diff --git a/examples/hello/fstream.xml b/examples/hello/fstream.xml
index 405eb95d458f5458bfe02387eaa8e517eaadbf56..937edb602ec895c7f6132fde5e88c4ed7d592df7 100644
--- a/examples/hello/fstream.xml
+++ b/examples/hello/fstream.xml
@@ -1,12 +1,12 @@
<?xml version="1.0"?>
<adios-config host-language="C++">
<adios-group name="Types">
- <var name="Numbers" type="Vinteger"/>
+ <var name="Numbers" type="std::vector<int>"/>
<attribute name="description" value="1 to 10"/>
</adios-group>
- <transport group="Vector" method="FStream">verbose=3</transport>
+ <transport group="Types" method="FStream">verbose=3</transport>
<!-- <buffer size-MB="40" allocate-time="now"/> -->
diff --git a/examples/hello/helloFStream.cpp b/examples/hello/helloFStream.cpp
index d9bcc449e878191b2a7709c5f51ddc7da69f2a53..0903c19981ec3d8835c10dbd0d30456ea77d89e5 100644
--- a/examples/hello/helloFStream.cpp
+++ b/examples/hello/helloFStream.cpp
@@ -6,8 +6,6 @@
*/
-
-
#include <stdexcept>
#include <iostream>
#include <fstream>
@@ -19,15 +17,15 @@
int main( int argc, char* argv [] )
{
- try
+ try //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
- const std::string group("Types");
- const std::string numbersVariable("Numbers");
+ const std::string group( "Types" );
+ const std::string numbersVariable( "Numbers" );
std::vector<int> myVector( 10 );
std::iota( myVector.begin(), myVector.end(), 1 );
- //testing with CPOSIXMPI
+ //testing with CFStream transport
adios::ADIOS adios( "fstream.xml", true );
adios.MonitorGroups( std::cout ); //Get Monitor info
adios.Write( group, numbersVariable, &myVector ); //Write
@@ -43,8 +41,9 @@ int main( int argc, char* argv [] )
std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
std::cout << e.what() << "\n";
}
- catch( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
+ catch( std::exception& e )
{
+ std::cout << "Exception, STOPPING PROGRAM\n";
std::cout << e.what() << "\n";
}
diff --git a/include/core/CGroup.h b/include/core/CGroup.h
index 7d91f590a65fe188e6b65e109fd962e006b7b2cb..926506efd1b2fddbf968a8c00b629cd1b7042176 100644
--- a/include/core/CGroup.h
+++ b/include/core/CGroup.h
@@ -42,11 +42,11 @@ public:
/**
* @brief Constructor for XML config file
* @param hostLanguage reference from ADIOS class
- * @param xmlGroup contains <adios-group....</adios-group> single group definition from XML config file
+ * @param xmlGroup contains <adios-group (tag excluded)....</adios-group> single group definition from XML config file
* @param groupName returns the groupName from <adios-group name=" "
- * @param debugMode
+ * @param debugMode from ADIOS
*/
- CGroup( const std::string& hostLanguage, const std::string& xmlGroup, std::string& groupName, const bool debugMode = false );
+ CGroup( const std::string& hostLanguage, const std::string& xmlGroup, const bool debugMode = false );
/**
* Non-XML empty constructor
@@ -128,7 +128,10 @@ public:
private:
- const std::string& m_HostLanguage; ///< reference to class ADIOS m_HostLanguage, this erases the copy constructor
+ const std::string& m_HostLanguage; ///< reference to class ADIOS m_HostLanguage, this erases the copy constructor. Might be moved later to non-reference const
+ const bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code
+
+ bool m_IsOpen = false; ///< checks if group was opened for operations;
/**
* @brief Contains all group variables (from XML Config file).
* <pre>
@@ -136,7 +139,7 @@ private:
* Value: Polymorphic value is always unique child defined in SVariableTemplate.h, allow different variable types
* </pre>
*/
- std::map< std::string, std::unique_ptr<CVariableBase> > m_Variables;
+ std::map< std::string, std::shared_ptr<CVariableBase> > m_Variables;
/**
* @brief Contains all group attributes from SAttribute.h
@@ -150,21 +153,17 @@ private:
std::vector<std::string> m_GlobalDimensions; ///< from global-bounds in XML File, data in global space
std::vector<std::string> m_GlobalOffsets; ///< from global-bounds in XML File, data in global space
- std::unique_ptr<CTransport> m_Transport; ///< transport method defined in XML File, using unique_ptr as copy constructor is removed
+ std::shared_ptr<CTransport> m_Transport; ///< transport method defined in XML File, using shared_ptr as CGroup is put in a map copy constructor deleted
std::string m_ActiveTransport;
- bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code
- bool m_IsOpen = false; ///< checks if group was opened for operations;
std::string m_FileName; ///< associated fileName is the Group is opened.
std::string m_AcessMode; ///< file access mode "r"->read, "w"->write, "a"->append
/**
* Called from XML constructor
- * @param hostLanguage from ADIOS class, used to determine allowed variable types (Fortran -> real, C++-> std::vector )
* @param xmlGroup contains <adios-group....</adios-group> single group definition from XML config file passing by reference as it could be big
- * @param groupName returns the groupName from <adios-group name=" "
*/
- void ParseXMLGroup( const std::string& xmlGroup, std::string& groupName );
+ void ParseXMLGroup( const std::string& xmlGroup );
/**
* Function that checks if transport method is valid, called from overloaded SetTransform functions
diff --git a/include/core/CTransport.h b/include/core/CTransport.h
index f95ba1250626f3994f09d1558c46276a1d5c44dc..012f210adb065f90c9b6f777447617511542b237 100644
--- a/include/core/CTransport.h
+++ b/include/core/CTransport.h
@@ -19,9 +19,6 @@
#endif
-#include "core/CVariableBase.h"
-
-
namespace adios
{
@@ -36,7 +33,6 @@ public:
MPI_Comm m_MPIComm;
std::string m_FileName; ///< file name associated with a group that owns the transport
- std::string m_AccessMode; ///< read, write, append
CTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
MPI_Comm mpiComm ):
@@ -50,13 +46,14 @@ public:
{ }
- void Open( const std::string fileName, const std::string accessMode = "w" )
- {
- m_FileName = fileName;
- m_AccessMode = accessMode;
- }
+ /**
+ * Open Output file accesing a mode
+ * @param fileName name of file
+ * @param accessMode r or read, w or write, a or append
+ */
+ virtual void Open( const std::string fileName, const std::string accessMode ) = 0;
- virtual void Write( const CVariableBase& variable ) = 0;
+ virtual void Close( ) = 0; //here think what needs to be passed
};
diff --git a/include/functions/ADIOSFunctions.h b/include/functions/ADIOSFunctions.h
index 628ba6da88cbff751b7863952cbbc37de9ea1ed9..85e9b1f128cff11b4cedd19ba219788001872d87 100644
--- a/include/functions/ADIOSFunctions.h
+++ b/include/functions/ADIOSFunctions.h
@@ -88,11 +88,12 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, std::st
* Called inside the ADIOS XML constructors to get contents from file, broadcast and set hostLanguage and groups from ADIOS class
* @param xmlConfigFile xml config file name
* @param mpiComm communicator used from broadcasting
+ * @param debugMode from ADIOS m_DebugMode passed to CGroup in groups
* @param hostLanguage set from host-language in xml file
* @param groups passed returns the map of groups defined in fileContent
* @param debugMode if true will do more checks, exceptions, warnings, expect slower code
*/
-void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, std::string& hostLanguage,
+void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const bool debugMode, std::string& hostLanguage,
std::map< std::string, CGroup >& groups );
} //end namespace
diff --git a/include/functions/GroupFunctions.h b/include/functions/GroupFunctions.h
index f70c6b425902be7aeaef28e42256bf0b254e8237..d3258044d414fe626823734a11b09e5a550bf4fe 100644
--- a/include/functions/GroupFunctions.h
+++ b/include/functions/GroupFunctions.h
@@ -21,6 +21,7 @@
#endif
#include "core/CVariableBase.h"
+#include "core/CTransport.h"
namespace adios
{
@@ -37,7 +38,7 @@ namespace adios
*/
void CreateVariableLanguage( const std::string hostLanguage, const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map<std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept;
+ std::map<std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
/**
* Create a C++ supported variable, including STL vector types
@@ -50,7 +51,7 @@ void CreateVariableLanguage( const std::string hostLanguage, const std::string n
*/
void CreateVariableCpp( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept;
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
/**
* Create a C supported variable, including STL vector types
@@ -63,7 +64,7 @@ void CreateVariableCpp( const std::string name, const bool isGlobal,
*/
void CreateVariableC( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept;
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
/**
* Create a Fortran supported variable, including STL vector types
@@ -76,7 +77,17 @@ void CreateVariableC( const std::string name, const bool isGlobal,
*/
void CreateVariableFortran( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept;
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept;
+
+
+/**
+ * Looks up the variable type and cast the appropriate values type to m_Value in CVariable
+ * Maybe it produces exceptions? Must double-check
+ * @param variables always a derived CVariable object from CVariableBase
+ * @param values to be casted to the right type
+ */
+void SetVariableValues( CVariableBase& variable, const void* values ) noexcept;
+
/**
@@ -88,7 +99,7 @@ void CreateVariableFortran( const std::string name, const bool isGlobal,
* @param transport passed from CGroup m_Transport member
*/
void CreateTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
- const MPI_Comm mpiComm, std::unique_ptr<CTransport>& transport ) noexcept;
+ const MPI_Comm mpiComm, std::shared_ptr<CTransport>& transport ) noexcept;
diff --git a/include/transport/CFStream.h b/include/transport/CFStream.h
index c62212d70a70c4cda2ff4b8cb67090aa169f297f..ab8e72b8c15e22701f3f3c08beeada335275db1b 100644
--- a/include/transport/CFStream.h
+++ b/include/transport/CFStream.h
@@ -8,6 +8,7 @@
#ifndef CFSTREAM_H_
#define CFSTREAM_H_
+#include <fstream>
#include "core/CTransport.h"
@@ -27,7 +28,14 @@ public:
~CFStream( );
- void Write( const CVariableBase& variable );
+ void Open( const std::string fileName, const std::string accessMode );
+
+ void Close( );
+
+private:
+
+ std::fstream m_FStream; ///< file stream corresponding to this transport
+
};
diff --git a/include/transport/CPOSIX.h b/include/transport/CPOSIX.h
index ab2c48f985922af30d0dbdc67b91abf3cb3f6481..125413137bb31c67b9b708566fd7cf4244ad12a1 100644
--- a/include/transport/CPOSIX.h
+++ b/include/transport/CPOSIX.h
@@ -25,7 +25,9 @@ public:
~CPOSIX( );
- void Write( const CVariableBase& variable );
+ void Open( const std::string fileName, const std::string accessMode );
+
+ void Close( );
};
diff --git a/src/core/CGroup.cpp b/src/core/CGroup.cpp
index 84a510cf951628f0a8218b101a039517b959c182..58d8af5a318cc824ad47bfc48cdbb2105531b5ae 100644
--- a/src/core/CGroup.cpp
+++ b/src/core/CGroup.cpp
@@ -12,7 +12,8 @@
#include "core/CGroup.h"
#include "functions/GroupFunctions.h" //for CreateVariableLanguage
#include "public/SSupport.h"
-#include "functions/ADIOSFunctions.h" //for XML Parsing GetTag
+#include "functions/ADIOSFunctions.h" //for XML Parsing functions (e.g. GetTag)
+#include "core/CVariable.h" //for cast implementation of CVariableBase::Set that calls CVariable::Set
namespace adios
@@ -25,11 +26,11 @@ CGroup::CGroup( const std::string& hostLanguage, const bool debugMode ):
{ }
-CGroup::CGroup( const std::string& hostLanguage, const std::string& xmlGroup, std::string& groupName, const bool debugMode ):
+CGroup::CGroup( const std::string& hostLanguage, const std::string& xmlGroup, const bool debugMode ):
m_HostLanguage{ hostLanguage },
m_DebugMode{ debugMode }
{
- ParseXMLGroup( xmlGroup, groupName );
+ ParseXMLGroup( xmlGroup );
}
@@ -49,6 +50,9 @@ void CGroup::SetVariable( const std::string name, const bool isGlobal, const std
{
if( m_DebugMode == true )
{
+ if( SSupport::Datatypes.at( m_HostLanguage ).count( type ) == 0 )
+ throw std::invalid_argument( "ERROR: type " + type + " for variable " + name + " is not supported.\n" );
+
if( m_Variables.count( name ) == 0 ) //variable doesn't exists
CreateVariableLanguage( m_HostLanguage, name, isGlobal, type, dimensionsCSV, transform, m_Variables );
else //name is found
@@ -110,7 +114,7 @@ void CGroup::SetTransport( const std::string method, const unsigned int priority
throw std::invalid_argument( "ERROR: transport method " + method + " not supported. Check spelling or case sensitivity.\n" );
}
- if( m_ActiveTransport.empty() == false ) //there is an existing transport method
+ if( m_ActiveTransport.empty() == false ) //there is an existing transport method, so reset
m_Transport.reset();
CreateTransport( method, priority, iteration, mpiComm, m_Transport );
@@ -127,27 +131,16 @@ void CGroup::Write( const std::string variableName, const void* values )
if( itVariable == m_Variables.end() )
throw std::invalid_argument( "ERROR: variable " + variableName + " is undefined.\n" );
}
- // must move this to GroupFunctions.h
-
- const std::string type = itVariable->second->m_Type;
- auto& variable = itVariable->second;
-
- //Set variable values
- if( type == "double" ) variable->Set<double>( values );
- else if( type == "integer" ) variable->Set<int>( values );
- else if( type == "std::vector<int>" || type == "vector<int>" ) variable->Set<std::vector<int>>( values );
-// else if( type == "unsigned integer" ) variable->Set<unsigned int>( values );
-// else if( type == "float" ) variable->Set<float>( values );
-
- std::cout << "Hello from " << type << " variable " << variableName << "\n";
- m_Transport->Write( *variable ); //Using shared_ptr for Variable, must dereference
+ SetVariableValues( *itVariable->second, values ); //will check type and cast to appropriate template<type>
+ //here must do something with Capsule
}
void CGroup::Close( )
{
//here must think what to do with Capsule and close Transport
+ m_Transport->Close( );
}
//PRIVATE FUNCTIONS BELOW
@@ -172,33 +165,31 @@ void CGroup::Monitor( std::ostream& logStream ) const
}
-void CGroup::ParseXMLGroup( const std::string& xmlGroup, std::string& groupName )
+void CGroup::ParseXMLGroup( const std::string& xmlGroup )
{
- //get name
- std::string tag;
std::string::size_type currentPosition( 0 );
- GetSubString( "<adios-group ", ">", xmlGroup, tag, currentPosition );
- tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
-
- std::vector< std::pair<const std::string, const std::string> > pairs;
- GetPairsFromTag( xmlGroup, tag, pairs );
-
- for( auto& pair : pairs )
- {
- if( pair.first == "name") groupName = pair.second;
- }
-
bool isGlobal = false;
while( currentPosition != std::string::npos )
{
+ //Get tag
+ std::string tag;
GetSubString( "<", ">", xmlGroup, tag, currentPosition );
if( tag == "</adios-group>" ) break;
if( tag == "</global-bounds>" ) isGlobal = false;
- tag = tag.substr( 1, tag.size() - 2 ); //eliminate < > needs an exception?
+ if( m_DebugMode == true )
+ {
+ if( tag.size() < 2 )
+ throw std::invalid_argument( "ERROR: wrong tag " + tag + " when reading group \n" ); //check < or <=)
+ }
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+
+ //Get pairs from tag
+ std::vector< std::pair<const std::string, const std::string> > pairs;
GetPairsFromTag( xmlGroup, tag, pairs );
+ //Check based on tagName
const std::string tagName( tag.substr( 0, tag.find_first_of(" \t\n\r") ) );
if( tagName == "var" ) //assign a Group variable
@@ -241,10 +232,4 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup, std::string& groupName
}
-void CGroup::CheckTransport( const std::string method )
-{
-
-}
-
-
} //end namespace
diff --git a/src/functions/ADIOSFunctions.cpp b/src/functions/ADIOSFunctions.cpp
index 06c03d68f8914554e965bf41077e2cc30c79f3b4..024ca5d871ef44d8671337593a8b4a2eae1630be 100644
--- a/src/functions/ADIOSFunctions.cpp
+++ b/src/functions/ADIOSFunctions.cpp
@@ -42,13 +42,22 @@ void DumpFileToStream( const std::string fileName, std::string& fileContent )
void GetSubString( const std::string initialTag, const std::string finalTag, const std::string content,
std::string& subString, std::string::size_type& currentPosition )
{
- auto lf_Wipe =[]( std::string& subString, std::string::size_type& currentPosition )
+ auto lf_Wipe = []( std::string& subString, std::string::size_type& currentPosition )
{
subString.clear();
currentPosition = std::string::npos;
};
- std::string::size_type start( content.find(initialTag, currentPosition ) );
+ auto lf_SetPositions = []( const char quote, const std::string::size_type quotePosition, const std::string& content,
+ std::string::size_type& currentPosition, std::string::size_type& closingQuotePosition )
+ {
+ currentPosition = quotePosition;
+ closingQuotePosition = content.find( quote, currentPosition+1 );
+ };
+
+
+ //BODY OF FUNCTION STARTS HERE
+ std::string::size_type start( content.find( initialTag, currentPosition ) );
if( start == content.npos )
{
lf_Wipe( subString, currentPosition );
@@ -68,38 +77,40 @@ void GetSubString( const std::string initialTag, const std::string finalTag, con
while( isValue == true )
{
- std::string::size_type quotePosition = content.find( '\'', currentPosition );
+ std::string::size_type singleQuotePosition = content.find( '\'', currentPosition );
std::string::size_type doubleQuotePosition = content.find( '\"', currentPosition );
- if( ( quotePosition == content.npos && doubleQuotePosition == content.npos ) ||
- ( quotePosition == content.npos && end < doubleQuotePosition ) ||
- ( doubleQuotePosition == content.npos && end < quotePosition ) ||
- ( end < quotePosition && end < doubleQuotePosition )
+ if( ( singleQuotePosition == content.npos && doubleQuotePosition == content.npos ) ||
+ ( singleQuotePosition == content.npos && end < doubleQuotePosition ) ||
+ ( doubleQuotePosition == content.npos && end < singleQuotePosition ) ||
+ ( end < singleQuotePosition && end < doubleQuotePosition )
) break;
- //first case
- std::string::size_type closingPosition;
- if( quotePosition < doubleQuotePosition ) //find the closing "
- {
- currentPosition = quotePosition;
- closingPosition = content.find( '\'', currentPosition+1 );
- }
- else //find the closing '
+ //find the closing corresponding quote
+ std::string::size_type closingQuotePosition;
+
+ if( singleQuotePosition == content.npos ) //no ' anywhere
+ lf_SetPositions( '\"', doubleQuotePosition, content, currentPosition, closingQuotePosition );
+ else if( doubleQuotePosition == content.npos ) //no " anywhere
+ lf_SetPositions( '\'', singleQuotePosition, content, currentPosition, closingQuotePosition );
+ else
{
- currentPosition = doubleQuotePosition;
- closingPosition = content.find( '\"', currentPosition+1 );
+ if( singleQuotePosition < doubleQuotePosition )
+ lf_SetPositions( '\'', singleQuotePosition, content, currentPosition, closingQuotePosition );
+ else //find the closing "
+ lf_SetPositions( '\"', doubleQuotePosition, content, currentPosition, closingQuotePosition );
}
- if( closingPosition == content.npos ) //if can't find closing it's open until the end
+ if( closingQuotePosition == content.npos ) //if can't find closing it's open until the end
{
lf_Wipe( subString, currentPosition );
return;
}
- if( closingPosition < end )
- {
- currentPosition = closingPosition+1;
+
+ currentPosition = closingQuotePosition+1;
+
+ if( closingQuotePosition < end )
continue;
- }
//if this point is reached it means it's a value inside " " or ' ', move to the next end
end = content.find( finalTag, currentPosition );
@@ -157,9 +168,8 @@ void GetPairsFromTag( const std::string& fileContent, const std::string tag,
{ }
else // opening tag
{
- //check for closing tagName
const std::string tagName( tag.substr( 0, tag.find_first_of(" \t\n\r") ) );
- const std::string closingTagName( "</" + tagName + ">" );
+ const std::string closingTagName( "</" + tagName + ">" ); //check for closing tagName
if( fileContent.find( closingTagName ) == fileContent.npos )
throw std::invalid_argument( "ERROR: closing tag " + closingTagName + " missing, check XML file\n");
@@ -168,7 +178,8 @@ void GetPairsFromTag( const std::string& fileContent, const std::string tag,
}
}
-void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
+
+void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, const bool debugMode,
std::string& hostLanguage, std::map< std::string, CGroup >& groups )
{
//adios-config
@@ -186,44 +197,92 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
startComment = currentContent.find( "<!--" );
}
- std::string tag; //use for < > tags
- std::vector< std::pair<const std::string, const std::string> > pairs; // pairs in tag
-
//Tag <adios-config
currentPosition = 0;
- GetSubString( "<", ">", currentContent, tag, currentPosition );
+
+ std::string tag; //use for < > tags
+ GetSubString( "<adios-config", ">", currentContent, tag, currentPosition );
tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+
+ std::vector< std::pair<const std::string, const std::string> > pairs; // pairs in tag
GetPairsFromTag( currentContent, tag, pairs );
for( auto& pair : pairs )
+ if( pair.first == "host-language" )
+ hostLanguage = pair.second;
+
+ if( debugMode == true )
{
- if( pair.first == "host-language" ) hostLanguage = pair.second;
- }
+ if( SSupport::HostLanguages.count( hostLanguage ) == 0 )
+ throw std::invalid_argument("ERROR: host language " + hostLanguage + " not supported.\n" );
- if( SSupport::HostLanguages.count( hostLanguage ) == 0 )
- throw std::invalid_argument("ERROR: host language " + hostLanguage + " not supported.\n" );
+ if( hostLanguage.empty() == true )
+ throw std::invalid_argument("ERROR: host language is empty.\n" );
+ }
//adios-group
- std::string xmlGroup;
+ currentPosition = 0;
+
while( currentPosition != std::string::npos )
{
- GetSubString("<adios-group ", "</adios-group>", currentContent, xmlGroup, currentPosition );
- if( xmlGroup.empty() ) break;
+ std::string xmlGroup;
+ GetSubString("<adios-group ", "</adios-group>", currentContent, xmlGroup, currentPosition ); //Get all group contents
+ if( xmlGroup.empty() ) //no more groups to find
+ break;
+ //get group name
+ std::string::size_type groupPosition( 0 );
+ GetSubString( "<adios-group ", ">", xmlGroup, tag, groupPosition );
+ if( debugMode == true )
+ {
+ if( tag.size() < 2 )
+ throw std::invalid_argument( "ERROR: wrong tag " + tag + " in adios-group\n" ); //check < or <=
+ }
+
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+ GetPairsFromTag( xmlGroup, tag, pairs );
std::string groupName;
- CGroup group( hostLanguage, xmlGroup, groupName ); //need to change formulation to be able to emplace
- if( groups.count( groupName ) == 1 ) //group exists
- throw std::invalid_argument("ERROR: group " + groupName + " defined twice.\n" );
+ for( auto& pair : pairs )
+ {
+ if( pair.first == "name")
+ groupName = pair.second;
+ }
+
+ if( debugMode == true )
+ {
+ if( groupName.empty() )
+ throw std::invalid_argument( "ERROR: group name not found. \n" );
+
+ if( groups.count( groupName ) == 1 ) //group exists
+ throw std::invalid_argument( "ERROR: group " + groupName + " defined twice.\n" );
+ }
- groups.insert( std::make_pair( groupName, std::move( group ) ) ); //move rvalue as it has const members
+ groups.emplace( groupName, CGroup( hostLanguage, xmlGroup, debugMode ) );
currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size() );
currentPosition = 0;
}
//transport
+ //lambda function to check priority and iteration casting to unsigned int
+ auto lf_UIntCheck = []( const std::string method, const std::string fieldStr, const std::string fieldName,
+ const bool debugMode, int& field )
+ {
+ field = 0;
+ if( fieldStr.empty() == false )
+ {
+ field = std::stoi( fieldStr ); //throws invalid_argument
+
+ if( debugMode == true )
+ {
+ if( field < 0 )
+ throw std::invalid_argument("ERROR: " + fieldName + " in transport " + method + " can't be negative\n" );
+ }
+ }
+ };
+
currentPosition = 0;
while( currentPosition != std::string::npos )
{
@@ -243,33 +302,22 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
}
auto itGroup = groups.find( groupName );
- if( itGroup == groups.end() ) //not found
+ if( debugMode == true )
{
- std::cout << "WARNING: group " << groupName << " in transport line not found \n";
- continue;
+ if( itGroup == groups.end() ) //not found
+ throw std::invalid_argument( "ERROR: in transport " + method + " group " + groupName + " not found.\n" );
}
- //lambda function to check priority and iteration
- auto lf_UIntCheck = []( const std::string method, const std::string fieldStr, const std::string fieldName, int& field )
- {
- field = 0;
- if( fieldStr.empty() == false )
- {
- field = std::stoi( fieldStr ); //throws invalid_argument
- if( field < 0 ) throw std::invalid_argument("ERROR: " + fieldName + " in transport " + method + " can't be negative\n" );
- }
- };
-
int priority, iteration;
- lf_UIntCheck( method, priorityStr, "priority", priority );
- lf_UIntCheck( method, iterationStr, "iteration", iteration );
+ lf_UIntCheck( method, priorityStr, "priority", debugMode, priority );
+ lf_UIntCheck( method, iterationStr, "iteration", debugMode, iteration );
itGroup->second.SetTransport( method, (unsigned int)priority, (unsigned int)iteration, mpiComm );
}
}
-void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm,
+void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const bool debugMode,
std::string& hostLanguage, std::map< std::string, CGroup >& groups )
{
int xmlFileContentSize;
@@ -297,7 +345,7 @@ void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm,
delete []( xmlFileContentMPI ); //delete char* needed for MPI, might add size is moving to C++14 for optimization, avoid memory leak
}
- SetMembers( xmlFileContent, mpiComm, hostLanguage, groups );
+ SetMembers( xmlFileContent, mpiComm, debugMode, hostLanguage, groups );
}
diff --git a/src/functions/GroupFunctions.cpp b/src/functions/GroupFunctions.cpp
index 88936be0f4fac6e79a530b9613250fea326a97fc..e2679bc5fd87c28164c18c44ce310e6258072bf9 100644
--- a/src/functions/GroupFunctions.cpp
+++ b/src/functions/GroupFunctions.cpp
@@ -20,7 +20,7 @@ namespace adios
void CreateVariableLanguage( const std::string hostLanguage, const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map<std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept
+ std::map<std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
{
if( hostLanguage == "C++" )
CreateVariableCpp( name, isGlobal, type, dimensionsCSV, transform, variables );
@@ -35,7 +35,7 @@ void CreateVariableLanguage( const std::string hostLanguage, const std::string n
void CreateVariableCpp( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
{
using PVar = std::unique_ptr<CVariableBase>; //might be modified in C++17 if std::make_unique is available, local scope
//using emplace to create object in-place, can't use copy constructors with unique_ptr
@@ -113,27 +113,44 @@ void CreateVariableCpp( const std::string name, const bool isGlobal,
variables.emplace( name, PVar( new CVariable< std::vector< std::complex<long double> > >( isGlobal, type, dimensionsCSV, transform ) ) );
}
+
void CreateVariableC( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
{
}
+
void CreateVariableFortran( const std::string name, const bool isGlobal,
const std::string type, const std::string dimensionsCSV, const std::string transform,
- std::map< std::string, std::unique_ptr<CVariableBase> >& variables ) noexcept
+ std::map< std::string, std::shared_ptr<CVariableBase> >& variables ) noexcept
{
}
+void SetVariableValues( CVariableBase& variable, const void* values ) noexcept
+{
+ const std::string type = variable.m_Type;
+
+ //Set variable values, add more support
+ if( type == "double" )
+ variable.Set<double>( values );
+
+ else if( type == "integer" )
+ variable.Set<int>( values );
+
+ else if( type == "std::vector<int>" || type == "vector<int>" )
+ variable.Set<std::vector<int>>( values );
+
+}
void CreateTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
- const MPI_Comm mpiComm, std::unique_ptr<CTransport>& transport )
+ const MPI_Comm mpiComm, std::shared_ptr<CTransport>& transport ) noexcept
{
- using PCT = std::unique_ptr<CTransport>; //might be modified in C++17 if std::make_unique is available, local scope
+ using PCT = std::shared_ptr<CTransport>; //might be modified in C++14 if std::make_unique is available, local scope
if( method == "POSIX" )
transport = PCT( new CPOSIX( priority, iteration, mpiComm ) );
@@ -142,6 +159,7 @@ void CreateTransport( const std::string method, const unsigned int priority, con
transport = PCT( new CFStream( priority, iteration, mpiComm ) );
}
+
} //end namespace
diff --git a/src/public/ADIOS.cpp b/src/public/ADIOS.cpp
index 27f9486a623e26a081d0891df33a471fbab40fc8..3286340266dae5ba16a30666ca00b7a45678f48d 100644
--- a/src/public/ADIOS.cpp
+++ b/src/public/ADIOS.cpp
@@ -29,7 +29,7 @@ ADIOS::ADIOS( const std::string xmlConfigFile, const bool debugMode ):
m_XMLConfigFile{ xmlConfigFile },
m_DebugMode{ debugMode }
{
- InitXML( m_XMLConfigFile, m_MPIComm, m_HostLanguage, m_Groups );
+ InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage, m_Groups );
}
@@ -38,7 +38,7 @@ ADIOS::ADIOS( const std::string xmlConfigFile, const MPI_Comm mpiComm, const boo
m_MPIComm{ mpiComm },
m_DebugMode{ debugMode }
{
- InitXML( m_XMLConfigFile, m_MPIComm, m_HostLanguage, m_Groups );
+ InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage, m_Groups );
}
diff --git a/src/transport/CFStream.cpp b/src/transport/CFStream.cpp
index ec6e77a634033fa7f9a38952e76d4afb19287343..f25850ba0aca11d0909a78ba322a59c7ba8808d0 100644
--- a/src/transport/CFStream.cpp
+++ b/src/transport/CFStream.cpp
@@ -9,7 +9,6 @@
#include <iostream>
#include "transport/CFStream.h"
-#include "core/CVariable.h" // implements CVariableBase Get function
namespace adios
@@ -25,27 +24,43 @@ CFStream::~CFStream( )
{ }
-void CFStream::Write( const CVariableBase& variable )
+void CFStream::Open( const std::string fileName, const std::string accessMode )
{
- int rank, size;
- MPI_Comm_rank( m_MPIComm, &rank );
- MPI_Comm_size( m_MPIComm, &size ); //would write to file
-
- const std::string type( variable.m_Type );
- std::cout << "My variable type is " << variable.m_Type << "\n";
-
- if( type[0] == 'V' ) //meaning it's a vector
- {
- //pointer to vector
- auto values = variable.Get< std::vector<int> >();
- std::cout << "Vector of size " << values->size() << "\n";
- unsigned int i = 0;
- for( auto element : *values )
- {
- std::cout << "var[" << i << "] = " << element << "\n";
- ++i;
- }
- }
+ if( accessMode == "w" || accessMode == "write" )
+ m_FStream.open( fileName, std::fstream::out );
+
+ else if( accessMode == "r" || accessMode == "read" )
+ m_FStream.open( fileName, std::fstream::in );
+
+ else if( accessMode == "a" || accessMode == "append" )
+ m_FStream.open( fileName, std::fstream::out | std::fstream::app );
+}
+
+
+void CFStream::Close( )
+{
+ m_FStream.close( ); //close the file
+
+ //This part should go to a capsule
+// int rank, size;
+// MPI_Comm_rank( m_MPIComm, &rank );
+// MPI_Comm_size( m_MPIComm, &size ); //would write to file
+//
+// const std::string type( variable.m_Type );
+// std::cout << "My variable type is " << variable.m_Type << "\n";
+//
+// if( type[0] == 'V' ) //meaning it's a vector
+// {
+// //pointer to vector
+// auto values = variable.Get< std::vector<int> >();
+// std::cout << "Vector of size " << values->size() << "\n";
+// unsigned int i = 0;
+// for( auto element : *values )
+// {
+// std::cout << "var[" << i << "] = " << element << "\n";
+// ++i;
+// }
+// }
}
diff --git a/src/transport/CPOSIX.cpp b/src/transport/CPOSIX.cpp
index bb80dd304aedcaa42a3cabb2806b857936e11488..27092be94cec25d1125b8e26f94841382c979917 100644
--- a/src/transport/CPOSIX.cpp
+++ b/src/transport/CPOSIX.cpp
@@ -24,14 +24,16 @@ CPOSIX::~CPOSIX( )
{ }
-void CPOSIX::Write( const CVariableBase& variable )
+void CPOSIX::Open( const std::string fileName, const std::string accessMode )
{
- int rank, size;
- MPI_Comm_rank( m_MPIComm, &rank );
- MPI_Comm_size( m_MPIComm, &size );
- std::cout << "Just saying Hello from CPOSIX Write from process " << rank << "/" << size << "\n";
}
+void CPOSIX::Close( )
+{
+
+}
+
+
-} //end namespace
+}//end namespace