From eab9abecc6590ff7cddd9465f37c07037fe3c02e Mon Sep 17 00:00:00 2001
From: wfg <wfg@pc0098504.ornl.gov>
Date: Mon, 3 Oct 2016 17:01:59 -0400
Subject: [PATCH] Redesign to separate MPI and noMPI code
To do:
1) Test Makefile with and without MPI
---
doc/CodingGuidelines | 32 ++++++------
include/ADIOS.h | 86 +++++++++++++++++++++++++++++++++
include/CADIOS.h | 70 ---------------------------
include/CFile.h | 52 ++++++++++++++++++++
include/SMetadata.h | 4 +-
include/file_mpi/CFileMPI.h | 48 ++++++++++++++++++
include/file_nompi/CFileNoMPI.h | 44 +++++++++++++++++
src/{CADIOS.cpp => ADIOS.cpp} | 0
8 files changed, 249 insertions(+), 87 deletions(-)
create mode 100644 include/ADIOS.h
delete mode 100644 include/CADIOS.h
create mode 100644 include/CFile.h
create mode 100644 include/file_mpi/CFileMPI.h
create mode 100644 include/file_nompi/CFileNoMPI.h
rename src/{CADIOS.cpp => ADIOS.cpp} (100%)
diff --git a/doc/CodingGuidelines b/doc/CodingGuidelines
index 3a03572fa..724365f30 100644
--- a/doc/CodingGuidelines
+++ b/doc/CodingGuidelines
@@ -10,10 +10,10 @@ Many items from this list are taken from Stroustrup, Sutter, and Meyers books.
Objectives:
1) Improve collaboration:
- 1.a. Reduce new code development and integration times for developers and users, by making code easy to understand
- 1.b. Allocate more time for discussion and pathfinding rather than understanding developers' coding
- 1.c. Expand developers and users base
-
+ 1.a. Reduce new code development and integration times for developers and users, by making code easy to understand
+ 1.b. Allocate more time for discussion and pathfinding rather than understanding developers' coding
+ 1.c. Expand developers and users base
+
2) Execute new ideas faster
3) Allocate more time to research and publication from new ideas
@@ -47,23 +47,23 @@ Text style for readability (Coding format setup in Eclipse with Window > Prefere
5) Brackets: use an extra space for brackets
- Do:
- if( number < 1 )
- {
- number = 4;
- ...
- }
-
- Don't:
- if( number < 1 ){
- number = 4; .....
+ Do:
+ if( number < 1 )
+ {
+ number = 4;
+ ...
+ }
+
+ Don't:
+ if( number < 1 ){
+ number = 4; .....
.....}
-
+
6) Prefer the keyword "using" over "typedef". Only rename complex types, do not rename standard types (int, double, std::vector)
Don't: typedef std::vector<std::vector<double>> Vector2D;
Do: using std::vector<std::vector<double>> = Vector2D;
-
+
Documentation/Comments
1) Use Doxygen as the official API documentation tool. Eclipse has a template autocomplete option for function declarations.
diff --git a/include/ADIOS.h b/include/ADIOS.h
new file mode 100644
index 000000000..cf471d2b4
--- /dev/null
+++ b/include/ADIOS.h
@@ -0,0 +1,86 @@
+/*
+ * ADIOS.h
+ *
+ * Created on: Oct 3, 2016
+ * Author: wfg
+ */
+
+#ifndef ADIOS_H_
+#define ADIOS_H_
+
+#include <string>
+#include <memory>
+
+//#ifdef USE_MPI
+#include <mpi.h>
+//#endif
+
+#include "SMetadata.h"
+
+
+namespace adios
+{
+/**
+ * Class ADIOS, interface between user call and ADIOS library
+ */
+class ADIOS
+{
+
+public: // can be accessed by anyone
+
+ std::string m_XMLConfigFile; ///< XML File to be read containing configuration information
+ bool m_IsUsingMPI = false; ///< bool flag false: sequential, true: parallel MPI, to be checked instead of communicator
+ std::unique_ptr<CFile> m_File;
+
+ ADIOS( ); ///< empty constructor, to be defined. Since we have an empty constructor we can't have const variables not defined by this constructor
+
+ /**
+ * Serial constructor for XML config file
+ * @param xmlConfigFile passed to m_XMLConfigFile
+ */
+ ADIOS( const std::string xmlConfigFile );
+
+ //#ifdef USE_MPI //MPI only section
+ MPI_Comm* m_MPIComm = nullptr; ///< only used as reference to MPI communicator passed from parallel constructor, using pointer instead of reference as null is a possible value
+ /**
+ * Parallel constructor for XML config file and MPI
+ * @param xmlConfigFile passed to m_XMLConfigFile
+ * @param mpiComm MPI communicator ...const to be discussed
+ */
+ ADIOS( const std::string xmlConfigFile, const MPI_Comm& mpiComm );
+
+ /**
+ * Parallel MPI communicator without XML config
+ * @param mpiComm MPI communicator passed to m_MPIComm ...const to be discussed
+ */
+ ADIOS( const MPI_Comm& mpiComm );
+ //#endif //MPI only section
+
+ virtual ~ADIOS( ); ///< virtual destructor overriden by children's own destructors
+
+ virtual void Init( ) = 0; ///< calls to read XML file among other initialization tasks
+
+private:
+
+ SMetadata m_Metadata; ///< contains all metadata information from XML Config File
+ bool m_IsUsingMPI = false; ///< bool flag false: sequential, true: parallel MPI, to be checked instead of communicator
+
+ void InitNoMPI( ); ///< called from Init, initialize Serial
+
+ //#ifdef USE_MPI
+ void InitMPI( ); ///< called from Init, initialize parallel MPI
+ //#endif
+
+ void ReadXMLConfigFile( ); ///< populates SMetadata by reading the XML Config File
+
+
+};
+
+
+
+} //end namespace
+
+
+
+
+#endif /* ADIOS_H_ */
diff --git a/include/CADIOS.h b/include/CADIOS.h
deleted file mode 100644
index 6222bce38..000000000
--- a/include/CADIOS.h
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * CADIOS.h
- *
- * Created on: Sep 29, 2016
- * Author: William F Godoy
- */
-
-#ifndef CADIOS_H_
-#define CADIOS_H_
-
-#include <string>
-#include <mpi.h>
-#include <memory> // unique_ptr
-
-#include "include/SMetadata.h"
-
-namespace adios
-{
-/**
- * Class CADIOS, interface between user call and ADIOS library
- */
-class CADIOS
-{
-
-public: // can be accessed by anyone
-
- std::string m_XMLConfigFile; ///< XML File to be read containing configuration information
- bool m_IsUsingMPI = false; ///< bool flag false: sequential, true: parallel MPI, to be checked instead of communicator
- MPI_Comm* m_MPIComm = nullptr; ///< only used as reference to MPI communicator passed from parallel constructor, using pointer instead of reference as null is a possible value
-
- CADIOS( ); ///< empty constructor, to be defined. Since we have an empty constructor we can't have const variables not defined by this constructor
-
- /**
- * Serial constructor for XML config file
- * @param xmlConfigFile passed to m_XMLConfigFile
- */
- CADIOS( const std::string xmlConfigFile );
-
- /**
- * Parallel constructor for XML config file and MPI
- * @param xmlConfigFile passed to m_XMLConfigFile
- * @param mpiComm MPI communicator ...const to be discussed
- */
- CADIOS( const std::string xmlConfigFile, const MPI_Comm& mpiComm );
-
- ~CADIOS( ); ///< virtual destructor overriden by children's own destructors
-
- void Init( ); ///< calls to read XML file among other initialization tasks
-
-private:
-
- SMetadata m_Metadata; ///< contains all metadata information from XML Config File
-
- void InitSerial( ); ///< called from Init, initialize Serial
- void InitMPI( ); ///< called from Init, initialize parallel MPI
-
- void ReadXMLConfigFile( ); ///< populates SMetadata by reading the XML Config File
-
-
-};
-
-
-
-
-
-
-
-}
-
-#endif /* CADIOS_H_ */
diff --git a/include/CFile.h b/include/CFile.h
new file mode 100644
index 000000000..3402acb79
--- /dev/null
+++ b/include/CFile.h
@@ -0,0 +1,52 @@
+/*
+ * CFile.h
+ *
+ * Created on: Oct 3, 2016
+ * Author: wfg
+ */
+
+#ifndef CFILE_H_
+#define CFILE_H_
+
+#include <string>
+
+#include "SMetadata.h"
+
+namespace adios
+{
+
+class CFile
+{
+
+public:
+
+ const std::string m_FileName; ///< serial: file name, MPI: prefix for file name
+ const std::string m_FileType; ///< netCDF, PHDF5, POSIX
+ const bool m_IsUsingMPI; ///< true: Communicator is passed, false: serial process (might include threads)
+ const SMetadata& m_Metadata; ///< reference to metadata info
+
+ CFile( const std::string fileName, const std::string fileType, const SMetadata& metadata, const bool isUsingMPI ):
+ m_FileName{ fileName },
+ m_FileType{ fileType },
+ m_Metadata{ metadata },
+ m_IsUsingMPI{ isUsingMPI }
+ { }
+
+ virtual ~CFile( ) { };
+
+ virtual void Open( const std::string fileName, const std::string groupName, const std::string accessMode ) = 0;
+
+ virtual unsigned long int GroupSize( const std::string fileName, const std::string groupName ) const = 0;
+
+ virtual void Write( const std::string fileName, const std::string variableName ) = 0;
+
+ virtual void Close( ) = 0;
+
+};
+
+
+} //end namespace
+
+
+
+#endif /* CFILE_H_ */
diff --git a/include/SMetadata.h b/include/SMetadata.h
index b4044cd4b..6d30dedf5 100644
--- a/include/SMetadata.h
+++ b/include/SMetadata.h
@@ -16,6 +16,8 @@ namespace adios
struct SMetadata
{
std::string hostLanguage; ///< Supported: C, C++, Fortran
+ ///add more Metadata?
+
@@ -23,6 +25,6 @@ struct SMetadata
};
-}
+} //end namespace
#endif /* SMETADATA_H_ */
diff --git a/include/file_mpi/CFileMPI.h b/include/file_mpi/CFileMPI.h
new file mode 100644
index 000000000..8c58e93fb
--- /dev/null
+++ b/include/file_mpi/CFileMPI.h
@@ -0,0 +1,48 @@
+/*
+ * CFileMPI.h
+ *
+ * Created on: Oct 3, 2016
+ * Author: wfg
+ */
+
+#ifndef CFILEMPI_H_
+#define CFILEMPI_H_
+
+#include <mpi.h>
+
+#include "CFile.h"
+
+
+namespace adios
+{
+
+class CFileMPI : public CFile
+{
+
+public:
+
+ MPI_Comm* m_MPIComm;
+
+ CFileMPI( const std::string fileName, const std::string fileType, const SMetadata& metadata, const MPI_Comm& mpiComm ):
+ CFile( fileName, fileType, metadata, true ),
+ m_MPIComm{ mpiComm }
+ { }
+
+ virtual ~CFileMPI( ) { };
+
+ virtual void Open( const std::string fileName, const std::string groupName, const std::string accessMode );
+
+ virtual unsigned long int GroupSize( const std::string fileName, const std::string groupName ) const = 0;
+
+ virtual void Write( const std::string fileName, const std::string variableName ) = 0;
+
+ virtual void Close( ) = 0;
+
+};
+
+
+} //end namespace
+
+
+
+#endif /* CFILEMPI_H_ */
diff --git a/include/file_nompi/CFileNoMPI.h b/include/file_nompi/CFileNoMPI.h
new file mode 100644
index 000000000..9a86f7d5c
--- /dev/null
+++ b/include/file_nompi/CFileNoMPI.h
@@ -0,0 +1,44 @@
+/*
+ * CFileNoMPI.h
+ *
+ * Created on: Oct 3, 2016
+ * Author: wfg
+ */
+
+#ifndef CFILENOMPI_H_
+#define CFILENOMPI_H_
+
+
+#include "CFile.h"
+
+
+namespace adios
+{
+
+class CFileNoMPI : public CFile
+{
+
+public:
+
+ CFileNoMPI( const std::string fileName, const std::string fileType, const SMetadata& metadata ):
+ CFile( fileName, fileName, metadata, false )
+ { };
+
+ virtual ~CFileNoMPI( ){ };
+
+ virtual void Open( const std::string fileName, const std::string groupName, const std::string accessMode ) = 0;
+
+ virtual unsigned long int GroupSize( const std::string fileName, const std::string groupName ) const = 0;
+
+ virtual void Write( const std::string fileName, const std::string variableName ) = 0;
+
+ virtual void Close( ) = 0;
+
+};
+
+
+} //end namespace
+
+
+
+#endif /* CFILENOMPI_H_ */
diff --git a/src/CADIOS.cpp b/src/ADIOS.cpp
similarity index 100%
rename from src/CADIOS.cpp
rename to src/ADIOS.cpp
--
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