diff --git a/include/core/Engine.h b/include/core/Engine.h
index 5f053edeeb9f1254092c2fb548c5bb249c65f1d6..7c9b2b65f53b96f6b2192396553045833098e8b3 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -170,9 +170,10 @@ protected:
const std::string parameterName,
const std::string hint ) const;
-
void CheckDefaultGroup( ) const; ///< checks if default group m_Group is nullptr, throws exception if trying to use
+ bool TransportNamesUniqueness( ) const; ///< checks if transport names are unique among the same types (file I/O)
+
std::string GetName( const std::vector<std::string>& arguments ) const; //might move this to adiosFunctions
};
diff --git a/include/core/Support.h b/include/core/Support.h
index f472ce127ceca86872f29144e1f6d7426cd5c5a9..36f75e80b5e42b63876d749ee3a5fbe477bd56dc 100644
--- a/include/core/Support.h
+++ b/include/core/Support.h
@@ -28,6 +28,8 @@ struct Support
static const std::set<std::string> Transforms; ///< supported data transform methods
static const std::map<std::string, std::set<std::string> > Datatypes; ///< supported data types, key: host language, value: all supported types
static const std::map<std::string, std::set<std::string> > DatatypesAliases; ///< all supported int aliases, key: C++ type (e.g. int), value: aliases to type in key (e.g. int, integer)
+
+ static const std::set<std::string> FileTransports; ///< file I/O transports
};
diff --git a/include/format/BP1.h b/include/format/BP1.h
index ab6f371b2e78fec75fd956cf692a294edd9325c9..6b32c836e7c1b341a8daf141c993c087a2e80e8a 100644
--- a/include/format/BP1.h
+++ b/include/format/BP1.h
@@ -96,8 +96,6 @@ enum VariableStatistics
-
-
} //end namespace format
} //end namespace adios
diff --git a/include/format/BP1Writer.h b/include/format/BP1Writer.h
index f984c2748e1d2ca5b70519b9d3e19c8f69f1b17a..bf15ddd46f4144ed835b20d17a3085bb926fad1c 100644
--- a/include/format/BP1Writer.h
+++ b/include/format/BP1Writer.h
@@ -51,6 +51,15 @@ public:
~BP1Writer( );
+ std::size_t GetProcessIndexSize( const std::string name, const std::string timeStepName );
+
+ void WriteProcessGroupIndex( const bool isFortran, const std::string name, const unsigned int processID,
+ const std::string timeStepName, const unsigned int timeStep,
+ 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 );
+
/**
* Returns the estimated variable index size
* @param group
@@ -69,7 +78,7 @@ public:
indexSize += variableName.size();
// characteristics 3 and 4, check variable number of dimensions
- std::size_t dimensions = std::count( variable.DimensionsCSV.begin(), variable.DimensionsCSV.end(), ',' ) + 1; //number of commas in CSV + 1
+ const std::size_t dimensions = std::count( variable.DimensionsCSV.begin(), variable.DimensionsCSV.end(), ',' ) + 1; //number of commas in CSV + 1
indexSize += 28 * dimensions; //28 bytes per dimension
indexSize += 1; //id
@@ -129,7 +138,7 @@ public:
//memberID
MemcpyToBuffers( metadataBuffers, metadataPositions, &m_VariablesCount, 4 );
- //group, only in metadata
+ //group name, only in metadata
const std::uint16_t lengthGroupName = group.m_Name.length();
WriteNameRecord( group.m_Name, lengthGroupName, metadataBuffers, metadataPositions );
@@ -291,12 +300,15 @@ public:
++m_VariablesCount;
} //end of function
-
void Close( const BP1MetadataSet& metadataSet, Capsule& capsule, Transport& transport );
private:
+
+
+
+
/**
* Writes name record using a
* @param name to be written
@@ -304,7 +316,7 @@ private:
* @param buffers to be written
* @param positions to be moved
*/
- void WriteNameRecord( const std::string& name, const std::uint16_t& length,
+ void WriteNameRecord( const std::string name, const std::uint16_t length,
std::vector<char*>& buffers, std::vector<std::size_t>& positions );
void WriteDimensionRecord( std::vector<char*>& buffers, std::vector<std::size_t>& positions,
diff --git a/include/functions/adiosFunctions.h b/include/functions/adiosFunctions.h
index afb081c92abad6f03490cfcae492aa61507a1c72..f43a7f3c9b44e027164234e3e4880acc5d3a6cd8 100644
--- a/include/functions/adiosFunctions.h
+++ b/include/functions/adiosFunctions.h
@@ -178,6 +178,7 @@ int GrowBuffer( const std::size_t incomingDataSize, const float growthFactor, co
*/
void MovePositions( const int bytes, std::vector<std::size_t>& positions );
+
} //end namespace
diff --git a/include/functions/engineTemplates.h b/include/functions/engineTemplates.h
deleted file mode 100644
index 626755a6d1ec1841a5643667b3e92b98a3ce41bb..0000000000000000000000000000000000000000
--- a/include/functions/engineTemplates.h
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * GroupTemplates.h
- *
- * Created on: Nov 7, 2016
- * Author: wfg
- */
-
-#ifndef ENGINETEMPLATES_H_
-#define ENGINETEMPLATES_H_
-
-/// \cond EXCLUDE_FROM_DOXYGEN
-#include <string>
-#include <stdexcept>
-/// \endcond
-
-
-#include "core/Group.h"
-#include "core/Variable.h"
-#include "core/Capsule.h"
-#include "functions/adiosFunctions.h"
-
-
-
-namespace adios
-{
-
-
-/**
- * Intermediate function that assigns values from user to a Variable.Values pointer reference
- * and dispatches it to different capsules.
- * A variable's numerical dimensions are obtained from previously set variables in group.
- * @param group variable owner, used to get all dimensions as numerical values
- * @param variable variable to be written
- * @param capsules container of capsules coming from an Engine
- * @param transports used only if buffer size is larger than a certain maximum
- */
-template<class T>
-void WriteToCapsules( const Group& group, Variable<T>& variable, const T* values,
- std::vector< std::shared_ptr<Capsule> >& capsules,
- std::vector< std::shared_ptr<Transport> >& transports )
-{
- variable.Values = values;
- auto localDimensions = group.GetDimensions( variable.DimensionsCSV );
-
- std::vector< unsigned long long int > globalDimensions;
- std::vector< unsigned long long int > globalOffsets;
-
- if( variable.GlobalBoundsIndex > -1 ) //global variable
- {
- globalDimensions = group.GetDimensions( group.m_GlobalBounds[ variable.GlobalBoundsIndex ].first );
- globalOffsets = group.GetDimensions( group.m_GlobalBounds[ variable.GlobalBoundsIndex ].second );
- }
-
- for( auto& capsule : capsules )
- {
- //capsule->Write( variable, localDimensions, globalDimensions, globalOffsets, transports );
- }
-}
-
-
-} //end namespace
-
-
-
-#endif /* ENGINETEMPLATES_H_ */
diff --git a/src/core/Engine.cpp b/src/core/Engine.cpp
index 7293df87dd22276bf6a230378409fe8098563e91..55eff35a845dee6468393991adabe68ffae00679 100644
--- a/src/core/Engine.cpp
+++ b/src/core/Engine.cpp
@@ -106,6 +106,42 @@ void Engine::CheckDefaultGroup( ) const
}
+bool Engine::TransportNamesUniqueness( ) const
+{
+ auto lf_CheckTransportsType = [&]( const std::set<std::string>& specificType ) -> bool
+ {
+ std::set<std::string> transportNames;
+
+ for( const auto& parameters : m_Method.m_TransportParameters )
+ {
+ auto itTransport = parameters.find( "transport" );
+ if( m_DebugMode == true )
+ {
+ if( itTransport == parameters.end() )
+ throw std::invalid_argument( "ERROR: transport not defined in Method input to Engine " + m_Name );
+ }
+
+ const std::string type( itTransport->second );
+ if( specificType.count( type ) == 1 ) //file transports type
+ {
+ std::string name( m_Name );
+ auto itName = parameters.find("name");
+ if( itName != parameters.end() )
+ name = itName->second;
+
+ if( transportNames.count( name ) == 0 )
+ transportNames.insert( name );
+ else
+ return false;
+ }
+ }
+ return true;
+ };
+
+ return lf_CheckTransportsType( Support::FileTransports );
+}
+
+
std::string Engine::GetName( const std::vector<std::string>& arguments ) const
{
bool isNameFound = false;
diff --git a/src/core/Support.cpp b/src/core/Support.cpp
index 25804adb7432532874e15d128cf92a0a7160137d..670838cda448e5208dbe372f88afea56095c9935 100644
--- a/src/core/Support.cpp
+++ b/src/core/Support.cpp
@@ -104,5 +104,12 @@ const std::map<std::string, std::set<std::string> > Support::DatatypesAliases
};
+const std::set<std::string> Support::FileTransports{
+ { "POSIX", "File", "FStream", "MPIFile" }
+};
+
+
+
+
} //end namespace
diff --git a/src/engine/writer/Writer.cpp b/src/engine/writer/Writer.cpp
index 2ff46fa9a210e2fe85eb68afc01d40b19d189e80..aff6b34bae7dbf37359b43cc7b096d8527075dc9 100644
--- a/src/engine/writer/Writer.cpp
+++ b/src/engine/writer/Writer.cpp
@@ -261,7 +261,9 @@ void Writer::Write( const std::string variableName, const long double* values )
void Writer::InitTransports( )
{
- //Let BPFormat handle this??
+ //Let BPFormat handle this
+ //InitTransportsBP( m_Method.m_TransportParameters, m_Transports, m_Name+m_EndMessage );
+
std::set< std::string > transportStreamNames; //used to check for name conflict between transports
const unsigned int transportsSize = m_Method.m_TransportParameters.size();
diff --git a/src/format/BP1Writer.cpp b/src/format/BP1Writer.cpp
index b48a229bbc1b564ac7033c15fd52643ad16cdfa0..d7f2d398b8a8ec526c1b2942dd51d70192e24c07 100644
--- a/src/format/BP1Writer.cpp
+++ b/src/format/BP1Writer.cpp
@@ -25,6 +25,64 @@ BP1Writer::~BP1Writer( )
{ }
+std::size_t BP1Writer::GetProcessIndexSize( const std::string name, const std::string timeStepName )
+{
+ return name.length() + timeStepName.length() + 23;
+}
+
+
+void BP1Writer::WriteProcessGroupIndex( const bool isFortran, const std::string name, const unsigned int processID,
+ const std::string timeStepName, const unsigned int timeStep,
+ 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 )
+{
+ std::vector<std::size_t> metadataLengthPositions( metadataPositions ); //get length of pg position
+
+ MovePositions( 2, metadataPositions ); //skip length of pg in metadata, 2 bytes, would write at the end
+ MovePositions( 8, dataPositions ); //skip length of pg including data, 8 bytes, would write at the end
+
+ //write name to metadata
+ const std::uint16_t lengthOfName = name.length();
+ WriteNameRecord( name, lengthOfName, metadataBuffers, metadataPositions );
+
+ //write is host language Fortran in metadata and data
+ const char hostFortran = ( isFortran ) ? 'y' : 'n'; //if host language is fortran
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &hostFortran, 1 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &hostFortran, 1 );
+
+ //name in data
+ WriteNameRecord( name, lengthOfName, dataBuffers, dataPositions );
+
+ //processID,
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &processID, 4 );
+ //skip coordination var in data ....what is coordination var?
+ MovePositions( 4, dataPositions );
+
+ //time step name to metadata and data
+ const std::uint16_t lengthOfTimeStep = timeStepName.length();
+ WriteNameRecord( timeStepName, lengthOfTimeStep, metadataBuffers, metadataPositions );
+ WriteNameRecord( timeStepName, lengthOfTimeStep, dataBuffers, dataPositions );
+ //time step to metadata and data
+ MemcpyToBuffers( metadataBuffers, metadataPositions, &timeStep, 4 );
+ MemcpyToBuffers( dataBuffers, dataPositions, &timeStep, 4 );
+
+ //write offset to pg in data on metadata which is the current absolute position
+ MemcpyToBuffers( metadataBuffers, metadataPositions, dataAbsolutePositions, 8 );
+
+
+ //get pg index length
+ std::vector<std::uint16_t> metadataIndexLengths( metadataPositions.size() );
+ for( unsigned int i = 0; i < metadataPositions.size(); ++i )
+ metadataIndexLengths[i] = metadataPositions[i] - metadataLengthPositions[i];
+
+ //write to metadata length position the pgIndex length
+ MemcpyToBuffers( metadataBuffers, metadataLengthPositions, metadataIndexLengths, 2 );
+ MovePositions( -2, metadataLengthPositions ); //back to original position
+}
+
+
void BP1Writer::Close( const BP1MetadataSet& metadataSet, Capsule& capsule, Transport& transport )
{
@@ -34,7 +92,7 @@ void BP1Writer::Close( const BP1MetadataSet& metadataSet, Capsule& capsule, Tran
}
//PRIVATE FUNCTIONS
-void BP1Writer::WriteNameRecord( const std::string& name, const std::uint16_t& length,
+void BP1Writer::WriteNameRecord( const std::string name, const std::uint16_t length,
std::vector<char*>& buffers, std::vector<std::size_t>& positions )
{
MemcpyToBuffers( buffers, positions, &length, 2 );
diff --git a/src/transport/POSIX.cpp b/src/transport/POSIX.cpp
index dafd3d33d7de43840dadbc2c8137262809729a70..264ffb35b250d294858c4a25a46005ff86d6ad38 100644
--- a/src/transport/POSIX.cpp
+++ b/src/transport/POSIX.cpp
@@ -42,13 +42,17 @@ void POSIX::Open( const std::string name, const std::string accessMode )
m_AccessMode = accessMode;
if( accessMode == "w" || accessMode == "write" )
+ {
m_FileDescriptor = open( m_Name.c_str(), O_WRONLY | O_CREAT, 0666 );
-
+ }
else if( accessMode == "a" || accessMode == "append" )
+ {
m_FileDescriptor = open( m_Name.c_str(), O_WRONLY | O_APPEND );
-
+ }
else if( accessMode == "r" || accessMode == "read" )
+ {
m_FileDescriptor = open( m_Name.c_str(), O_RDONLY );
+ }
if( m_DebugMode == true )
{