From 52d0a7a6125d9cb91b3e5a9361c99be64d8b190a Mon Sep 17 00:00:00 2001
From: wfg <wfg@pc0098504.ornl.gov>
Date: Fri, 11 Nov 2016 18:03:02 -0500
Subject: [PATCH] Continue working with API changes
---
include/capsule/CBoostInterprocess.h | 12 +++++++++-
include/capsule/CEmptyCapsule.h | 6 ++---
include/core/CCapsule.h | 26 ++++++++++++++-------
include/core/CGroup.h | 4 ++--
include/public/ADIOS.h | 33 +++++++++++++++++++++++----
src/core/CCapsule.cpp | 27 ++++++++++++++++++++++
src/public/ADIOS.cpp | 34 +++++++++++++++++++++++++---
7 files changed, 121 insertions(+), 21 deletions(-)
create mode 100644 src/core/CCapsule.cpp
diff --git a/include/capsule/CBoostInterprocess.h b/include/capsule/CBoostInterprocess.h
index 427426d8e..24407c948 100644
--- a/include/capsule/CBoostInterprocess.h
+++ b/include/capsule/CBoostInterprocess.h
@@ -42,7 +42,17 @@ public:
template< class T>
- void WriteVariableToBuffer( const CGroup& group, const SVariable<T>& variable );
+ void WriteVariableToBuffer( const CGroup& group, const SVariable<T>& variable )
+ {
+// while
+// {
+//
+// send
+// receive status
+// if( status )
+// switch Transport
+// }
+ }
/**
* Closes the buffer and moves it into the
diff --git a/include/capsule/CEmptyCapsule.h b/include/capsule/CEmptyCapsule.h
index 332600fb8..dadaf9b9a 100644
--- a/include/capsule/CEmptyCapsule.h
+++ b/include/capsule/CEmptyCapsule.h
@@ -8,6 +8,9 @@
#ifndef CEMPTYCAPSULE_H_
#define CEMPTYCAPSULE_H_
+#include "core/CCapsule.h"
+
+
namespace adios
{
@@ -30,9 +33,6 @@ public:
void OpenGroupBuffer( const CGroup& group );
-
- void WriteVariableToBuffer( const CGroup& group, const SVariable<T>& variable );
-
/**
* Closes the buffer and moves it into the
* @param group
diff --git a/include/core/CCapsule.h b/include/core/CCapsule.h
index d926f9ce7..b078b32cb 100644
--- a/include/core/CCapsule.h
+++ b/include/core/CCapsule.h
@@ -39,21 +39,22 @@ public:
MPI_Comm m_MPIComm = 0; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
#endif
- unsigned long int m_BufferSize; ///< buffer size
- std::vector<char> m_Buffer; ///< buffer to be managed, just one type for now
+ std::map< std::string, std::vector<char> > m_Buffer; ///< buffer to be managed, just one type for now
std::map< std::string, std::shared_ptr<CTransform> > m_Transforms; ///< transforms associated with ADIOS run
std::map< std::string, std::shared_ptr<CTransport> > m_Transports; ///< transports associated with ADIOS run
/**
* Unique constructor
* @param mpiComm communicator passed from ADIOS
+ * @param bufferSize passed by the user
*/
- CCapsule( const MPI_Comm mpiComm, const unsigned long int bufferSize ):
- m_MPIComm{ mpiComm },
- m_BufferSize{ bufferSize }
- { }
+ CCapsule( const MPI_Comm mpiComm, const unsigned long int bufferSize );
- virtual ~CCapsule( ){ };
+ virtual ~CCapsule( );
+
+ void CreateTransform( const std::string transform );
+
+ void CreateTransport( const std::string transport );
/**
* This will add to the m_Transports and m_Transforms map
@@ -61,10 +62,19 @@ public:
*/
void OpenGroupBuffer( const CGroup& group ) = 0;
- virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<char>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned char>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<short>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned short>& variable );
virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<long int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned long int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<long long int>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<unsigned long long int>& variable );
virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<float>& variable );
virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<double>& variable );
+ virtual void WriteVariableToBuffer( const CGroup& group, const SVariable<long double>& variable );
/**
* Closes the buffer and moves it into the
diff --git a/include/core/CGroup.h b/include/core/CGroup.h
index c94f99c15..061c535a9 100644
--- a/include/core/CGroup.h
+++ b/include/core/CGroup.h
@@ -143,7 +143,7 @@ private:
std::string m_Transport; ///< current transport method associated with this group
std::string m_BufferName; ///< associated buffer (file, stream, vector, etc.) if the Group is opened.
- std::string m_AccessMode; /// associated access mode for associated buffer from m_BufferName
+ std::string m_AccessMode; ///< associated access mode for associated buffer from m_BufferName
unsigned long int m_SerialSize; ///< size used for potential serialization of metadata into a std::vector<char>. Counts sizes from m_Variables, m_Attributes, m_GlobalBounds
@@ -160,7 +160,7 @@ private:
* Used by SetVariable and SetAttribute to check if global bounds exist in m_GlobalBounds
* @param globalDimensionsCSV comma separated variables defining global dimensions (e.g. "Nx,NY,Nz")
* @param globalOffsetsCSV comma separated variables defining global offsets (e.g. "oNx,oNY,oNz")
- * @return -1 if not global -> both inputs are empty, otherwise index in m_GlobalBounds if exist or create a new element in m_GlobalBounds;
+ * @return -1 if not global --> both inputs are empty, otherwise index in m_GlobalBounds if exist or create a new element in m_GlobalBounds;
*/
const int SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept;
diff --git a/include/public/ADIOS.h b/include/public/ADIOS.h
index 97a8e4519..52e58ef0c 100644
--- a/include/public/ADIOS.h
+++ b/include/public/ADIOS.h
@@ -42,11 +42,13 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
MPI_Comm m_MPIComm = 0; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
#endif
+
/**
* @brief ADIOS empty constructor. Used for non XML config file API calls.
*/
ADIOS( );
+
/**
* @brief Serial constructor for XML config file
* @param xmlConfigFile passed to m_XMLConfigFile
@@ -54,6 +56,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
*/
ADIOS( const std::string xmlConfigFile, const bool debugMode = false );
+
/**
* @brief Parallel constructor for XML config file and MPI
* @param xmlConfigFile passed to m_XMLConfigFile
@@ -73,6 +76,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
~ADIOS( ); ///< virtual destructor overriden by children's own destructors
+
/**
* @brief Open or Append to an output file
* @param groupName should match an existing group from XML file or created through CreateGroup
@@ -81,13 +85,15 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
*/
void Open( const std::string groupName, const std::string fileName, const std::string accessMode = "w" );
+
/**
* Submits a data element values for writing and associates it with the given variableName
* @param groupName name of group that owns the variable
* @param variableName name of existing scalar or vector variable in the XML file or created with CreateVariable
* @param values pointer to the variable values passed from the user application, use dynamic_cast to check that pointer is of the same value type
*/
- void Write( const std::string groupName, const std::string variableName, T* values )
+ template< class T>
+ void Write( const std::string groupName, const std::string variableName, const T* values )
{
auto itGroup = m_Groups.find( groupName );
if( m_DebugMode == true )
@@ -100,12 +106,14 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
WriteVariable( variableName, values, itGroup->second, m_Capsule );
}
+
/**
* Close a particular group, group will be out of scope and destroyed
* @param groupName group to be closed
*/
void Close( const std::string groupName );
+
/**
* @brief Dumps groups information to a file stream or standard output.
* Note that either the user closes this fileStream or it's closed at the end.
@@ -114,10 +122,27 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
void MonitorGroups( std::ostream& logStream ) const;
+ /**
+ * @brief Create a new group or replace an existing one
+ * @param groupName unique name
+ * @param transport transport method
+ * @param streamFile
+ */
+ void CreateGroup( const std::string groupName, const std::string transport = "" );
+
+
+ void CreateVariable( const std::string groupName, const std::string variableName, const std::string type,
+ const std::string dimensionsCSV = "", const std::string transform = "",
+ const std::string globalDimensionsCSV = "", const std::string globalOffsetsCSV = "" );
+
+ void CreateAttribute( const std::string groupName, const std::string attributeName,
+ const std::string type, const std::string value,
+ const std::string globalDimensionsCSV = "", const std::string globalOffsetsCSV = "" );
+
+
private:
std::string m_XMLConfigFile; ///< XML File to be read containing configuration information
-
std::string m_HostLanguage = "C++"; ///< Supported languages: C, C++, Fortran, Python, etc.
bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code
@@ -138,10 +163,10 @@ private:
* ADIOS will allocate two separate buffers each with the specified maximum limit.
* Default = 0 means there is no limit
*/
- unsigned int MaxBufferSizeInMB = 0;
+ unsigned long int MaxBufferSizeInMB = 0;
/**
- * Checks for group existence in m_Groups, if failed throws std::invalid_argument exception
+ * @brief Checks for group existence in m_Groups, if failed throws std::invalid_argument exception
* @param itGroup group iterator, usually from find function
* @param groupName passed for thrown exception only
* @param hint adds information to thrown exception
diff --git a/src/core/CCapsule.cpp b/src/core/CCapsule.cpp
new file mode 100644
index 000000000..9bcbbeafe
--- /dev/null
+++ b/src/core/CCapsule.cpp
@@ -0,0 +1,27 @@
+/*
+ * CCapsule.cpp
+ *
+ * Created on: Nov 11, 2016
+ * Author: wfg
+ */
+
+#include "core/CCapsule.h"
+
+
+namespace adios
+{
+
+CCapsule::CCapsule( const MPI_Comm mpiComm, const unsigned long int bufferSize ):
+ m_MPIComm{ mpiComm },
+ m_BufferSize{ bufferSize }
+{ }
+
+
+CCapsule::~CCapsule( )
+{ }
+
+
+
+
+
+}
diff --git a/src/public/ADIOS.cpp b/src/public/ADIOS.cpp
index b22826238..16c47091a 100644
--- a/src/public/ADIOS.cpp
+++ b/src/public/ADIOS.cpp
@@ -46,14 +46,27 @@ ADIOS::~ADIOS( )
{ }
+void ADIOS::CreateGroup( const std::string groupName, const std::string transport )
+{
+ if( m_DebugMode == true )
+ {
+ if( m_Groups.find( groupName ) != m_Groups.end() )
+ throw std::invalid_argument( "ERROR: group " + groupName + " already exist, from call to CreateGroup\n" );
+ }
+
+ m_Groups.emplace( groupName, CGroup( m_HostLanguage, m_DebugMode ) );
+}
+
+
+
void ADIOS::Open( const std::string groupName, const std::string fileName, const std::string accessMode )
{
auto itGroup = m_Groups.find( groupName );
+
if( m_DebugMode == true )
CheckGroup( itGroup, groupName, " from call to Open with file " + fileName );
itGroup->second.Open( fileName, accessMode );
-
}
@@ -68,12 +81,27 @@ void ADIOS::Close( const std::string groupName )
throw std::invalid_argument( "ERROR: group " + groupName + " is not open in Write function.\n" );
}
- m_Capsule.CloseGroupBuffer( itGroup->second );
-
+ m_Capsule->CloseGroupBuffer( itGroup->second );
itGroup->second.Close( );
}
+void ADIOS::CreateVariable( const std::string groupName, const std::string variableName, const std::string type,
+ const std::string dimensionsCSV, const std::string transform,
+ const std::string globalDimensionsCSV, const std::string globalOffsetsCSV )
+{
+ auto itGroup = m_Groups.find( groupName );
+ if( m_DebugMode == true )
+ {
+ CheckGroup( itGroup, groupName, " from call to CreateVariable \n" );
+ }
+
+ itGroup->second.CreateVariable( variableName, type, dimensionsCSV, transform, globalDimensionsCSV, globalOffsetsCSV );
+
+
+
+}
+
void ADIOS::MonitorGroups( std::ostream& logStream ) const
{
for( auto& groupPair : m_Groups )
--
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