diff --git a/examples/dataman/datamanNoXML.cpp b/examples/dataman/datamanNoXML.cpp
index 4db4d4bb48aaa5e8a8f72fa1f4fe25534839bfd4..2323b6467149ba64849f4cdaa33320981a7d9d26 100644
--- a/examples/dataman/datamanNoXML.cpp
+++ b/examples/dataman/datamanNoXML.cpp
@@ -1,17 +1,16 @@
/*
- * dataman.cpp: Example for DataMan Transport usage
+ * datamanNoXML.cpp: Example for DataMan Transport usage also using POSIX as additional transport
*
* Created on: Nov 15, 2016
* Author: wfg
*/
-
-
-
#ifdef HAVE_MPI
#include <mpi.h>
#else
#include "public/mpidummy.h"
+ using adios::MPI_Init;
+ using adios::MPI_Comm_rank;
#endif
#include "public/ADIOS.h"
@@ -25,46 +24,30 @@ int main( int argc, char* argv [] )
try //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
+ //APP variables
const unsigned int myCharsSize = 10;
std::vector<char> myChars( myCharsSize, '1' ); // 10 chars with value '1'
- //Equivalent to adios_init debug mode is on, MPI_COMM_WORLD is dummy nothing to worry about
+ //ADIOS init here, non-XML, debug mode is ON
adios::ADIOS adios( MPI_COMM_WORLD, true );
- //Create group TCP and set up, this can be done from XML config file
- const std::string group1( "TCP" );
- const std::string group2( "TCP" );
-
-
- adios.CreateGroup( group );
- adios.CreateVariable( group, "myCharsSize", "unsigned int" ); //scalar : group, name, type
- adios.CreateVariable( group, "myChars", "char", "myCharsSize,Ny,Nz", "gNx,gNy,gNz", "oNx,oNy,oNz" ); //group, name, type, integer variable defining size
- //adios.SetVariableTransform( group, "myCharsSize", transform );
- //here we tell group to be associate with a DataMan transport
- //we can add more parameters if you require
- //adios.SetTransport( group, "DataMan" );
-
- const std::string streamName( "TCPStream" );
- adios.Open( streamName, "write", "DataMan" ); //here open a stream called TCPStream for writing (w or write)
- adios.AddTransport( streamName, "POSIX" );
-
- adios.Write( streamName1, "myChars" );
-
- //adios.Open( streamName, "read", "DataMan" ); //here open a stream called TCPStream for writing (w or write)
- //adios.Write( "TCPStream", group, "myCharsSize", &myCharsSize ); //calls your transport
- capsule.SetGroup( group );
-
-
- adios.Write( streamName2, group1, "myChars" , &myChars[0], transport1, transport2, transport3 ); //calls your transport
- adios.Write( "TCPStream", group2, "myChars" , &myChars[0] ); //calls current transport
- adios.Close( streamName );
-
- adios.Write( streamName, group1, "myChars" , &myChars[0] ); //calls your transport
-
- adios.Open( group, "G", "write" ); //here open a stream called TCPStream for writing (w or write)
- adios.Write( group, "myCharsSize", &myCharsSize ); //calls your transport
- adios.Write( group, "myChars" , &myChars[0] ); //calls your transport
- adios.Close( "TCPStream" );
+ //Create group TCP and define variables
+ const std::string groupTCP( "TCP" );
+ adios.DeclareGroup( groupTCP );
+ adios.DefineVariable( groupTCP, "myCharsSize", "unsigned int" ); //scalar : group, name, type
+ adios.DefineVariable( groupTCP, "myChars", "char", "myCharsSize" ); //group, name, type, integer variables defining dimensions
+
+ //Open stream using two transports, DataMan is default, POSIX is an additional one
+ const std::string streamTCP( "TCP" );
+ adios.Open( streamTCP, "write", "DataMan" ); //here open a stream called TCPStream for writing (w or write), name is the same as stream
+ adios.AddTransport( streamTCP, "write", "POSIX", "name=TCP.bp" ); //add POSIX transport with .bp name
+
+ //Writing
+ adios.SetCurrentGroup( streamTCP, groupTCP ); //no need to add group field in Write
+ adios.Write( streamTCP, "myCharsSize", &myCharsSize );
+ adios.Write( streamTCP, "myChars", &myChars );
+ //Close
+ adios.Close( streamTCP ); // Flush to all transports, DataMan and POSIX
}
catch( std::bad_alloc& e )
{
@@ -99,6 +82,7 @@ int main( int argc, char* argv [] )
}
}
+ MPI_Finalize( );
return 0;
}
diff --git a/include/core/CCapsule.h b/include/core/CCapsule.h
index a8c7d2a8b15ed4f96faa9bc55d14c67507406ebe..b71a9e8fc0eb334247f2c88b9287bc1f4d38ccb1 100644
--- a/include/core/CCapsule.h
+++ b/include/core/CCapsule.h
@@ -95,7 +95,7 @@ public:
WriteToBuffer( data, size, transportIndex, m_Transports, m_MaxBufferSize, m_Buffer );
}
- void Close( int transportIndex ); ///< Closes current Transport
+ void Close( int transportIndex ); ///< Closes a particular transport
private:
diff --git a/include/core/CGroup.h b/include/core/CGroup.h
index 6a6d83ec634d8740e188a43aa932a9fdccf8b2db..695f094936ef207c4a9021a7fe64ae637eced84e 100644
--- a/include/core/CGroup.h
+++ b/include/core/CGroup.h
@@ -27,13 +27,13 @@
#include "core/SVariable.h"
#include "core/SAttribute.h"
#include "core/CTransport.h"
+#include "core/CTransform.h"
namespace adios
{
-
/**
- * Class that defines each ADIOS Group composed of Variables, Attributes and a Transport method
+ * Class that defines each ADIOS Group composed of Variables, Attributes and GlobalBounds (if global variables exist)
*/
class CGroup
{
@@ -44,17 +44,18 @@ public:
* @brief Constructor for XML config file
* @param hostLanguage reference from ADIOS class
* @param xmlGroup contains <adios-group (tag excluded)....</adios-group> single group definition from XML config file
+ * @param transforms passed from ADIOS.m_Transforms
* @param debugMode from ADIOS
*/
- CGroup( const std::string& hostLanguage, const std::string& xmlGroup, const bool debugMode );
-
+ CGroup( const std::string hostLanguage, const std::string& xmlGroup,
+ std::vector< std::shared_ptr<CTransform> >& transforms, const bool debugMode );
/**
* Non-XML empty constructor
* @param hostLanguage reference from ADIOS class
* @param debugMode
*/
- CGroup( const std::string& hostLanguage, const bool debugMode );
+ CGroup( const std::string hostLanguage, const bool debugMode );
~CGroup( ); ///< Using STL containers, no deallocation
@@ -69,7 +70,8 @@ public:
*/
void DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV );
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV,
+ const int transformIndex = -1, const int compressionLevel = 0 );
/**
* Sets a variable transform contained in ADIOS.m_Transforms (single container for all groups and variables)
@@ -95,15 +97,20 @@ public:
*/
void Monitor( std::ostream& logStream ) const;
+ /**
+ * Looks for variables defining a variable dimensions and return their actual values in a vector
+ * @param dimensionsCSV comma separated dimensions "Nx,Ny,Nz"
+ * @return actual vector values = { Nx, Ny, Nz }
+ */
+ std::vector<unsigned long long int> GetDimensions( const std::string dimensionsCSV ) const;
- std::vector<unsigned long long int> CGroup::GetDimensions( const std::string dimensionsCSV ) const;
unsigned long long int m_SerialSize = 0; ///< size used for potential serialization of metadata into a std::vector<char>. Counts sizes from m_Variables, m_Attributes, m_GlobalBounds
private:
- 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 std::string m_HostLanguage; ///< copy of ADIOS m_HostLanguage
const bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code, known at compile time
std::map< std::string, std::pair< std::string, unsigned int > > m_Variables; ///< Makes variable name unique, key: variable name, value: pair.first = type, pair.second = index in corresponding vector of CVariable
@@ -139,10 +146,7 @@ private:
* Called from XML constructor
* @param xmlGroup contains <adios-group....</adios-group> single group definition from XML config file passing by reference as it could be big
*/
- void ParseXMLGroup( const std::string& xmlGroup );
-
-
- const unsigned int CurrentTypeIndex( const std::string type ) const noexcept;
+ void ParseXMLGroup( const std::string& xmlGroup, std::vector< std::shared_ptr<CTransform> >& transforms );
/**
* Used by SetVariable and SetAttribute to check if global bounds exist in m_GlobalBounds
@@ -159,6 +163,13 @@ private:
*/
const int SetTransforms( const std::string transform ) noexcept;
+ /**
+ * Retrieves the value of a variable representing another's variable dimensions. Set with Write
+ * Must of integer type (from short to unsigned long long int) and positive.
+ * used by function GetDimensions
+ * @param variableName variable to be searched in m_SetVariables
+ * @return variable value
+ */
const unsigned long long int GetIntVariableValue( const std::string variableName ) const;
};
diff --git a/include/core/CTransform.h b/include/core/CTransform.h
index fcdef4ce36c520ac84388f31aaa66748251a6031..979e4545bfd39016d5352f67175dc046cdc96c10 100644
--- a/include/core/CTransform.h
+++ b/include/core/CTransform.h
@@ -41,9 +41,9 @@ public:
virtual ~CTransform( ){ };
- void Compress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut );
+ virtual void Compress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut ) = 0;
- void DeCompress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut );
+ virtual void Decompress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut ) = 0;
};
diff --git a/include/functions/ADIOSFunctions.h b/include/functions/ADIOSFunctions.h
index f6bd0e6e3b7fbaf0b1c290a4e17fc8ba737bd60c..ea077e643e68d7e507b32e8a7095beef2ba3c349 100644
--- a/include/functions/ADIOSFunctions.h
+++ b/include/functions/ADIOSFunctions.h
@@ -46,6 +46,7 @@ void DumpFileToStream( const std::string fileName, std::string& fileContents );
*/
void GetSubString ( const std::string initialTag, const std::string finalTag, const std::string content, std::string& subString,
std::string::size_type& currentPosition );
+
/**
* Extracts the value inside quotes in a string currentTag ( Example: currentTag --> field1="value1" field2="value2" )
* @param quote double " or single '
@@ -56,6 +57,7 @@ void GetSubString ( const std::string initialTag, const std::string finalTag, co
void GetQuotedValue( const char quote, const std::string::size_type& quotePosition,
std::string& currentTag, std::string& value );
+
/**
* Get attributes field1="value1" field2="value2" by looping through a single XML tag
* @param tag field0="value0" field1="value1" in a single string
@@ -73,6 +75,7 @@ void GetPairs( const std::string tag, std::vector< std::pair<const std::string,
void GetPairsFromTag( const std::string& fileContent, const std::string tag,
std::vector< std::pair<const std::string, const std::string> >& pairs );
+
/**
* Set members m_Groups and m_HostLanguage from XML file content, called within Init functions
* @param fileContent file Content in a single string
@@ -83,6 +86,7 @@ void GetPairsFromTag( const std::string& fileContent, const std::string tag,
void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, std::string& hostLanguage,
std::map< std::string, CGroup >& groups );
+
/**
* 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
@@ -92,8 +96,9 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, std::st
* @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, const bool debugMode, std::string& hostLanguage,
- std::map< std::string, CGroup >& groups );
+void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const bool debugMode,
+ std::string& hostLanguage, std::map< std::string, CGroup >& groups );
+
/**
* Loops through a vector containing dimensions and returns the product of all elements
@@ -113,17 +118,19 @@ void CreateDirectory( const std::string fullPath ) noexcept;
/**
- * Identifies a char* variable, assigns a reference to the proper variable, and sends data to capsule so it can write to buffer
- * @param group
- * @param variableName
- * @param values
- * @param capsule
+ * Identifies, verifies the corresponding transform method and adds it the transforms container if neccesary.
+ * This functions must be updated as new transform methods are supported.
+ * @param transform method to be added to transforms with format "method:compressionLevel", or "method" with compressionLevel=0 (default)
+ * @param transforms container of existing transform methods, owned by ADIOS class
+ * @param debugMode if true will do more checks, exceptions, warnings, expect slower code
+ * @param transformIndex returns the corresponding transformIndex in transforms for this transport method
+ * @param compressionLevel returns the corresponding compression level from transport = "method:compressionLevel"
*/
-void WriteChar( CGroup& group, const std::string variableName, const char* values, CCapsule& capsule );
-
-
+void SetTransformHelper( const std::string transform, std::vector< std::shared_ptr<CTransform> >& transforms,
+ const bool debugMode, int& transformIndex, int& compressionLevel );
+bool IsTypeAlias( const std::string type, const std::set<std::string>& types );
diff --git a/include/functions/ADIOSTemplates.h b/include/functions/ADIOSTemplates.h
index 25df2c21cc4817e8b08bb7721bf33adbae6ff2fb..858eccd95a82fe884bbf408e1460e566ddcd13fa 100644
--- a/include/functions/ADIOSTemplates.h
+++ b/include/functions/ADIOSTemplates.h
@@ -25,7 +25,7 @@ namespace adios
template<class T>
void WriteHelperToCapsule( CCapsule& capsule, CGroup& group, SVariable<T>& variable, const T* values,
- const unsigned int cores ) noexcept
+ const int transportIndex ) noexcept
{
variable.m_Values = values;
auto localDimensions = group.GetDimensions( variable.m_DimensionsCSV );
@@ -38,12 +38,11 @@ void WriteHelperToCapsule( CCapsule& capsule, CGroup& group, SVariable<T>& varia
}
else //write local variable
{
- capsule.Write( variable.m_Values, GetTotalSize( localDimensions ), cores );
+ capsule.Write( variable.m_Values, GetTotalSize( localDimensions ), transportIndex );
}
}
-
/**
* Helper function called from ADIOS Write template function. Checks variable type, adds to group.m_SetVariables,
* and calls corresponding Capsule virtual function.
@@ -53,10 +52,19 @@ void WriteHelperToCapsule( CCapsule& capsule, CGroup& group, SVariable<T>& varia
* @param capsule
*/
template<class T>
-void WriteHelper( CCapsule& capsule, CGroup& group, const std::string variableName, const T* values, const bool debugMode,
- const unsigned int cores )
+void WriteHelper( CCapsule& capsule, CGroup& group, const std::string variableName, const T* values,
+ const int transportIndex, const bool debugMode )
{
- //variable
+ auto lf_DebugType = []( const bool debugMode, const std::string type, const std::set<std::string>& typeAliases )
+ {
+ if( debugMode == true )
+ {
+ if( typeAliases.count( type ) == 0 )
+ throw std::invalid_argument( "ERROR: variable " + variableName + " is not of type " + type +
+ " in call to Write\n" );
+ }
+ };
+
const auto itVariable = group.m_Variables.find( variableName );
if( debugMode == true )
@@ -64,57 +72,77 @@ void WriteHelper( CCapsule& capsule, CGroup& group, const std::string variableNa
if( itVariable == group.m_Variables.end() )
throw std::invalid_argument( "ERROR: from Write function, variable " + variableName + " doesn't exist\n" );
}
+
const std::string type( itVariable->first );
const unsigned int index = itVariable->second;
group.m_SetVariables.insert( variableName ); //should be done before writing to buffer, in case there is a crash?
+ //will need to add a lambda function later and put types in a set
if( std::is_same<T,char>::value )
{
- if( debugMode == true )
- {
- if( type != "char" )
- throw std::invalid_argument( "ERROR: variable " + variableName + " is not char\n" );
- }
- WriteHelperToCapsule( capsule, group, group.m_Char[index], values, cores );
- }
-
-// else if( std::is_same<T,unsigned char>::value )
-// group.m_UChar[index].m_Values = values;
-//
-// else if( std::is_same<T,short>::value )
-// group.m_Short[index].m_Values = values;
-//
-// else if( std::is_same<T,unsigned short>::value )
-// group.m_UShort[index].m_Values = values;
-//
-// else if( std::is_same<T,int>::value )
-// group.m_Int[index].m_Values = values;
-//
-// else if( std::is_same<T,unsigned int>::value )
-// group.m_UInt[index].m_Values = values;
-//
-// else if( std::is_same<T,long int>::value )
-// group.m_LInt[index].m_Values = values;
-//
-// else if( std::is_same<T,unsigned long int>::value )
-// group.m_ULInt[index].m_Values = values;
-//
-// else if( std::is_same<T,long long int>::value )
-// group.m_LLInt[index].m_Values = values;
-//
-// else if( std::is_same<T,unsigned long long int>::value )
-// group.m_ULLInt[index].m_Values = values;
-//
-// else if( std::is_same<T,float>::value )
-// group.m_Float[index].m_Values = values;
-//
-// else if( std::is_same<T,double>::value )
-// group.m_Double[index].m_Values = values;
-//
-// else if( std::is_same<T,long double>::value )
-// group.m_LDouble[index].m_Values = values;
-
-
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("char") );
+ WriteHelperToCapsule( capsule, group, group.m_Char[index], values, transportIndex );
+ }
+ else if( std::is_same<T,unsigned char>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("unsigned char") );
+ WriteHelperToCapsule( capsule, group, group.m_UChar[index], values, transportIndex );
+ }
+ else if( std::is_same<T,short>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("short") );
+ WriteHelperToCapsule( capsule, group, group.m_Short[index], values, transportIndex );
+ }
+ else if( std::is_same<T,unsigned short>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("unsigned short") );
+ WriteHelperToCapsule( capsule, group, group.m_UShort[index], values, transportIndex );
+ }
+ else if( std::is_same<T,int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("int") );
+ WriteHelperToCapsule( capsule, group, group.m_Int[index], values, transportIndex );
+ }
+ else if( std::is_same<T,unsigned int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("unsigned int") );
+ WriteHelperToCapsule( capsule, group, group.m_UInt[index], values, transportIndex );
+ }
+ else if( std::is_same<T,long int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("long int") );
+ WriteHelperToCapsule( capsule, group, group.m_LInt[index], values, transportIndex );
+ }
+ else if( std::is_same<T,unsigned long int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("unsigned long int") );
+ WriteHelperToCapsule( capsule, group, group.m_ULInt[index], values, transportIndex );
+ }
+ else if( std::is_same<T,long long int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("long long int") );
+ WriteHelperToCapsule( capsule, group, group.m_LLInt[index], values, transportIndex );
+ }
+ else if( std::is_same<T,unsigned long long int>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("unsigned long long int") );
+ WriteHelperToCapsule( capsule, group, group.m_ULLInt[index], values, transportIndex );
+ }
+ else if( std::is_same<T,float>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("float") );
+ WriteHelperToCapsule( capsule, group, group.m_Float[index], values, transportIndex );
+ }
+ else if( std::is_same<T,double>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("double") );
+ WriteHelperToCapsule( capsule, group, group.m_Double[index], values, transportIndex );
+ }
+ else if( std::is_same<T,long double>::value )
+ {
+ lf_DebugType( debugMode, type, SSupport::DatatypesAliases.at("long double") );
+ WriteHelperToCapsule( capsule, group, group.m_LDouble[index], values, transportIndex );
+ }
}
diff --git a/include/public/ADIOS.h b/include/public/ADIOS.h
index 3fa2eaafc8c0391fa05d1e3f30e1857766726198..35fc2dabffb21e369d9e0a12c49b3dbb6d44cfbb 100644
--- a/include/public/ADIOS.h
+++ b/include/public/ADIOS.h
@@ -101,7 +101,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* Sets a new transport method to be associated with a current stream.
* @param streamName must be created with Open
* @param transport
- * @return
+ * @return transport index
*/
template< class... Args >
int AddTransport( const std::string streamName, const std::string accessMode, const std::string transport, Args... args )
@@ -132,7 +132,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
template<class T>
void Write( const std::string streamName, const std::string groupName, const std::string variableName, const T* values,
- const int transportIndex )
+ const int transportIndex = -1 )
{
auto itCapsule = m_Capsules.find( streamName );
auto itGroup = m_Groups.find( groupName );
@@ -141,9 +141,12 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
{
CheckCapsule( itCapsule, streamName, " from call to Write variable " + variableName );
CheckGroup( itGroup, groupName, " from call to Write variable " + variableName );
+ if( transportIndex < -1 )
+ throw std::invalid_argument( "ERROR: transport index " + std::to_string( transportIndex ) +
+ " must be >= -1, in call to Write\n" );
}
- WriteHelper( itCapsule->second, itGroup->second, variableName, values, m_DebugMode );
+ WriteHelper( itCapsule->second, itGroup->second, variableName, values, transportIndex, m_DebugMode );
}
@@ -157,7 +160,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
*/
template<class T>
void Write( const std::string streamName, const std::string variableName, const T* values,
- const int transportIndex )
+ const int transportIndex = -1 )
{
auto itCapsule = m_Capsules.find( streamName );
if( m_DebugMode == true )
@@ -168,7 +171,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
if( m_DebugMode == true )
CheckGroup( itGroup, groupName, " from call to Write variable " + variableName );
- WriteHelper( itCapsule->second, itGroup->second, variableName, values, m_DebugMode );
+ WriteHelper( itCapsule->second, itGroup->second, variableName, values, transportIndex, m_DebugMode );
}
/**
diff --git a/include/public/SSupport.h b/include/public/SSupport.h
index 6584f145ed557701a9e7da3df324f64956df7833..9b90c520fdbdeee8657592ce4f249ace42355ade 100644
--- a/include/public/SSupport.h
+++ b/include/public/SSupport.h
@@ -25,6 +25,7 @@ struct SSupport
static const std::set<std::string> Transports; ///< supported transport methods
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
+ static const std::map<std::string, std::set<std::string> > DatatypesAliases;
};
diff --git a/include/transform/CBZIP2.h b/include/transform/CBZIP2.h
index f71dc8240d354dbcb381471051737a448116e03b..4fac24a2551f3272388f2317fbaf3098a8ccc767 100644
--- a/include/transform/CBZIP2.h
+++ b/include/transform/CBZIP2.h
@@ -9,9 +9,6 @@
#define CBZIP2_H_
-#include <bzip2.h> //bzip2 library header
-
-
#include "core/CTransform.h"
@@ -33,33 +30,9 @@ public:
~CBZIP2( );
- void Compress( const SVariable<char>& variableIn, SVariable<char>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<unsigned char>& variableIn, SVariable<unsigned char>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<short>& variableIn, SVariable<short>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<unsigned short>& variableIn, SVariable<unsigned short>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<int>& variableIn, SVariable<int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<unsigned int>& variableIn, SVariable<unsigned int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<long int>& variableIn, SVariable<long int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<unsigned long int>& variableIn, SVariable<unsigned long int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<long long int>& variableIn, SVariable<long long int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<unsigned long long int>& variableIn, SVariable<unsigned long long int>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<float>& variableIn, SVariable<float>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<double>& variableIn, SVariable<double>& variableOut, const unsigned int level ) const;
- void Compress( const SVariable<long double>& variableIn, SVariable<long double>& variableOut, const unsigned int level ) const;
-
- void Decompress( const SVariable<char>& variableIn, SVariable<char>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<unsigned char>& variableIn, SVariable<unsigned char>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<short>& variableIn, SVariable<short>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<unsigned short>& variableIn, SVariable<unsigned short>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<int>& variableIn, SVariable<int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<unsigned int>& variableIn, SVariable<unsigned int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<long int>& variableIn, SVariable<long int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<unsigned long int>& variableIn, SVariable<unsigned long int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<long long int>& variableIn, SVariable<long long int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<unsigned long long int>& variableIn, SVariable<unsigned long long int>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<float>& variableIn, SVariable<float>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<double>& variableIn, SVariable<double>& variableOut, const unsigned int level ) const;
- void Decompress( const SVariable<long double>& variableIn, SVariable<long double>& variableOut, const unsigned int level ) const;
+ void Compress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut );
+
+ void Decompress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut );
};
diff --git a/src/core/CGroup.cpp b/src/core/CGroup.cpp
index 015271e483e99e5bb2555198a26e6ee604b086b0..f9485989bc73d2e2686f46c0f78deab640945835 100644
--- a/src/core/CGroup.cpp
+++ b/src/core/CGroup.cpp
@@ -20,17 +20,18 @@ namespace adios
{
-CGroup::CGroup( const std::string& hostLanguage, const bool debugMode ):
+CGroup::CGroup( const std::string hostLanguage, const bool debugMode ):
m_HostLanguage{ hostLanguage },
m_DebugMode{ debugMode }
{ }
-CGroup::CGroup( const std::string& hostLanguage, const std::string& xmlGroup, const bool debugMode ):
+CGroup::CGroup( const std::string hostLanguage, const std::string& xmlGroup,
+ std::vector< std::shared_ptr<CTransform> >& transforms, const bool debugMode ):
m_HostLanguage{ hostLanguage },
m_DebugMode{ debugMode }
{
- ParseXMLGroup( xmlGroup );
+ ParseXMLGroup( xmlGroup, transforms );
}
@@ -40,62 +41,86 @@ CGroup::~CGroup( )
void CGroup::DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV,
- const std::string globalDimensionsCSV, const std::string globalOffsetsCSV )
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV,
+ const int transformIndex, const int compressionLevel )
{
if( m_DebugMode == true )
{
if( SSupport::Datatypes.at( m_HostLanguage ).count( type ) == 0 )
- throw std::invalid_argument( "ERROR: type " + type + " for variable " + variableName + " is not supported.\n" );
- if( m_Variables.count( variableName ) == 0 ) //variable doesn't exists
- m_Variables[variableName] = std::make_pair( type, CurrentTypeIndex( type ) );
- else //name is found
- throw std::invalid_argument( "ERROR: variable " + variableName + " exists more than once.\n" );
- }
- else
- {
- m_Variables[variableName] = std::make_pair( type, CurrentTypeIndex( type ) );
+ throw std::invalid_argument( "ERROR: type " + type + " for variable " + variableName +
+ " is not supported, in call to DefineVariable\n" );
+
+ if( m_Variables.count( variableName ) == 1 )
+ throw std::invalid_argument( "ERROR: variable " + variableName + " already exists, in call to DefineVariable\n" );
}
int globalBoundsIndex = SetGlobalBounds( globalDimensionsCSV, globalOffsetsCSV );
- if( type == "char" || type == "character" )
- m_Char.push_back( SVariable<char>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "unsigned char" )
- m_UChar.push_back( SVariable<unsigned char>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "short" || type == "integer*2" )
- m_Short.push_back( SVariable<short>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "unsigned short" )
- m_UShort.push_back( SVariable<unsigned short>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "int" || type == "integer" )
- m_Int.push_back( SVariable<int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "unsigned int" || type == "unsigned integer" )
- m_UInt.push_back( SVariable<unsigned int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "long int" || type == "long" || type == "long integer" )
- m_LInt.push_back( SVariable<long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "unsigned long int" || type == "unsigned long" || type == "unsigned long integer" )
- m_ULInt.push_back( SVariable<unsigned long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "long long int" || type == "long long" || type == "long long integer" )
- m_LLInt.push_back( SVariable<long long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "unsigned long long int" || type == "unsigned long long" || type == "unsigned long long integer" )
- m_ULLInt.push_back( SVariable<unsigned long long int>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "float" || type == "real" || type == "real*4" )
- m_Float.push_back( SVariable<float>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "double" || type == "double precision" || type == "real*8" )
- m_Double.push_back( SVariable<double>{ dimensionsCSV, nullptr, globalBoundsIndex } );
-
- else if( type == "long double" || type == "real*16" )
- m_LDouble.push_back( SVariable<long double>{ dimensionsCSV, nullptr, globalBoundsIndex } );
+ if( IsTypeAlias( type, SSupport::DatatypesAliases.at("char") ) == true )
+ {
+ m_Char.push_back( SVariable<char>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_Char.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned char") ) == true )
+ {
+ m_UChar.push_back( SVariable<unsigned char>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_UChar.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("short") ) == true )
+ {
+ m_Short.push_back( SVariable<short>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_Short.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned short") ) == true )
+ {
+ m_UShort.push_back( SVariable<unsigned short>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_UShort.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("int") ) == true )
+ {
+ m_Int.push_back( SVariable<int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_Int.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned int") ) == true )
+ {
+ m_UInt.push_back( SVariable<unsigned int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_UInt.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long int") ) == true )
+ {
+ m_LInt.push_back( SVariable<long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_LInt.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long int") ) == true )
+ {
+ m_ULInt.push_back( SVariable<unsigned long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_ULInt.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long long int") ) == true )
+ {
+ m_LLInt.push_back( SVariable<long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_LLInt.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long long int") ) == true )
+ {
+ m_ULLInt.push_back( SVariable<unsigned long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_ULLInt.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("float") ) == true )
+ {
+ m_Float.push_back( SVariable<float>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_Float.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("double") ) == true )
+ {
+ m_Double.push_back( SVariable<double>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_Double.size()-1 );
+ }
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long double") ) == true )
+ {
+ m_LDouble.push_back( SVariable<long double>{ dimensionsCSV, nullptr, globalBoundsIndex, transformIndex, compressionLevel } );
+ m_Variables[variableName] = std::make_pair( type, m_LDouble.size()-1 );
+ }
m_SerialSize += variableName.size() + type.size() + dimensionsCSV.size() + 4 * sizeof( char ); //4, adding one more for globalBoundsIndex
}
@@ -114,67 +139,62 @@ void CGroup::SetTransform( const std::string variableName, const unsigned int tr
const std::string type( itVariable->second.first );
const unsigned int index = itVariable->second.second;
- if( type == "char" || type == "character" )
+ if( IsTypeAlias( type, SSupport::DatatypesAliases.at("char") ) == true )
{
m_Char[index].TransformIndex = transformIndex;
m_Char[index].CompressionLevel = compressionLevel;
}
- else if( type == "unsigned char" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned char") ) == true )
{
m_UChar[index].TransformIndex = transformIndex;
m_UChar[index].CompressionLevel = compressionLevel;
}
- else if( type == "short" || type == "integer*2" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("short") ) == true )
{
m_Short[index].TransformIndex = transformIndex;
m_Short[index].CompressionLevel = compressionLevel;
}
- else if( type == "unsigned short" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned short") ) == true )
{
m_UShort[index].TransformIndex = transformIndex;
m_UShort[index].CompressionLevel = compressionLevel;
}
- else if( type == "int" || type == "integer" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("int") ) == true )
{
m_Int[index].TransformIndex = transformIndex;
m_Int[index].CompressionLevel = compressionLevel;
}
- else if( type == "unsigned int" || type == "unsigned integer" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned int") ) == true )
{
m_UInt[index].TransformIndex = transformIndex;
m_UInt[index].CompressionLevel = compressionLevel;
}
- else if( type == "long int" || type == "long" || type == "long integer" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long int") ) == true )
{
m_LInt[index].TransformIndex = transformIndex;
m_LInt[index].CompressionLevel = compressionLevel;
}
- else if( type == "unsigned long int" || type == "unsigned long" || type == "unsigned long integer" )
- {
- m_ULInt[index].TransformIndex = transformIndex;
- m_ULInt[index].CompressionLevel = compressionLevel;
- }
- else if( type == "long long int" || type == "long long" || type == "long long integer" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long int") ) == true )
{
m_ULInt[index].TransformIndex = transformIndex;
m_ULInt[index].CompressionLevel = compressionLevel;
}
- else if( type == "unsigned long long int" || type == "unsigned long long" || type == "unsigned long long integer" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long long int") ) == true )
{
m_ULLInt[index].TransformIndex = transformIndex;
m_ULLInt[index].CompressionLevel = compressionLevel;
}
- else if( type == "float" || type == "real" || type == "real*4" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("float") ) == true )
{
m_Float[index].TransformIndex = transformIndex;
m_Float[index].CompressionLevel = compressionLevel;
}
- else if( type == "double" || type == "double precision" || type == "real*8" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("double") ) == true )
{
m_Double[index].TransformIndex = transformIndex;
m_Double[index].CompressionLevel = compressionLevel;
}
- else if( type == "long double" || type == "real*16" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long double") ) == true )
{
m_LDouble[index].TransformIndex = transformIndex;
m_LDouble[index].CompressionLevel = compressionLevel;
@@ -210,34 +230,40 @@ const unsigned long long int CGroup::GetIntVariableValue( const std::string vari
const std::string type( m_Variables.at( variableName ).first );
const unsigned int index = m_Variables.at( variableName ).second;
- const unsigned long long int value = 0;
+ const long long int value = -1;
- if( type == "short" )
+ if( IsTypeAlias( type, SSupport::DatatypesAliases.at("short") ) == true )
value = *( m_Short[index].Values );
- else if( type == "unsigned short" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned short") ) == true )
value = *( m_UShort[index].Values );
- else if( type == "int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("int") ) == true )
value = *( m_Int[index].Values );
- else if( type == "unsigned int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned int") ) == true )
value = *( m_UInt[index].Values );
- else if( type == "long int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long int") ) == true )
value = *( m_LInt[index].Values );
- else if( type == "unsigned long int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long int") ) == true )
value = *( m_ULInt[index].Values );
- else if( type == "long long int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("long long int") ) == true )
value = *( m_LLInt[index].Values );
- else if( type == "unsigned long long int" )
+ else if( IsTypeAlias( type, SSupport::DatatypesAliases.at("unsigned long long int") ) == true )
value = *( m_ULLInt[index].Values );
else
- throw std::invalid_argument( "ERROR: variable " + variableName + " must be of short, int or associated type (long int, unsigned long int, etc.)\n" );
+ throw std::invalid_argument( "ERROR: variable " + variableName + " must be of integer type : short, int or associated type (long int, unsigned long int, etc.)\n" );
+
+ if( m_DebugMode == true )
+ {
+ if( value <= 0 )
+ throw std::invalid_argument( "ERROR: variable " + variableName + " must be >= 0 to represent a dimension\n" );
+ }
return value;
}
@@ -256,7 +282,7 @@ std::vector<unsigned long long int> CGroup::GetDimensions( const std::string dim
std::istringstream dimensionsSS( dimensionsCSV );
std::string dimension;
- while( std::getline( dimensionsSS, dimension, ',' ) )
+ while( std::getline( dimensionsSS, dimension, ',' ) ) //need to test
{
dimensions.push_back( GetIntVariableValue( dimension ) );
}
@@ -284,7 +310,7 @@ void CGroup::Monitor( std::ostream& logStream ) const
}
-void CGroup::ParseXMLGroup( const std::string& xmlGroup )
+void CGroup::ParseXMLGroup( const std::string& xmlGroup, std::vector< std::shared_ptr<CTransform> >& transforms )
{
std::string::size_type currentPosition( 0 );
std::string globalDimensionsCSV; //used to set variables
@@ -328,7 +354,14 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup )
else if( pair.first == "dimensions" ) dimensionsCSV = pair.second;
else if( pair.first == "transform" ) transform = pair.second;
}
- DefineVariable( name, type, dimensionsCSV, globalDimensionsCSV, globalOffsetsCSV );
+
+ int transformIndex = -1;
+ int compressionLevel = 0;
+
+ if( transform.empty() == false ) //if transform is present
+ SetTransformHelper( transform, transforms, m_DebugMode, transformIndex, compressionLevel );
+
+ DefineVariable( name, type, dimensionsCSV, globalDimensionsCSV, globalOffsetsCSV, transformIndex, compressionLevel );
}
else if( tagName == "attribute" )
{
@@ -364,53 +397,6 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup )
}
-const unsigned int CGroup::CurrentTypeIndex( const std::string type ) const noexcept
-{
- unsigned int index;
-
- if( type == "char" || type == "character" )
- index = m_Char.size();
-
- else if( type == "unsigned char" )
- index = m_UChar.size();
-
- else if( type == "short" || type == "integer*2" )
- index = m_Short.size();
-
- else if( type == "unsigned short" )
- index = m_UShort.size();
-
- else if( type == "int" || type == "integer" )
- index = m_Int.size();
-
- else if( type == "unsigned int" || type == "unsigned integer" )
- index = m_UInt.size();
-
- else if( type == "long int" || type == "long" || type == "long integer" )
- index = m_LInt.size();
-
- else if( type == "unsigned long int" || type == "unsigned long" || type == "unsigned long integer" )
- index = m_ULInt.size();
-
- else if( type == "long long int" || type == "long long" || type == "long long integer" )
- index = m_LLInt.size();
-
- else if( type == "unsigned long long int" || type == "unsigned long long" || type == "unsigned long long integer" )
- index = m_ULLInt.size();
-
- else if( type == "float" || type == "real" || type == "real*4" )
- index = m_Float.size();
-
- else if( type == "double" || type == "double precision" || type == "real*8" )
- index = m_Double.size();
-
- else if( type == "long double" || type == "real*16" )
- index = m_LDouble.size();
-
- return index;
-}
-
-
const int CGroup::SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept
{
if( globalDimensionsCSV.empty() || globalOffsetsCSV.empty() )
diff --git a/src/functions/ADIOSFunctions.cpp b/src/functions/ADIOSFunctions.cpp
index 8c059b2b4077727139a01801abea5a8a4c767704..8f8fef3ac757e3e7f6517796311f1f5eda05144d 100644
--- a/src/functions/ADIOSFunctions.cpp
+++ b/src/functions/ADIOSFunctions.cpp
@@ -284,6 +284,7 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, const b
}
};
+ //this section will have to change, doing nothing for now
currentPosition = 0;
while( currentPosition != std::string::npos )
{
@@ -312,8 +313,6 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, const b
int priority, iteration;
lf_UIntCheck( method, priorityStr, "priority", debugMode, priority );
lf_UIntCheck( method, iterationStr, "iteration", debugMode, iteration );
-
- itGroup->second.m_Transport = method;
//here do something with the capsule
}
}
@@ -396,59 +395,54 @@ void CreateDirectory( const std::string fullPath ) noexcept
}
-
-//Write helper functions
-void WriteChar( CGroup& group, const std::string variableName, const char* values, CCapsule& capsule, const unsigned int cores )
+void SetTransformHelper( const std::string transform, std::vector< std::shared_ptr<CTransform> >& transforms,
+ const bool debugMode, int& transformIndex, int& compressionLevel )
{
- if( group.m_DebugMode == true )
+ //get method:compressionLevel from transform
+ std::string method( transform ); //default
+ compressionLevel = 0; //default
+
+ auto colonPosition = transform.find( ":" );
+
+ if( colonPosition != transform.npos )
{
- const std::string type( group.m_Variables.at( variableName ).first );
- if( type != "char" )
- throw std::invalid_argument( "ERROR: variable " + variableName + " is not char\n" );
- }
+ if( debugMode == true )
+ {
+ if( colonPosition == transform.size() - 1 )
+ throw std::invalid_argument( "ERROR: wrong format for transform " + transform + ", in call to SetTransform\n" );
+ }
- const unsigned int index = group.m_Variables.at( variableName ).second;
- SVariable<char>& variable = group.m_Char[index];
- variable.m_Values = values;
- auto localDimensions = group.GetDimensions( variable.m_DimensionsCSV );
+ method = transform.substr( 0, colonPosition );
+ compressionLevel = std::stoi( transform.substr( colonPosition+1 ) ); //need to test
+ }
- if( variable.m_GlobalBoundsIndex > -1 ) //global variable
+ transformIndex = -1;
+ for( unsigned int i = 0; i < transforms.size(); ++i )
{
- auto globalDimensions = group.GetDimensions( group.m_GlobalBounds[ variable.m_GlobalBoundsIndex ].first );
- auto globalOffsets = group.GetDimensions( group.m_GlobalBounds[ variable.m_GlobalBoundsIndex ].second );
- //capsule.Write( group.m_StreamName, variable.m_Values, sizeof(char), localDimensions, globalDimensions, globalOffsets );
+ if( transforms[i]->m_Method == transform )
+ {
+ transformIndex = i;
+ break;
+ }
}
- else //write local variable
+
+ if( transformIndex == -1 ) //not found, then create a new transform
{
- capsule.Write( group.m_StreamName, variable.m_Values, GetTotalSize( localDimensions ), cores );
+ if( transform == "bzip2" )
+ transforms.push_back( std::make_shared<CBZIP2>( ) );
}
+
+ transformIndex = static_cast<int>( transforms.size() - 1 );
}
-void WriteUChar( CGroup& group, const std::string variableName, const char* values, CCapsule& capsule, const unsigned int cores )
+bool IsTypeAlias( const std::string type, const std::set<std::string>& types )
{
- if( group.m_DebugMode == true )
- {
- const std::string type( group.m_Variables.at( variableName ).first );
- if( type != "unsigned char" )
- throw std::invalid_argument( "ERROR: variable " + variableName + " is not char\n" );
- }
+ bool isAlias = false;
+ if( types.count( type ) == 1 )
+ isAlias = true;
- const unsigned int index = group.m_Variables.at( variableName ).second;
- SVariable<unsigned char>& variable = group.m_UChar[index];
- variable.m_Values = values;
- auto localDimensions = group.GetDimensions( variable.m_DimensionsCSV );
-
- if( variable.m_GlobalBoundsIndex > -1 ) //global variable
- {
- auto globalDimensions = group.GetDimensions( group.m_GlobalBounds[ variable.m_GlobalBoundsIndex ].first );
- auto globalOffsets = group.GetDimensions( group.m_GlobalBounds[ variable.m_GlobalBoundsIndex ].second );
- //capsule.Write( group.m_StreamName, variable.m_Values, sizeof(char), localDimensions, globalDimensions, globalOffsets );
- }
- else //write local variable
- {
- capsule.Write( group.m_StreamName, variable.m_Values, GetTotalSize( localDimensions ), cores );
- }
+ return isAlias;
}
diff --git a/src/public/ADIOS.cpp b/src/public/ADIOS.cpp
index 961d1d8e213ef8587cd27b0e7efde3a1b1faa790..bb8027c5b1ebf83151e9ddc8805e8c24ef29f21d 100644
--- a/src/public/ADIOS.cpp
+++ b/src/public/ADIOS.cpp
@@ -122,52 +122,18 @@ void ADIOS::SetTransform( const std::string groupName, const std::string variabl
CheckGroup( itGroup, groupName, " from call to SetTransform \n" );
if( SSupport::Transforms.count( transform ) == 0 )
- throw std::invalid_argument( "ERROR: transform method " + transform + " not supported, in call to SetTransform\n" );
- }
-
- //get method:compressionLevel from transform
- std::string method( transform );
- int compressionLevel = 0;
-
- auto colonPosition = transform.find( ":" );
-
- if( colonPosition != transform.npos )
- {
- if( m_DebugMode == true )
- {
- if( colonPosition == transform.size() - 1 )
- throw std::invalid_argument( "ERROR: wrong format for transform " + transform + ", in call to SetTransform\n" );
- }
-
- method = transform.substr( 0, colonPosition );
- compressionLevel = std::stoi( transform.substr( colonPosition+1 ) );
- }
-
- int transformIndex = -1;
- for( unsigned int i = 0; i < m_Transforms.size(); ++i )
- {
- if( m_Transforms[i]->m_Method == transform )
- {
- transformIndex = i;
- break;
- }
- }
-
- if( transformIndex == -1 ) //not found, then create a new transform
- {
- if( transform == "bzip2" )
- {
- m_Transforms.push_back( std::make_shared<CBZIP2>( ) );
- }
+ throw std::invalid_argument( "ERROR: transform method " + transform +
+ " not supported, in call to SetTransform\n" );
}
+ int transformIndex, compressionLevel;
+ //set m_Transforms, transformIndex, compressionLevel
+ SetTransformHelper( transform, m_Transforms, m_DebugMode, transformIndex, compressionLevel );
+ //set Variable with transformIndex, compressionLevel
itGroup->second.SetTransform( variableName, transformIndex, compressionLevel );
}
-
-
-
void ADIOS::DefineAttribute( const std::string groupName, const std::string attributeName,
const std::string type, const std::string value )
diff --git a/src/public/SSupport.cpp b/src/public/SSupport.cpp
index b0a2d38084a14dab88f4cc032d35138df8e41097..893e28fc519ada6be0a9beff44b64bb8e69a8dd5 100644
--- a/src/public/SSupport.cpp
+++ b/src/public/SSupport.cpp
@@ -85,6 +85,23 @@ const std::map<std::string, std::set<std::string> > SSupport::Datatypes
};
+const std::map<std::string, std::set<std::string> > SSupport::DatatypesAliases
+{
+ { "char", { "char", "character" } },
+ { "unsigned char", { "unsigned char", "unsigned character" } },
+ { "short", { "short", "integer*2" } },
+ { "unsigned short", { "unsigned short" } },
+ { "int", { "int", "integer" } },
+ { "unsigned int", { "unsigned int", "unsigned integer" } },
+ { "long int", { "long int", "long", "long integer" } },
+ { "unsigned long int", { "unsigned long int", "unsigned long", "unsigned long integer" } },
+ { "long long int", { "long long int", "long long", "long long integer" } },
+ { "unsigned long long int", { "unsigned long long int", "unsigned long long", "unsigned long long integer" } },
+ { "float", { "float", "real", "real*4" } },
+ { "double", { "double", "double precision", "real*8" } },
+ { "long double", { "long double", "long double precision", "real*16" } }
+};
+
} //end namespace
diff --git a/src/transform/CBZIP2.cpp b/src/transform/CBZIP2.cpp
index 4678fb0a33c3fb74ef95400fd1afffd2e94d5494..23d32c495fcb2a5a333dd24c93ba6c35d7405965 100644
--- a/src/transform/CBZIP2.cpp
+++ b/src/transform/CBZIP2.cpp
@@ -15,7 +15,8 @@ namespace adios
{
-CBZIP2::CBZIP2( )
+CBZIP2::CBZIP2( ):
+ CTransform( "bzip2" )
{ }
@@ -23,108 +24,18 @@ CBZIP2::~CBZIP2( )
{ }
-void CBZIP2::Compress( const SVariable<char>& variableIn, SVariable<char>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<unsigned char>& variableIn, SVariable<unsigned char>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<short>& variableIn, SVariable<short>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<unsigned short>& variableIn, SVariable<unsigned short>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<int>& variableIn, SVariable<int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<unsigned int>& variableIn, SVariable<unsigned int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<long int>& variableIn, SVariable<long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<unsigned long int>& variableIn, SVariable<unsigned long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<long long int>& variableIn, SVariable<long long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<unsigned long long int>& variableIn, SVariable<unsigned long long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<float>& variableIn, SVariable<float>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<double>& variableIn, SVariable<double>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Compress( const SVariable<long double>& variableIn, SVariable<long double>& variableOut, const unsigned int level ) const
-{ }
-
-//DECOMPRESS
-void CBZIP2::Decompress( const SVariable<char>& variableIn, SVariable<char>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<unsigned char>& variableIn, SVariable<unsigned char>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<short>& variableIn, SVariable<short>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<unsigned short>& variableIn, SVariable<unsigned short>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<int>& variableIn, SVariable<int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<unsigned int>& variableIn, SVariable<unsigned int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<long int>& variableIn, SVariable<long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<unsigned long int>& variableIn, SVariable<unsigned long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<long long int>& variableIn, SVariable<long long int>& variableOut, const unsigned int level ) const
-{ }
-
-
-void CBZIP2::Decompress( const SVariable<unsigned long long int>& variableIn, SVariable<unsigned long long int>& variableOut, const unsigned int level ) const
-{ }
+void CBZIP2::Compress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut )
+{
-void CBZIP2::Decompress( const SVariable<float>& variableIn, SVariable<float>& variableOut, const unsigned int level ) const
-{ }
+}
-void CBZIP2::Decompress( const SVariable<double>& variableIn, SVariable<double>& variableOut, const unsigned int level ) const
-{ }
+void CBZIP2::Decompress( const std::vector<char>& bufferIn, std::vector<char>& bufferOut )
+{
+}
-void CBZIP2::Decompress( const SVariable<long double>& variableIn, SVariable<long double>& variableOut, const unsigned int level ) const
-{ }
} //end namespace