adios::Var ioNumbers = wanGroup.DefineVariable<double>( "myNumbers", ioDim1D );
+
+ adios::Method& wanMethod = adios.DeclareMethod( "WAN_Method", "DataMan" ); //name and type
+ wanMethod.AddTransport( "Mdtm", "localIP=128.0.0.0.1", "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );//add as many as you want
+ //wanMethod.AddTransport( "POSIX", "have_metadata_file=true" );
+ wanMethod.SetDefaultGroup( wanGroup );
+
+ auto dataManWriter = adios.Open( "hello_dataman", "w", wanMethod ); //here pass the method to your engine
+ dataManWriter->Write<int>( ioDim1D, &myNX ); //a template Write is good to have
+ dataManWriter->Write<double>( ioNumbers, myNumbers.data() );
+ dataManWriter->Close( );
}
catch( std::invalid_argument& e )
{
diff --git a/include/core/Engine.h b/include/core/Engine.h
index 2094f6882f6265a656bc8cff5233065af6307a15..65e41b5de2964cde22ecf3b513abce7120bb70bd 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -135,7 +135,7 @@ public:
protected:
- std::vector< std::shared_ptr<Capsule> > m_Capsules; ///< managed Capsules
+ //std::vector< std::shared_ptr<Capsule> > m_Capsules; ///< managed Capsules might not be needed by certain engines
std::vector< std::shared_ptr<Transport> > m_Transports; ///< transports managed
const bool m_DebugMode = false; ///< true: additional checks, false: by-pass checks
unsigned int m_Cores = 1;
@@ -143,9 +143,9 @@ protected:
std::vector< std::pair<Group*, std::string> > m_WrittenVariables;
- virtual void Init( ) = 0; ///< Initialize m_Capsules and m_Transports, called from constructor
- virtual void InitCapsules( ) = 0; ///< Initialize transports from Method, called from Init in constructor.
- virtual void InitTransports( ) = 0; ///< Initialize transports from Method, called from Init in constructor.
+ virtual void Init( ); ///< Initialize m_Capsules and m_Transports, called from constructor
+ virtual void InitCapsules( ); ///< Initialize transports from Method, called from Init in constructor.
+ virtual void InitTransports( ); ///< Initialize transports from Method, called from Init in constructor.
/**
* Performs preliminary checks before writing a variable. Throws an exception if checks fail.
diff --git a/include/engine/dataman/DataMan.h b/include/engine/dataman/DataMan.h
index 69fa69ec23b33f0d8b7b886a99dfbfb92305dd9e..6ba92d7f0ad9a3971e174cb55ca0aebe929c6a6c 100644
--- a/include/engine/dataman/DataMan.h
+++ b/include/engine/dataman/DataMan.h
@@ -10,6 +10,8 @@
#include "core/Engine.h"
+#include "capsule/Heap.h"
+#include "format/BP1Writer.h"
namespace adios
@@ -66,10 +68,20 @@ public:
private:
+ Heap m_Buffer; ///< heap capsule, contains data and metadata buffers
+ format::BP1Writer m_BP1Writer; ///< format object will provide the required BP functionality to be applied on m_Buffer and m_Transports
+
void Init( ); ///< calls InitCapsules and InitTransports based on Method, called from constructor
- void InitCapsules( ); ///< from Method
void InitTransports( ); ///< from Transports
+ /**
+ * From transport Mdtm in m_Method
+ * @param parameter must be an accepted parameter
+ * @param mdtmParameters
+ * @return value either returns user-defined from "parameter=value" or a default
+ */
+ std::string GetMdtmParameter( const std::string parameter, const std::map<std::string,std::string>& mdtmParameters );
+
};
diff --git a/include/engine/dataman/DataManTemplates.h b/include/engine/dataman/DataManTemplates.h
index f6a6140533c5c19f44a5381ffd41b6c59df36be7..2051dd5dfdc2fb5a785fac76bee52903e2ed193e 100644
--- a/include/engine/dataman/DataManTemplates.h
+++ b/include/engine/dataman/DataManTemplates.h
@@ -14,19 +14,35 @@
#include "core/Group.h"
#include "core/Variable.h"
-#include "core/Capsule.h"
+#include "capsule/Heap.h"
#include "core/Transport.h"
+#include "format/BP1Writer.h"
namespace adios
{
+/**
+ *
+ * @param group variable owner
+ * @param variableName string type
+ * @param variable
+ * @param buffer heap buffer to writer variables to for disk I/O
+ * @param transports
+ * @param bp1Writer
+ */
template<class T>
-void DataManWriteVariable( Group& group, const std::string variableName, Variable<T>& variable, std::vector<std::shared_ptr<Capsule> >& capsules,
- std::vector<std::shared_ptr<Transport> >& transports )
+void DataManWriteVariable( const Group& group, const Var variableName, Variable<T>& variable,
+ Heap& buffer, std::vector< std::shared_ptr<Transport> >& transports,
+ format::BP1Writer& bp1Writer )
+
{
- //here write your magic, this template replaces MACRO
- std::cout << "Hello from DataMan Write variable " << variableName << "\n";
+ //here write your magic, this template replaces C MACROS
+ std::cout << "Hello from DataMan, writing variable " << variableName << " of typeid(T).name() = " << typeid(T).name() << "\n";
+ if( variable.IsDimension )
+ {
+ std::cout << "Which is a dimension variable\n";
+ }
}
diff --git a/include/engine/writer/Writer.h b/include/engine/writer/Writer.h
index 676faa488cedf7556a0033403f7886e5eb3b1720..7e455e563d36c73508fdde136648c0d267d0075b 100644
--- a/include/engine/writer/Writer.h
+++ b/include/engine/writer/Writer.h
@@ -10,6 +10,7 @@
#include "core/Engine.h"
#include "format/BP1Writer.h"
+#include "capsule/Heap.h"
namespace adios
@@ -66,10 +67,10 @@ public:
private:
- format::BP1Writer m_BP1Writer; ///< format object will provide the required BP functionality to be applied on m_Capsules and m_Transports
+ Heap m_Buffer; ///< heap capsule
+ format::BP1Writer m_BP1Writer; ///< format object will provide the required BP functionality to be applied on m_Buffer and m_Transports
void Init( );
- void InitCapsules( );
void InitTransports( );
};
diff --git a/include/engine/writer/WriterTemplates.h b/include/engine/writer/WriterTemplates.h
index 37f2a4ea125d8388846178c8a43c28e3f4fce726..d21dd82b1580fbd7012e10599f0c32af94507802 100644
--- a/include/engine/writer/WriterTemplates.h
+++ b/include/engine/writer/WriterTemplates.h
@@ -34,7 +34,7 @@ namespace adios
*/
template <class T>
void WriterWriteVariable( const Group& group, const std::string variableName, const Variable<T>& variable,
- Capsule& buffers, std::vector< std::shared_ptr<Transport> >& transports,
+ Heap& buffer, std::vector< std::shared_ptr<Transport> >& transports,
format::BP1Writer& bp1Writer )
{
diff --git a/include/format/BP1Writer.h b/include/format/BP1Writer.h
index 73a92cbfeef5a0f4a5f9e2a35dc5b099c53ef304..dbb0070463ad3af7c7d40d64b19bf24f3ed6ad1c 100644
--- a/include/format/BP1Writer.h
+++ b/include/format/BP1Writer.h
@@ -11,7 +11,7 @@
#include <vector>
#include <cstdint>
-#include <algorithm> //std::count, std::copy
+#include <algorithm> //std::count, std::copy, std::for_each
#include <cstring> //std::memcpy
#include "core/Variable.h"
@@ -104,52 +104,6 @@ public:
};
- /**
- * Returns data type index from enum Datatypes
- * @param variable input variable
- * @return data type
- */
- template< class T >
- std::int8_t GetDataType( const Variable<T>& variable ) noexcept
- {
- std::int8_t dataType = -1;
- if( std::is_same<T,char>::value )
- dataType = type_byte;
-
- else if( std::is_same<T,short>::value )
- dataType = type_short;
-
- else if( std::is_same<T,int>::value )
- dataType = type_integer;
-
- else if( std::is_same<T,long int>::value )
- dataType = type_long;
-
- else if( std::is_same<T,unsigned char>::value )
- dataType = type_unsigned_byte;
-
- else if( std::is_same<T,unsigned short>::value )
- dataType = type_unsigned_short;
-
- else if( std::is_same<T,unsigned int>::value )
- dataType = type_unsigned_integer;
-
- else if( std::is_same<T,unsigned long int>::value )
- dataType = type_unsigned_long;
-
- else if( std::is_same<T,float>::value )
- dataType = type_real;
-
- else if( std::is_same<T,double>::value )
- dataType = type_double;
-
- else if( std::is_same<T,long double>::value )
- dataType = type_long_double;
- //need to implement complex and string
- return dataType;
- }
-
-
/**
* Returns the estimated variable index size
* @param group
@@ -208,71 +162,117 @@ public:
* @param offset
*/
template< class T >
- void WriteToBuffers( std::vector<char*>& buffers, const T* source, std::size_t size, std::size_t& offset ) noexcept
+ void MemcpyToBuffers( std::vector<char*>& buffers, std::vector<std::size_t>& positions, const T* source, std::size_t size ) noexcept
+ {
+ const unsigned int length = buffers.size( );
+
+ for( unsigned int i = 0; i < length; ++i )
+ {
+ std::memcpy( &buffers[positions[i]], source, size );
+ positions[i] += size;
+ }
+ }
+
+ template< class T >
+ void MemcpyToBuffers( std::vector<char*>& buffers, std::vector<std::size_t>& positions,
+ const std::vector<T>& source, std::size_t size ) noexcept
{
- for( auto& buffer : buffers )
+ const unsigned int length = buffers.size( );
+
+ for( unsigned int i = 0; i < length; ++i )
{
- std::memcpy( &buffer[offset], source, size );
+ std::memcpy( &buffers[positions[i]], &source[i], size );
+ positions[i] += size;
}
- offset += size;
}
+
+
template< class T, class U >
- void CopyToBuffers( std::vector<char*>& buffers, const T* source, U size, std::size_t& offset ) noexcept
+ void CopyToBuffers( std::vector<char*>& buffers, std::vector<std::size_t>& positions, const T* source, U size ) noexcept
{
- for( auto& buffer : buffers )
+ const unsigned int length = buffers.size( );
+
+ for( unsigned int i = 0; i < length; ++i )
{
- std::copy( source, source+size, &buffer[offset] );
+ std::copy( source, source+size, &buffers[ positions[i] ] );
+ positions[i] += size;
+ }
+ }
+
+
+ template< class T, class U >
+ void CopyToBuffers( std::vector<char*>& buffers, std::vector<std::size_t>& positions, const std::vector<T>& source, U size ) noexcept
+ {
+ const unsigned int length = buffers.size( );
+
+ for( unsigned int i = 0; i < length; ++i )
+ {
+ std::copy( &source[i], &source[i]+size, &buffers[ positions[i] ] );
+ positions[i] += size;
}
- offset += size;
}
/**
- * Writes a variable to BP format in data and metadata (index) buffers
* @param group variable owner
* @param variableName name of variable to be written
* @param variable object carrying variable information
* @param dataBuffers buffers to which variable metadata and payload (values) will be written. Metadata is added in case of system corruption to allow regeneration.
- * @param dataPosition initial data position
+ * @param dataPosition initial data relative position
+ * @param dataAbsolutePosition data absolute position will be updated with dataPosition, needed for variable offset and variable payload offset
* @param metadataBuffers buffers to which only variable metadata will be written
- * @param metadataPosition
- * @param memberID
- * @return number of bytes written, needed for variable entry length
+ * @param metadataPosition position in metadataBuffer
*/
template< class T >
- void WriteVariable( const Group& group, const Var variableName,
- const Variable<T>& variable,
- std::vector<char*>& dataBuffers, const std::size_t dataPosition,
- std::vector<char*>& metadataBuffers, const std::size_t metadataPosition ) noexcept
+ void WriteVariable( const Group& group, const Var variableName, const Variable<T>& variable,
+ std::vector<char*>& dataBuffers,
+ std::vector<std::size_t>& dataPositions,
+ std::vector<std::size_t>& dataAbsolutePositions,
+ std::vector<char*>& metadataBuffers,
+ std::vector<std::size_t>& metadataPositions ) noexcept
{
- std::size_t metadataOffset = metadataPosition + 4; //length of var, will come at the end from this offset
- std::size_t dataOffset = dataPosition + 8; //length of var, will come at the end from this offset
+ auto lf_MovePositions = []( const int bytes, std::vector<std::size_t>& positions )
+ {
+ for( auto& position : positions ) // value or reference?
+ position += bytes;
+ };
+
+ const std::vector<std::size_t> metadataLengthPositions( metadataPositions );
+ const std::vector<std::size_t> dataLengthPositions( dataPositions );
+
+ lf_MovePositions( 4, metadataPositions ); //length of var, will come at the end from this offset
+ lf_MovePositions( 8, dataPositions ); //length of var, will come at the end from this offset
//memberID
- WriteToBuffers( metadataBuffers, &m_VariablesCount, 4, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &m_VariablesCount, 4 );
//group, only in metadata
const std::uint16_t lengthGroupName = group.m_Name.length();
- WriteToBuffers( metadataBuffers, &lengthGroupName, 2, metadataOffset ); //2 bytes
- WriteToBuffers( metadataBuffers, group.m_Name.c_str(), lengthGroupName, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &lengthGroupName, 2 ); //2 bytes
+ MemcpyToBuffers( metadataBuffers, metadataPositions, group.m_Name.c_str(), lengthGroupName );
+
//variable name to metadata and data
const std::uint16_t lengthVariableName = variableName.length();
- WriteToBuffers( metadataBuffers, &lengthVariableName, 2, metadataOffset );
- WriteToBuffers( metadataBuffers, variableName.c_str(), lengthVariableName, metadataOffset );
- WriteToBuffers( dataBuffers, &lengthVariableName, 2, dataOffset );
- WriteToBuffers( dataBuffers, variableName.c_str(), lengthVariableName, dataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &lengthVariableName, 2 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, variableName.c_str(), lengthVariableName );
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthVariableName, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, variableName.c_str(), lengthVariableName );
+
//skip path (jump 2 bytes, already set to zero)
- metadataOffset += 2;
- dataOffset += 2;
+ lf_MovePositions( 2, metadataPositions ); //length of var, will come at the end from this offset
+ lf_MovePositions( 2, dataPositions ); //length of var, will come at the end from this offset
+
//dataType
- const std::uint8_t dataType = GetDataType( variable );
- WriteToBuffers( metadataBuffers, &dataType, 1, metadataOffset );
- WriteToBuffers( dataBuffers, &dataType, 1, dataOffset );
+ const std::uint8_t dataType = GetDataType<T>();
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &dataType, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dataType, 1 );
//Characteristics Sets in Metadata and Data
- //const std::size_t metadataCharacteristicsSetsCountPosition = metadataOffset; //very important piece
- std::size_t dataCharacteristicsCountPosition = dataOffset;
+ //const std::vector<std::size_t> metadataCharacteristicsSetsCountPosition( metadataPositions ); //very important piece
+ std::vector<std::size_t> dataCharacteristicsCountPositions( dataPositions ); //very important piece
+
const std::uint64_t sets = 1; //write one for now
- WriteToBuffers( metadataBuffers, &sets, 8, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &sets, 8 );
+ std::vector<std::size_t> metadataCharacteristicsCountPositions( metadataPositions ); //very important, can't be const as it is updated by MemcpyToBuffer
std::uint8_t characteristicsCounter = 0; //used for characteristics count, characteristics length will be calculated at the end
@@ -282,94 +282,92 @@ public:
//write to metadata characteristic
//characteristic: dimension
std::uint8_t characteristicID = characteristic_dimensions;
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 );
const std::uint8_t dimensions = localDimensions.size();
- WriteToBuffers( metadataBuffers, &dimensions, 1, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &dimensions, 1 );
const std::uint16_t dimensionsLength = dimensions * 24; //24 is from 8 bytes for each: local dimension, global dimension, global offset
- WriteToBuffers( metadataBuffers, &dimensionsLength, 2, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &dimensionsLength, 2 );
//write in data if it's a dimension variable (scalar) y or n
const char dimensionYorN = ( variable.IsDimension ) ? 'y' : 'n';
- WriteToBuffers( dataBuffers, &dimensionYorN, 1, dataOffset );
- WriteToBuffers( dataBuffers, &dimensions, 1, dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensionYorN, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensions, 1 );
const std::uint16_t dimensionsLengthInData = dimensions * 27; //27 is from 9 bytes for each: var y/n + local, var y/n + global dimension, var y/n + global offset
- WriteToBuffers( dataBuffers, &dimensionsLengthInData, 2, dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensionsLengthInData, 2 );
if( variable.GlobalBoundsIndex == -1 ) //local variable
{
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
//metadata characteristics
- WriteToBuffers( metadataBuffers, &localDimensions[d], 8, metadataOffset );
- metadataOffset += 16; //skipping global dimension(8), global offset (8)
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &localDimensions[d], 8 );
+ lf_MovePositions( 16, metadataPositions ); //skipping global dimension(8), global offset (8)
}
const char no = 'n'; //dimension format unsigned int value (not using memberID for now)
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
//data dimensions
- WriteToBuffers( dataBuffers, &no, 1, dataOffset );
- WriteToBuffers( dataBuffers, &localDimensions[d], 8, dataOffset );
- dataOffset += 18; //skipping var no + global dimension(8), var no + global offset (8)
+ MemcpyToBuffers( dataBuffers, dataPositions, &no, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &localDimensions[d], 8 );
+ lf_MovePositions( 18, dataPositions ); //skipping var no + global dimension(8), var no + global offset (8)
}
//dimensions in data characteristic entry
- dataCharacteristicsCountPosition = dataOffset;
- dataOffset += 5; //skip characteristics count(1) + length (4)
- WriteToBuffers( dataBuffers, &characteristicID, 1, dataOffset );
+ dataCharacteristicsCountPositions = dataPositions; //very important
- std::int16_t lengthOfDimensionsCharacteristic = 3 + 24 * dimensions; // 3 = dimension(1) + length(2) ; 24 = 3 local, global, global offset x 8 bytes/each
- WriteToBuffers( dataBuffers, &lengthOfDimensionsCharacteristic, 2, dataOffset );
+ lf_MovePositions( 5, dataPositions ); //skip characteristics count(1) + length (4)
+ MemcpyToBuffers( dataBuffers, dataPositions, &characteristicID, 1 );
- WriteToBuffers( dataBuffers, &dimensions, 1, dataOffset );
- WriteToBuffers( dataBuffers, &dimensionsLength, 2, dataOffset );
+ const std::int16_t lengthOfDimensionsCharacteristic = 3 + 24 * dimensions; // 3 = dimension(1) + length(2) ; 24 = 3 local, global, global offset x 8 bytes/each
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthOfDimensionsCharacteristic, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensions, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensionsLength, 2 );
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
- //data characteristics
- WriteToBuffers( dataBuffers, &localDimensions[d], 8, dataOffset );
- metadataOffset += 16; //skipping global dimension(8), global offset (8)
+ MemcpyToBuffers( dataBuffers, dataPositions, &localDimensions[d], 8 );
+ lf_MovePositions( 16, dataPositions );
}
}
else //global variable
{
- std::vector<unsigned long long int> globalDimensions = group.GetDimensions( group.m_GlobalBounds[variable.GlobalBoundsIndex].first );
- std::vector<unsigned long long int> globalOffsets = group.GetDimensions( group.m_GlobalBounds[variable.GlobalBoundsIndex].second );
+ const std::vector<unsigned long long int> globalDimensions = group.GetDimensions( group.m_GlobalBounds[variable.GlobalBoundsIndex].first );
+ const std::vector<unsigned long long int> globalOffsets = group.GetDimensions( group.m_GlobalBounds[variable.GlobalBoundsIndex].second );
//metadata, writing in characteristics
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
- WriteToBuffers( metadataBuffers, &localDimensions[d], 8, metadataOffset );
- WriteToBuffers( metadataBuffers, &globalDimensions[d], 8, metadataOffset );
- WriteToBuffers( metadataBuffers, &globalOffsets[d], 8, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &localDimensions[d], 8 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &globalDimensions[d], 8 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &globalOffsets[d], 8 );
}
//data dimensions entry
+ const char no = 'n'; //dimension format unsigned int value
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
- const char no = 'n'; //dimension format unsigned int value
- WriteToBuffers( dataBuffers, &no, 1, dataOffset );
- WriteToBuffers( dataBuffers, &localDimensions[d], 8, dataOffset );
- WriteToBuffers( dataBuffers, &no, 1, dataOffset );
- WriteToBuffers( dataBuffers, &localDimensions[d], 8, dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &no, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &localDimensions[d], 8 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &no, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &localDimensions[d], 8 );
}
- //dimensions in data characteristic entry (might not be required)
- dataCharacteristicsCountPosition = dataOffset;
- dataOffset += 5; //skip characteristics count(1) + length (4)
- WriteToBuffers( dataBuffers, &characteristicID, 1, dataOffset ); //id
-
- std::int16_t lengthOfDimensionsCharacteristic = 3 + 24 * dimensions; // 3 = dimension(1) + length(2) ; 24 = 3 local, global, global offset x 8 bytes/each
- WriteToBuffers( dataBuffers, &lengthOfDimensionsCharacteristic, 2, dataOffset );
+ //dimensions in data characteristic entry
+ dataCharacteristicsCountPositions = dataPositions;
+ lf_MovePositions( 5, dataPositions ); //skip characteristics count(1) + length (4)
+ MemcpyToBuffers( dataBuffers, dataPositions, &characteristicID, 1 ); //id
- WriteToBuffers( dataBuffers, &dimensions, 1, dataOffset );
- WriteToBuffers( dataBuffers, &dimensionsLength, 2, dataOffset );
+ const std::int16_t lengthOfDimensionsCharacteristic = 3 + 24 * dimensions; // 3 = dimension(1) + length(2) ; 24 = 3 local, global, global offset x 8 bytes/each
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthOfDimensionsCharacteristic, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensions, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &dimensionsLength, 2 );
for( unsigned int d = 0; d < (unsigned int)localDimensions.size(); ++d )
{
- WriteToBuffers( dataBuffers, &localDimensions[d], 8, dataOffset );
- WriteToBuffers( dataBuffers, &globalDimensions[d], 8, dataOffset );
- WriteToBuffers( dataBuffers, &globalOffsets[d], 8, dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &localDimensions[d], 8 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &globalDimensions[d], 8 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &globalOffsets[d], 8 );
}
}
++characteristicsCounter;
@@ -379,18 +377,18 @@ public:
if( variable.DimensionsCSV == "1" ) //scalar //just doing string scalars for now (by name), needs to be modified when user passes value
{
characteristicID = characteristic_value;
- std::int16_t lenghtOfName = variableName.length();
+ const std::int16_t lenghtOfName = variableName.length();
//metadata
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset );
- WriteToBuffers( metadataBuffers, &lenghtOfName, 2, metadataOffset );
- WriteToBuffers( metadataBuffers, variableName.c_str(), lenghtOfName, metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &lenghtOfName, 2 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, variableName.c_str(), lenghtOfName );
//data
- WriteToBuffers( dataBuffers, &characteristicID, 1, dataOffset );
- std::int16_t lengthOfCharacteristic = 2 + lenghtOfName;
- WriteToBuffers( dataBuffers, &lengthOfCharacteristic, 2, dataOffset );
- WriteToBuffers( dataBuffers, &lenghtOfName, 2, dataOffset );
- WriteToBuffers( dataBuffers, variableName.c_str(), lenghtOfName, dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &characteristicID, 1 );
+ const std::int16_t lengthOfCharacteristic = 2 + lenghtOfName;
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthOfCharacteristic, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &lenghtOfName, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, variableName.c_str(), lenghtOfName );
}
else // Stat -> Min, Max for arrays,
{
@@ -398,10 +396,9 @@ public:
{
//Get min and max
const std::size_t valuesSize = GetTotalSize( localDimensions );
- //here we can make decisions for threads based on valuesSize
T min, max;
- if( valuesSize >= 10000000 ) //ten million? this needs actual results
+ if( valuesSize >= 10000000 ) //ten million? this needs actual results //here we can make decisions for threads based on valuesSize
GetMinMax( variable.Values, valuesSize, min, max, m_Cores ); //here we can add cores from constructor
else
GetMinMax( variable.Values, valuesSize, min, max );
@@ -412,55 +409,98 @@ public:
const std::int8_t statisticMaxID = statistic_max;
//write min and max to metadata
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset ); //min
- WriteToBuffers( metadataBuffers, &statisticMinID, 1, metadataOffset );
- WriteToBuffers( metadataBuffers, &min, sizeof(T), metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 ); //min
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &statisticMinID, 1 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &min, sizeof(T) );
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset ); //max
- WriteToBuffers( metadataBuffers, &statisticMaxID, 1, metadataOffset );
- WriteToBuffers( metadataBuffers, &max, sizeof(T), metadataOffset );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 ); //max
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &statisticMaxID, 1 );
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &max, sizeof(T) );
//write min and max to data
- WriteToBuffers( dataBuffers, &characteristicID, 1, dataOffset ); //min
+ MemcpyToBuffers( dataBuffers, dataPositions, &characteristicID, 1 ); //min
const std::int16_t lengthCharacteristic = 1 + sizeof( T );
- WriteToBuffers( dataBuffers, &lengthCharacteristic, 2, dataOffset );
- WriteToBuffers( dataBuffers, &statisticMinID, 1, dataOffset );
- WriteToBuffers( dataBuffers, &min, sizeof(T), dataOffset );
-
- WriteToBuffers( dataBuffers, &characteristicID, 1, dataOffset ); //max
- WriteToBuffers( dataBuffers, &lengthCharacteristic, 2, dataOffset );
- WriteToBuffers( dataBuffers, &statisticMaxID, 1, dataOffset );
- WriteToBuffers( dataBuffers, &max, sizeof(T), dataOffset );
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthCharacteristic, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &statisticMinID, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &min, sizeof(T) );
+
+ MemcpyToBuffers( dataBuffers, dataPositions, &characteristicID, 1 ); //max
+ MemcpyToBuffers( dataBuffers, dataPositions, &lengthCharacteristic, 2 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &statisticMaxID, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &max, sizeof(T) );
}
}
++characteristicsCounter;
- //here write characteristics count and length to data
- std::uint32_t characteristicsLengthInData = dataOffset - dataCharacteristicsCountPosition;
- WriteToBuffers( dataBuffers, &characteristicsCounter, 1, dataCharacteristicsCountPosition );
- WriteToBuffers( dataBuffers, &characteristicsLengthInData, 4, dataCharacteristicsCountPosition );
- dataCharacteristicsCountPosition -= 5;
- //Offsets should be last and only written to metadata
+ //Characteristics count and length in Data
+ std::vector<std::uint32_t> dataCharacteristicsLengths( dataPositions );
+ std::transform( dataCharacteristicsLengths.begin( ), dataCharacteristicsLengths.end( ),
+ dataCharacteristicsCountPositions.begin(), dataCharacteristicsCountPositions.end(),
+ std::minus<std::uint32_t>() );
+
+ MemcpyToBuffers( dataBuffers, dataCharacteristicsCountPositions, &characteristicsCounter, 1 );
+ MemcpyToBuffers( dataBuffers, dataCharacteristicsCountPositions, dataCharacteristicsLengths, 4 ); //vector to vector
+ lf_MovePositions( -5, dataCharacteristicsCountPositions ); //back to original position
+
+ //Offsets should be last and only written to metadata, they come from absolute positions
characteristicID = characteristic_offset;
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset ); //variable offset id
- WriteToBuffers( metadataBuffers, &dataPosition, 8, metadataOffset ); //variable offset
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 ); //variable offset id
+ MemcpyToBuffers( metadataBuffers, metadataPositions, dataAbsolutePositions, 8 ); //variable offset
++characteristicsCounter;
+ //update absolute positions with dataPositions, this is the payload offset
+ std::transform( dataAbsolutePositions.begin(), dataAbsolutePositions.end(),
+ dataPositions.begin(), dataPositions.end(), std::plus<std::size_t>() );
+
characteristicID = characteristic_payload_offset;
- WriteToBuffers( metadataBuffers, &characteristicID, 1, metadataOffset ); //variable payload offset id
- WriteToBuffers( metadataBuffers, &dataOffset, 8, metadataOffset ); //variable offset
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &characteristicID, 1 ); //variable payload offset id
+ MemcpyToBuffers( metadataBuffers, metadataPositions, dataAbsolutePositions, 8 ); //variable payload offset
++characteristicsCounter;
- //here write var entry length in metadata
+ //Characteristics count and length in Metadata
+ std::vector<std::uint32_t> metadataCharacteristicsLengths( metadataPositions );
+ std::transform( metadataCharacteristicsLengths.begin( ), metadataCharacteristicsLengths.end( ),
+ metadataCharacteristicsCountPositions.begin(), metadataCharacteristicsCountPositions.end(),
+ std::minus<std::uint32_t>() );
+ MemcpyToBuffers( metadataBuffers, metadataCharacteristicsCountPositions, &characteristicsCounter, 1 );
+ MemcpyToBuffers( metadataBuffers, metadataCharacteristicsCountPositions, metadataCharacteristicsLengths, 4 ); //vector to vector
+ lf_MovePositions( -5, metadataCharacteristicsCountPositions ); //back to original position
+
+ //here write payload
+
+
++m_VariablesCount;
} //end of function
+
+private:
+
+ /**
+ * Returns data type index from enum Datatypes
+ * @param variable input variable
+ * @return data type
+ */
+ template< class T > inline std::int8_t GetDataType( ) noexcept { return type_unknown; }
+
};
+//Moving template BP1Writer::GetDataType template specializations outside of the class
+template< > inline std::int8_t BP1Writer::GetDataType<char>( ) noexcept { return type_byte; }
+template< > inline std::int8_t BP1Writer::GetDataType<short>( ) noexcept{ return type_short; }
+template< > inline std::int8_t BP1Writer::GetDataType<int>( ) noexcept{ return type_integer; }
+template< > inline std::int8_t BP1Writer::GetDataType<long int>( ) noexcept{ return type_long; }
+
+template< > inline std::int8_t BP1Writer::GetDataType<unsigned char>( ) noexcept { return type_unsigned_byte; }
+template< > inline std::int8_t BP1Writer::GetDataType<unsigned short>( ) noexcept{ return type_unsigned_short; }
+template< > inline std::int8_t BP1Writer::GetDataType<unsigned int>( ) noexcept{ return type_unsigned_integer; }
+template< > inline std::int8_t BP1Writer::GetDataType<unsigned long int>( ) noexcept{ return type_unsigned_long; }
+template< > inline std::int8_t BP1Writer::GetDataType<float>( ) noexcept{ return type_real; }
+template< > inline std::int8_t BP1Writer::GetDataType<double>( ) noexcept{ return type_double; }
+template< > inline std::int8_t BP1Writer::GetDataType<long double>( ) noexcept{ return type_long_double; }
diff --git a/include/functions/adiosFunctions.h b/include/functions/adiosFunctions.h
index 17697adcf989a4e757c52fd14123bac3579ed5f0..8ee76b130ae5c728d72f7993d24687e1f095403c 100644
--- a/include/functions/adiosFunctions.h
+++ b/include/functions/adiosFunctions.h
@@ -142,6 +142,23 @@ void SetTransformsHelper( const std::vector<std::string>& transformNames, std::v
std::map<std::string, std::string> BuildParametersMap( const std::vector<std::string>& parameters, const bool debugMode );
+/**
+ * Single call that extract data buffers information from Capsule. That way virtual Capsule functions are called a few times
+ * @param capsules input
+ * @param dataBuffers from Capsule.GetData()
+ * @param positions
+ * @param absolutePositions
+ */
+//void GetDataBuffers( const std::vector<Capsule*>& capsules, std::vector<char*>& dataBuffers, std::vector<std::size_t>& positions,
+// std::vector<std::size_t>& absolutePositions );
+
+/**
+ * Converts comma-separated values to a vector of integers
+ * @param csv "1,2,3"
+ * @return vector<int> = { 1, 2, 3 }
+ */
+std::vector<int> CSVToVectorInt( const std::string csv );
+
} //end namespace
diff --git a/include/functions/adiosTemplates.h b/include/functions/adiosTemplates.h
index e8cf5c2f17e871a24b083accd52bcc526956d798..1e675933e3daf4d178e9f252968829971cbb618f 100644
--- a/include/functions/adiosTemplates.h
+++ b/include/functions/adiosTemplates.h
@@ -11,43 +11,23 @@
namespace adios
{
+/**
+ * Get the primitive type in a string from a template
+ * @return if T is a char, returns string = "char"
+ */
+template< class T> inline std::string GetType( ) noexcept { return ""; }
-template< class T> inline
-std::string GetType( ) noexcept
-{ return ""; }
-
-template<> inline
-std::string GetType<char>() noexcept { return "char"; }
-
-template<> inline
-std::string GetType<unsigned char>() noexcept { return "unsigned char"; }
-
-template<> inline
-std::string GetType<short>() noexcept { return "short"; }
-
-template<> inline
-std::string GetType<unsigned short>() noexcept { return "unsigned short"; }
-
-template<> inline
-std::string GetType<int>() noexcept { return "int"; }
-
-template<> inline
-std::string GetType<unsigned int>() noexcept { return "unsigned int"; }
-
-template<> inline
-std::string GetType<long int>() noexcept { return "long int"; }
-
-template<> inline
-std::string GetType<unsigned long int>() noexcept { return "unsigned long int"; }
-
-template<> inline
-std::string GetType<float>() noexcept { return "float"; }
-
-template<> inline
-std::string GetType<double>() noexcept { return "double"; }
-
-template<> inline
-std::string GetType<long double>() noexcept { return "long double"; }
+template<> inline std::string GetType<char>() noexcept { return "char"; }
+template<> inline std::string GetType<unsigned char>() noexcept { return "unsigned char"; }
+template<> inline std::string GetType<short>() noexcept { return "short"; }
+template<> inline std::string GetType<unsigned short>() noexcept { return "unsigned short"; }
+template<> inline std::string GetType<int>() noexcept { return "int"; }
+template<> inline std::string GetType<unsigned int>() noexcept { return "unsigned int"; }
+template<> inline std::string GetType<long int>() noexcept { return "long int"; }
+template<> inline std::string GetType<unsigned long int>() noexcept { return "unsigned long int"; }
+template<> inline std::string GetType<float>() noexcept { return "float"; }
+template<> inline std::string GetType<double>() noexcept { return "double"; }
+template<> inline std::string GetType<long double>() noexcept { return "long double"; }
/**
@@ -61,7 +41,7 @@ template<class T>
bool IsTypeAlias( const std::string type,
const std::map<std::string, std::set<std::string>>& aliases ) noexcept
{
- if( type == GetType<T>() ) //most of the time we will pass the same type
+ if( type == GetType<T>() ) //most of the time we will pass the same type, which is a key in aliases
return true;
bool isAlias = false;
diff --git a/src/engine/dataman/DataMan.cpp b/src/engine/dataman/DataMan.cpp
index 9c918fb7764cfe615fdaed1cbf149a0bb22c97cf..59ba6306ea0b3dcd50dd79dfd8391f20383b7256 100644
--- a/src/engine/dataman/DataMan.cpp
+++ b/src/engine/dataman/DataMan.cpp
@@ -11,6 +11,7 @@
#include "engine/dataman/DataMan.h"
#include "engine/dataman/DataManTemplates.h"
#include "core/Support.h"
+#include "functions/adiosFunctions.h" //CSVToVector
//supported capsules
#include "capsule/Heap.h"
@@ -19,6 +20,7 @@
#include "transport/POSIX.h"
#include "transport/FStream.h"
#include "transport/File.h"
+#include "transport/MdtmMan.h"
namespace adios
@@ -28,7 +30,8 @@ namespace engine
DataMan::DataMan( const std::string streamName, const std::string accessMode, const MPI_Comm mpiComm,
const Method& method, const bool debugMode, const unsigned int cores ):
- Engine( "DataMan", streamName, accessMode, mpiComm, method, debugMode, cores, " DataMan constructor (or call to ADIOS Open).\n" )
+ Engine( "DataMan", streamName, accessMode, mpiComm, method, debugMode, cores, " DataMan constructor (or call to ADIOS Open).\n" ),
+ m_Buffer{ Heap( accessMode, m_RankMPI, m_DebugMode, cores ) }
{
Init( );
}
@@ -50,7 +53,7 @@ void DataMan::Write( Group& group, const std::string variableName, const char* v
auto index = PreSetVariable( group, variableName, " from call to Write char*" );
Variable<char>& variable = group.m_Char[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -59,7 +62,7 @@ void DataMan::Write( Group& group, const std::string variableName, const unsigne
auto index = PreSetVariable( group, variableName, " from call to Write unsigned char*" );
Variable<unsigned char>& variable = group.m_UChar[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -68,7 +71,7 @@ void DataMan::Write( Group& group, const std::string variableName, const short*
auto index = PreSetVariable( group, variableName, " from call to Write short*" );
Variable<short>& variable = group.m_Short[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -77,7 +80,7 @@ void DataMan::Write( Group& group, const std::string variableName, const unsigne
auto index = PreSetVariable( group, variableName, " from call to Write unsigned short*" );
Variable<unsigned short>& variable = group.m_UShort[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -86,7 +89,7 @@ void DataMan::Write( Group& group, const std::string variableName, const int* va
auto index = PreSetVariable( group, variableName, " from call to Write int*" );
Variable<int>& variable = group.m_Int[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -95,7 +98,7 @@ void DataMan::Write( Group& group, const std::string variableName, const unsigne
auto index = PreSetVariable( group, variableName, " from call to Write unsigned int*" );
Variable<unsigned int>& variable = group.m_UInt[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -104,7 +107,7 @@ void DataMan::Write( Group& group, const std::string variableName, const long in
auto index = PreSetVariable( group, variableName, " from call to Write long int*" );
Variable<long int>& variable = group.m_LInt[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -113,7 +116,7 @@ void DataMan::Write( Group& group, const std::string variableName, const unsigne
auto index = PreSetVariable( group, variableName, " from call to Write unsigned long int*" );
Variable<unsigned long int>& variable = group.m_ULInt[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -122,7 +125,7 @@ void DataMan::Write( Group& group, const std::string variableName, const long lo
auto index = PreSetVariable( group, variableName, " from call to Write long long int*" );
Variable<long long int>& variable = group.m_LLInt[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -131,15 +134,16 @@ void DataMan::Write( Group& group, const std::string variableName, const unsigne
auto index = PreSetVariable( group, variableName, " from call to Write unsigned long long int*" );
Variable<unsigned long long int>& variable = group.m_ULLInt[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
+
void DataMan::Write( Group& group, const std::string variableName, const float* values )
{
auto index = PreSetVariable( group, variableName, " from call to Write float*" );
Variable<float>& variable = group.m_Float[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void DataMan::Write( Group& group, const std::string variableName, const double* values )
@@ -147,7 +151,7 @@ void DataMan::Write( Group& group, const std::string variableName, const double*
auto index = PreSetVariable( group, variableName, " from call to Write double*" );
Variable<double>& variable = group.m_Double[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -156,7 +160,7 @@ void DataMan::Write( Group& group, const std::string variableName, const long do
auto index = PreSetVariable( group, variableName, " from call to Write long double*" );
Variable<long double>& variable = group.m_LDouble[index]; //must be a reference
variable.Values = values;
- DataManWriteVariable( group, variableName, variable, m_Capsules, m_Transports );
+ DataManWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
//USING Preset Group
@@ -239,18 +243,11 @@ void DataMan::Write( const std::string variableName, const long double* values )
}
-void DataMan::InitCapsules( )
-{
- //Create single capsule of type heap
- m_Capsules.push_back( std::make_shared<Heap>( m_AccessMode, m_RankMPI, m_Cores ) );
-}
-
-
void DataMan::InitTransports( ) //maybe move this?
{
std::set< std::string > transportStreamNames; //used to check for name conflict between transports
- const unsigned int transportsSize = m_Method.m_TransportParameters.size();
+ //const unsigned int transportsSize = m_Method.m_TransportParameters.size();
for( const auto& parameters : m_Method.m_TransportParameters )
{
@@ -258,7 +255,6 @@ void DataMan::InitTransports( ) //maybe move this?
if( m_DebugMode == true )
CheckParameter( itTransport, parameters, "transport", ", in " + m_Name + m_EndMessage );
-
if( itTransport->second == "POSIX" )
{
m_Transports.push_back( std::make_shared<POSIX>( m_MPIComm, m_DebugMode ) );
@@ -271,9 +267,21 @@ void DataMan::InitTransports( ) //maybe move this?
{
m_Transports.push_back( std::make_shared<FStream>( m_MPIComm, m_DebugMode ) );
}
+ else if( itTransport->second == "Mdtm" || itTransport->second == "MdtmMan" )
+ {
+ const std::string localIP( GetMdtmParameter( "localIP", parameters ) ); //mandatory
+ const std::string remoteIP( GetMdtmParameter( "remoteIP", parameters ) ); //mandatory
+ const std::string prefix( GetMdtmParameter( "prefix", parameters ) );
+ const int numberOfPipes = std::stoi( GetMdtmParameter( "pipes", parameters ) );
+ const std::vector<int> tolerances = CSVToVectorInt( GetMdtmParameter( "tolerances", parameters ) );
+ const std::vector<int> priorities = CSVToVectorInt( GetMdtmParameter( "priorities", parameters ) );
+
+ m_Transports.push_back( std::make_shared<MdtmMan>( localIP, remoteIP, m_AccessMode, prefix, numberOfPipes,
+ tolerances, priorities, m_MPIComm, m_DebugMode ) );
+ }
else if( itTransport->second == "MPIFile" )
{
- //m_Transports.push_back( std::make_shared<MPIFile>( m_MPIComm, m_DebugMode ) ); not yet supported
+ //m_Transports.push_back( std::make_shared<MPIFile>( m_MPIComm, m_DebugMode ) ); //not yet supported
}
else
{
@@ -281,36 +289,46 @@ void DataMan::InitTransports( ) //maybe move this?
throw std::invalid_argument( "ERROR: transport + " + itTransport->second + " not supported, in " +
m_Name + m_EndMessage );
}
- //name
- if( transportsSize > 1 )
- {
- auto itName = parameters.find( "name" ); //first check name
+ }
+}
- if( m_DebugMode == true )
- CheckParameter( itName, parameters, "name", " in transport " + itTransport->second +
- ", in " + m_Name + m_EndMessage );
- m_Transports.back()->Open( itName->second, m_AccessMode );
- }
- else if( transportsSize == 1 )
- {
- auto itName = parameters.find( "name" );
+std::string DataMan::GetMdtmParameter( const std::string parameter, const std::map<std::string,std::string>& mdtmParameters )
+{
+ auto itParam = mdtmParameters.find( parameter );
+ if( itParam != mdtmParameters.end() ) //found
+ {
+ return itParam->second; //return value
+ }
+ // if not found
+ //mandatory ones
+ if( parameter == "localIP" || parameter == "remoteIP" )
+ {
+ if( m_DebugMode == true )
+ throw std::invalid_argument( "ERROR: " + parameter + " parameter not found in Method, in call to DataMan constructor\n" );
+ }
+ else if( parameter == "prefix" )
+ {
+ return "";
+ }
+ else if( parameter == "pipes" )
+ {
+ return "0"; // or 1?
+ }
+ else if( parameter == "tolerances" ) //so far empty string
+ {
- if( itName == parameters.end() ) //take streamName
- m_Transports.back()->Open( m_Name, m_AccessMode );
- else
- m_Transports.back()->Open( m_Name, m_AccessMode );
+ }
+ else if( parameter == "priority" )
+ {
- }
- else if( transportsSize == 0 )
- {
- if( m_DebugMode == true )
- throw std::invalid_argument( "ERROR: transport not defined for engine " + m_Name + m_EndMessage );
- }
}
+
+ return ""; //return empty string
}
+
} //end namespace engine
} //end namespace adios
diff --git a/src/engine/writer/Writer.cpp b/src/engine/writer/Writer.cpp
index 89f832d613ceae67eb5d5df0bda3f2f3ddd4ef75..9e5fc7c22e8ce822dcf70e02ad339ce6ae0d0558 100644
--- a/src/engine/writer/Writer.cpp
+++ b/src/engine/writer/Writer.cpp
@@ -27,7 +27,8 @@ namespace adios
Writer::Writer( const std::string streamName, const std::string accessMode, const MPI_Comm mpiComm,
const Method& method, const bool debugMode, const unsigned int cores ):
- Engine( "Writer", streamName, accessMode, mpiComm, method, debugMode, cores, " Writer constructor (or call to ADIOS Open).\n" )
+ Engine( "Writer", streamName, accessMode, mpiComm, method, debugMode, cores, " Writer constructor (or call to ADIOS Open).\n" ),
+ m_Buffer{ Heap( accessMode, m_RankMPI, m_DebugMode, cores ) }
{
Init( );
}
@@ -49,7 +50,7 @@ void Writer::Write( Group& group, const std::string variableName, const char* va
auto index = PreSetVariable( group, variableName, " from call to Write char*" );
Variable<char>& variable = group.m_Char[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const unsigned char* values )
@@ -57,7 +58,7 @@ void Writer::Write( Group& group, const std::string variableName, const unsigned
auto index = PreSetVariable( group, variableName, " from call to Write unsigned char*" );
Variable<unsigned char>& variable = group.m_UChar[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const short* values )
@@ -65,7 +66,7 @@ void Writer::Write( Group& group, const std::string variableName, const short* v
auto index = PreSetVariable( group, variableName, " from call to Write short*" );
Variable<short>& variable = group.m_Short[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const unsigned short* values )
@@ -73,7 +74,7 @@ void Writer::Write( Group& group, const std::string variableName, const unsigned
auto index = PreSetVariable( group, variableName, " from call to Write unsigned short*" );
Variable<unsigned short>& variable = group.m_UShort[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const int* values )
@@ -81,7 +82,7 @@ void Writer::Write( Group& group, const std::string variableName, const int* val
auto index = PreSetVariable( group, variableName, " from call to Write int*" );
Variable<int>& variable = group.m_Int[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const unsigned int* values )
@@ -89,7 +90,7 @@ void Writer::Write( Group& group, const std::string variableName, const unsigned
auto index = PreSetVariable( group, variableName, " from call to Write unsigned int*" );
Variable<unsigned int>& variable = group.m_UInt[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const long int* values )
@@ -97,7 +98,7 @@ void Writer::Write( Group& group, const std::string variableName, const long int
auto index = PreSetVariable( group, variableName, " from call to Write long int*" );
Variable<long int>& variable = group.m_LInt[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const unsigned long int* values )
@@ -105,7 +106,7 @@ void Writer::Write( Group& group, const std::string variableName, const unsigned
auto index = PreSetVariable( group, variableName, " from call to Write unsigned long int*" );
Variable<unsigned long int>& variable = group.m_ULInt[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const long long int* values )
@@ -113,7 +114,7 @@ void Writer::Write( Group& group, const std::string variableName, const long lon
auto index = PreSetVariable( group, variableName, " from call to Write long long int*" );
Variable<long long int>& variable = group.m_LLInt[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const unsigned long long int* values )
@@ -121,7 +122,7 @@ void Writer::Write( Group& group, const std::string variableName, const unsigned
auto index = PreSetVariable( group, variableName, " from call to Write unsigned long long int*" );
Variable<unsigned long long int>& variable = group.m_ULLInt[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
void Writer::Write( Group& group, const std::string variableName, const float* values )
@@ -129,7 +130,7 @@ void Writer::Write( Group& group, const std::string variableName, const float* v
auto index = PreSetVariable( group, variableName, " from call to Write float*" );
Variable<float>& variable = group.m_Float[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -138,7 +139,7 @@ void Writer::Write( Group& group, const std::string variableName, const double*
auto index = PreSetVariable( group, variableName, " from call to Write double*" );
Variable<double>& variable = group.m_Double[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -147,7 +148,7 @@ void Writer::Write( Group& group, const std::string variableName, const long dou
auto index = PreSetVariable( group, variableName, " from call to Write long double*" );
Variable<long double>& variable = group.m_LDouble[index]; //must be a reference
variable.Values = values;
- WriterWriteVariable( group, variableName, variable, *m_Capsules[0], m_Transports, m_BP1Writer );
+ WriterWriteVariable( group, variableName, variable, m_Buffer, m_Transports, m_BP1Writer );
}
@@ -242,12 +243,6 @@ void Writer::Write( const std::string variableName, const long double* values )
}
-void Writer::InitCapsules( )
-{
- m_Capsules.push_back( std::make_shared<Heap>( m_AccessMode, m_RankMPI, m_Cores ) );
-}
-
-
void Writer::InitTransports( )
{
//Let BPFormat handle this??
diff --git a/src/functions/adiosFunctions.cpp b/src/functions/adiosFunctions.cpp
index 94230cff119a970f3a9474957be5f675673ca542..426b9c2cf549c4758498fc3b347b7f2a7b16bcce 100644
--- a/src/functions/adiosFunctions.cpp
+++ b/src/functions/adiosFunctions.cpp
@@ -12,6 +12,7 @@
#include <iostream>
#include <thread> //std::thread
#include <cstring> //std::memcpy
+#include <algorithm> //std::count
#include <sys/types.h> //CreateDirectory
#include <sys/stat.h> //stat
@@ -510,6 +511,32 @@ std::map<std::string, std::string> BuildParametersMap( const std::vector<std::st
}
+std::vector<int> CSVToVectorInt( const std::string csv )
+{
+ std::vector<int> numbers;
+ if( csv.empty() )
+ return numbers;
+
+ if( csv.find(",") == csv.npos ) //check if no commas, one int
+ {
+ numbers.push_back( std::stoi( csv ) ); //might need to be checked
+ }
+ else
+ {
+ int count = std::count( csv.begin(), csv.end(), ',' );
+ numbers.reserve( count );
+
+ std::istringstream csvSS( csv );
+ std::string value;
+ while( std::getline( csvSS, value, ',' ) ) //need to test
+ {
+ numbers.push_back( std::stoi( csv ) );
+ }
+ }
+
+ return numbers;
+}
+