From 3397c5e54d08f5571beb46e8b35cd9c3f62d9e4d Mon Sep 17 00:00:00 2001
From: wfg <wfg@pc0098504.ornl.gov>
Date: Thu, 13 Oct 2016 18:02:05 -0400
Subject: [PATCH] Ready to start testing hello Transport MPI and nonMPI POSIX
methods.
Warning: Makefile only compiling for all, not nompi or mpi
---
Makefile | 42 ++---
doc/Doxyfile | 14 +-
examples/hello/helloADIOS_nompi.cpp | 2 +-
examples/hello/writer2Groups.xml | 72 +++++++++
include/ADIOS.h | 16 +-
include/ADIOSFunctions.h | 15 ++
include/CGroup.h | 65 +++++++-
include/CTransport.h | 11 +-
include/CVariable.h | 7 +-
include/SSupport.h | 23 +--
include/mpi/transport/CPOSIXMPI.h | 2 +-
include/mpi/transport/CTransportMPI.h | 2 +-
include/nompi/transport/CPOSIXNoMPI.h | 2 +-
include/nompi/transport/CTransportNoMPI.h | 2 +-
src/ADIOS.cpp | 50 ++++--
src/ADIOSFunctions.cpp | 177 +++++++++++++++++-----
src/CGroup.cpp | 51 ++++++-
src/mpi/transport/CPOSIXMPI.cpp | 2 +-
src/nompi/transport/CPOSIXNoMPI.cpp | 2 +-
19 files changed, 437 insertions(+), 120 deletions(-)
create mode 100644 examples/hello/writer2Groups.xml
diff --git a/Makefile b/Makefile
index bf31f7bae..000cffe96 100644
--- a/Makefile
+++ b/Makefile
@@ -22,56 +22,46 @@ ADIOS_INC=-I./include
INCLUDE=$(ADIOS_INC)
#Build Header Dependencies, if one changes it will rebuild
-MPI_HFiles=$(shell find ./include/mpi/ -type f -name "*MPI.h")
-NoMPI_HFiles=$(shell find ./include/nompi/ -type f -name "*NoMPI.h")
-Local_HFiles=$(shell find ./include/ -type f -name "*.h")
+MPI_HFiles=$(shell find ./include/mpi -type f -name "*MPI.h")
+NoMPI_HFiles=$(shell find ./include/nompi -type f -name "*NoMPI.h")
+Local_HFiles=$(shell find ./include -type f -name "*.h")
HFiles=$(MPI_HFiles) $(NoMPI_HFiles) $(Local_HFiles)
#Source *.cpp Files and Object Files
-MPI_CPPFiles=$(shell find ./src/mpi/ -type f -name "*MPI.cpp")
+MPI_CPPFiles=$(shell find ./src/mpi -type f -name "*MPI.cpp")
MPI_ObjFiles=$(patsubst ./src/mpi/transport/%.cpp, ./bin/%.o, $(MPI_CPPFiles))
-NoMPI_CPPFiles=$(shell find ./src/nompi/ -type f -name "*NoMPI.cpp")
+NoMPI_CPPFiles=$(shell find ./src/nompi -type f -name "*NoMPI.cpp")
NoMPI_ObjFiles=$(patsubst ./src/nompi/transport/%.cpp, ./bin/%.o, $(NoMPI_CPPFiles))
+Common_CPPFiles=$(wildcard ./src/*.cpp)
+Common_ObjFiles=$(patsubst ./src/%.cpp, ./bin/%.o, $(Common_CPPFiles))
+
+
ObjFiles=$(MPI_ObjFiles) $(NoMPI_ObjFiles)
#Build all MPI and noMPI
-all: $(MPI_ObjFiles) $(NoMPI_ObjFiles) ./bin/ADIOS.o ./bin/ADIOSFunctions.o $(HFiles)
- @echo "ADIOS MPI headers" $(MPI_HFiles);
- @echo "ADIOS No MPI headers" $(NoMPI_HFiles);
+all: $(MPI_ObjFiles) $(NoMPI_ObjFiles) $(Common_ObjFiles) $(HFiles)
$(AR) rcs ./lib/libadios.a $(MPI_ObjFiles) $(NoMPI_ObjFiles) ./bin/ADIOS.o ./bin/ADIOSFunctions.o ./bin/CGroup.o
#MPI build
-mpi: $(MPI_ObjFiles) ./bin/ADIOS.o $(MPI_HFiles) $(Local_HFiles)
+mpi: $(MPI_ObjFiles) $(Common_ObjFiles) $(MPI_HFiles) $(Local_HFiles)
$(AR) rcs ./lib/libadios.a $(MPI_ObjFiles) ./bin/ADIOS.o ./bin/ADIOSFunctions.o ./bin/CGroup.o
./bin/%.o: ./src/mpi/transport/%.cpp
$(MPICC) $(CFLAGS) -DHAVE_MPI $(INCLUDE) -o $@ $<
-
-./bin/ADIOS.o: ./src/ADIOS.cpp
+
+./bin/%.o: ./src/%.cpp
$(MPICC) $(CFLAGS) -DHAVE_MPI $(INCLUDE) -o $@ $<
-
#NoMPI build
-nompi: $(NoMPI_ObjFiles) ./bin/ADIOS_nompi.o ./bin/ADIOSFunctions.o ./bin/CGroup.o $(NoMPI_HFiles) $(Local_HFiles)
- $(AR) rcs ./lib/libadios_nompi.a $(NoMPI_ObjFiles) ./bin/ADIOS_nompi.o ./bin/ADIOSFunctions.o ./bin/CGroup.o
+nompi: $(NoMPI_ObjFiles) $(Common_ObjFiles) $(NoMPI_HFiles) $(Local_HFiles)
+ $(AR) rcs ./lib/libadios_nompi.a $(NoMPI_ObjFiles) $(Common_ObjFiles)
./bin/%.o: ./src/nompi/transport/%.cpp $(NoMPI_HFiles) $(Local_HFiles)
$(CC) $(CFLAGS) $(INCLUDE) -o $@ $<
-
-./bin/ADIOS_nompi.o: ./src/ADIOS.cpp $(NoMPI_HFiles) $(Local_HFiles)
- $(CC) $(CFLAGS) $(INCLUDE) -o $@ $<
-
-
-#Local common files
-./bin/ADIOSFunctions.o: ./src/ADIOSFunctions.cpp $(NoMPI_HFiles) $(Local_HFiles)
- $(CC) $(CFLAGS) $(INCLUDE) -o $@ $<
-
-./bin/CGroup.o: ./src/CGroup.cpp $(NoMPI_HFiles) $(Local_HFiles)
- $(CC) $(CFLAGS) $(INCLUDE) -o $@ $<
-
+
clean:
rm ./bin/*.o ./lib/libadios.a ./lib/libadios_nompi.a
diff --git a/doc/Doxyfile b/doc/Doxyfile
index 0b9aae509..f4d1ec3b4 100644
--- a/doc/Doxyfile
+++ b/doc/Doxyfile
@@ -434,7 +434,7 @@ EXTRACT_PACKAGE = NO
# included in the documentation.
# The default value is: NO.
-EXTRACT_STATIC = YES
+EXTRACT_STATIC = NO
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
@@ -771,7 +771,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
-INPUT = /home/wfg/workspace/ADIOSPP/include /home/wfg/workspace/ADIOSPP/include/mpi/transport /home/wfg/workspace/ADIOSPP/include/nompi/transport
+INPUT = /home/wfg/workspace/ADIOSPP/include /home/wfg/workspace/ADIOSPP/include/mpi/transport /home/wfg/workspace/ADIOSPP/include/nompi/transport /home/wfg/workspace/ADIOSPP/src /home/wfg/workspace/ADIOSPP/src/mpi/transport /home/wfg/workspace/ADIOSPP/src/nompi/transport
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -2218,7 +2218,7 @@ GROUP_GRAPHS = YES
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
-UML_LOOK = NO
+UML_LOOK = YES
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
@@ -2239,7 +2239,7 @@ UML_LIMIT_NUM_FIELDS = 10
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
-TEMPLATE_RELATIONS = NO
+TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
@@ -2281,7 +2281,7 @@ CALL_GRAPH = YES
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
-CALLER_GRAPH = NO
+CALLER_GRAPH = YES
# If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
# hierarchy of all classes instead of a textual one.
@@ -2339,7 +2339,7 @@ DOT_PATH =
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
-DOTFILE_DIRS =
+DOTFILE_DIRS = /home/wfg/workspace/ADIOSPP/include /home/wfg/workspace/ADIOSPP/include/mpi/transport /home/wfg/workspace/ADIOSPP/include/nompi/transport
# The MSCFILE_DIRS tag can be used to specify one or more directories that
# contain msc files that are included in the documentation (see the \mscfile
@@ -2388,7 +2388,7 @@ DOT_GRAPH_MAX_NODES = 50
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
-MAX_DOT_GRAPH_DEPTH = 0
+MAX_DOT_GRAPH_DEPTH = 3
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
diff --git a/examples/hello/helloADIOS_nompi.cpp b/examples/hello/helloADIOS_nompi.cpp
index e617aeef3..e01949eaa 100644
--- a/examples/hello/helloADIOS_nompi.cpp
+++ b/examples/hello/helloADIOS_nompi.cpp
@@ -18,7 +18,7 @@ int main( int argc, char* argv [] )
{
adios::ADIOS adiosFile( "writer2Groups.xml" ); //testing with CPOSIXNoMPI
adiosFile.Init( );
- adiosFile.MonitorGroups( );
+ adiosFile.MonitorGroups( std::cout );
std::cout << "Finished initializing ADIOS\n";
}
catch( std::exception& e )
diff --git a/examples/hello/writer2Groups.xml b/examples/hello/writer2Groups.xml
new file mode 100644
index 000000000..d019bdfdc
--- /dev/null
+++ b/examples/hello/writer2Groups.xml
@@ -0,0 +1,72 @@
+<?xml version="1.0"?>
+<adios-config host-language="Fortran">
+ <adios-group name="writer2D">
+
+ <var name="nproc" path="/info" type="integer"/>
+ <attribute name="description" path="/info/nproc" value="Number of writers"/>
+ <var name="npx" path="/info" type="integer"/>
+ <attribute name="description" path="/info/npx" value="Number of processors in x dimension"/>
+ <var name="npy" path="/info" type="integer"/>
+ <attribute name="description" path="/info/npy" value="Number of processors in y dimension"/>
+
+ <var name="gdx" type="integer"/>
+ <attribute name="description" path="/gdx" value="Global array size in x dimension"/>
+ <var name="gdy" type="integer"/>
+ <attribute name="description" path="/gdy" value="Global array size in y dimension"/>
+
+ <!-- Auxiliary variables for global array indexing written (overwritten) by each process -->
+ <var name="ox" type="integer"/>
+ <var name="oy" type="integer"/>
+ <var name="ldx" type="integer"/>
+ <var name="ldy" type="integer"/>
+
+ <!-- 2D array to write with block,block decomposition -->
+ <global-bounds dimensions="gdx,gdy" offsets="ox,oy">
+ <var name="xy" type="double" dimensions="ldx,ldy"/>
+ </global-bounds>
+ <attribute name="description" path="/xy"
+ value="2D array with 2D decomposition"/>
+
+ </adios-group>
+
+ <!-- Use transport method
+ DATASPACES for staging data in memory coupling or
+ FLEXPATH for socket based staging between applications
+ MPI for file-based coupling
+ -->
+ <!--transport group="writer2D" method="MPI">verbose=2</transport-->
+ <!--transport group="writer2D" method="DATASPACES">verbose=3</transport-->
+ <transport group="writer2D" method="DIMES">verbose=3</transport>
+ <!--transport group="writer2D" method="FLEXPATH">QUEUE_SIZE=10;verbose=3</transport-->
+ <adios-group name="writer3D">
+
+ <var name="nproc" path="/info" type="integer"/>
+ <attribute name="description" path="/info/nproc" value="Number of writers"/>
+ <var name="npx" path="/info" type="integer"/>
+ <attribute name="description" path="/info/npx" value="Number of processors in x dimension"/>
+ <var name="npy" path="/info" type="integer"/>
+ <attribute name="description" path="/info/npy" value="Number of processors in y dimension"/>
+
+ <var name="gdx" type="integer"/>
+ <attribute name="description" path="/gdx" value="Global array size in x dimension"/>
+ <var name="gdy" type="integer"/>
+ <attribute name="description" path="/gdy" value="Global array size in y dimension"/>
+
+ <!-- Auxiliary variables for global array indexing written (overwritten) by each process -->
+ <var name="ox" type="integer"/>
+ <var name="oy" type="integer"/>
+ <var name="ldx" type="integer"/>
+ <var name="ldy" type="integer"/>
+
+ <!-- 2D array to write with block,block decomposition -->
+ <global-bounds dimensions="gdx,gdy" offsets="ox,oy">
+ <var name="xy" type="double" dimensions="ldx,ldy"/>
+ </global-bounds>
+ <attribute name="description" path="/xy"
+ value="2D array with 2D decomposition"/>
+
+ </adios-group>
+
+ <buffer size-MB="40" allocate-time="now"/>
+
+</adios-config>
diff --git a/include/ADIOS.h b/include/ADIOS.h
index be8e79247..825bb0dbe 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -10,6 +10,7 @@
#include <string>
#include <memory>
+#include <ostream>
#ifdef HAVE_MPI
#include <mpi.h>
@@ -78,16 +79,21 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
*/
unsigned long int GroupSize( const std::string groupName ) const;
-
/**
* 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
*/
template<class T>
void Write( const std::string groupName, const std::string variableName, const T* values );
- void MonitorGroups( );
+ /**
+ * @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.
+ * @param logStream either std::cout standard output, or a std::ofstream file
+ */
+ void MonitorGroups( std::ostream& logStream ) const;
void Close( ); // dumps to file?
@@ -124,6 +130,12 @@ private:
#ifdef HAVE_MPI
void InitMPI( ); ///< called from Init, initialize parallel MPI
#endif
+
+ /**
+ * Checks for group existence in m_Groups
+ * @param groupName to be checked
+ */
+ void CheckGroup( const std::string groupName );
};
diff --git a/include/ADIOSFunctions.h b/include/ADIOSFunctions.h
index 8e20700a2..5b57869fa 100644
--- a/include/ADIOSFunctions.h
+++ b/include/ADIOSFunctions.h
@@ -12,6 +12,10 @@
#include <vector>
#include <map>
+#ifdef HAVE_MPI
+#include <mpi.h> //Just for MPI_Comm argument in SetMembersMPI
+#endif
+
#include "CGroup.h"
@@ -72,6 +76,17 @@ void GetPairsFromTag( const std::string& fileContent, const std::string tag,
void SetMembers( const std::string& fileContent, std::string& hostLanguage, std::map< std::string, CGroup >& groups );
+#ifdef HAVE_MPI
+/**
+ * Set members m_Groups and m_HostLanguage from XML file content, called within Init functions
+ * @param fileContent file Content in a single string
+ * @param hostLanguage return the host language from fileContent
+ * @param groups passed returns the map of groups defined in fileContent
+ */
+void SetMembers( const std::string& fileContent, std::string& hostLanguage, std::map< std::string, CGroup >& groups,
+ const MPI_Comm mpiComm );
+#endif
+
} //end namespace
diff --git a/include/CGroup.h b/include/CGroup.h
index a38f98189..018a021df 100644
--- a/include/CGroup.h
+++ b/include/CGroup.h
@@ -12,6 +12,11 @@
#include <string>
#include <memory> //for shared_pointer
#include <vector>
+#include <ostream>
+
+#ifdef HAVE_MPI
+#include <mpi.h> //for MPI_Comm in overloaded SetTransform
+#endif
#include "CVariable.h"
#include "SAttribute.h"
@@ -37,6 +42,23 @@ public:
~CGroup( ); ///< Using STL containers
+ /**
+ * Opens group and passes fileName and accessMode to m_Transport
+ * @param fileName
+ * @param accessMode
+ */
+ void Open( const std::string fileName, const std::string accessMode = "w" );
+
+
+ /**
+ * Passes variableName and values to m_Transport
+ * @param variableName
+ * @param values
+ */
+ template<class T>
+ void Write( const std::string variableName, const T* values );
+
+
/**
* @brief Sets a variable in current Group, name must be unique
* @param name
@@ -46,7 +68,7 @@ public:
* @param transform method, format = lib or lib:level, where lib = zlib, bzip2, szip, and level=1:9 . If no level is defined then library default is taken
*/
void SetVariable( const std::string name, const bool isGlobal, const std::string type,
- const std::string dimensionsCSV = {1}, const std::string transform = "" );
+ const std::string dimensionsCSV = "1", const std::string transform = "" );
/**
* @brief Sets a variable in current Group
@@ -66,16 +88,34 @@ public:
*/
void SetGlobalBounds( const std::string dimensionsCSV, const std::string offsetsCSV = "" );
+
/**
- * Set a transport method for this group
- * @param transport supported values in SSupport.h TransportMethods
+ * @brief Set a transport method for this group, if existing it will replace current transport method
+ * @param method supported values in SSupport.h TransportMethods
* @param priority numeric priority for the I/O to schedule this write with others that might be pending
* @param iteration iterations between writes of a group to gauge how quickly this data should be evacuated from the compute node
- * @param verbose level
*/
- void SetTransportMethod( const std::string transport, unsigned int priority = 1, unsigned int iteration=1, unsigned int verbose = 0 );
+ void SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration );
- void MonitorGroup( ); ///< Dumps information about Group variables
+ #ifdef HAVE_MPI
+ /**
+ * @brief MPI version of SetTransport, includes the communicator
+ * @param method supported values in SSupport.h TransportMethods
+ * @param priority numeric priority for the I/O to schedule this write with others that might be pending
+ * @param iteration iterations between writes of a group to gauge how quickly this data should be evacuated from the compute node
+ * @param mpiComm MPI communicator from User->ADIOS->Group
+ */
+ void SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
+ const MPI_Comm mpiComm );
+ #endif
+
+
+ /**
+ * @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.
+ * @param logStream either std::cout standard output, or a std::ofstream file
+ */
+ void Monitor( std::ostream& logStream ) const; ///< Dumps information about Group variables
private:
@@ -93,9 +133,12 @@ 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::shared_ptr< CTransport > m_TransportMethod; ///< transport method defined in XML File, using shared pointer as SGroup can be uninitialized
- std::string m_ActiveMethod;
+ std::shared_ptr< CTransport > m_Transport; ///< transport method defined in XML File, using shared pointer as SGroup can be uninitialized
+ std::string m_ActiveTransport;
+ 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
/**
* Called from XML constructor
@@ -103,6 +146,12 @@ private:
* @param groupName returns the groupName from <adios-group name=" "
*/
void ParseXMLGroup( const std::string& xmlGroup, std::string& groupName );
+
+ /**
+ * Function that checks if transport method is valid, called from overloaded SetTransform functions
+ * @param method transport method to be checked from SSupport
+ */
+ void CheckTransport( const std::string method );
};
diff --git a/include/CTransport.h b/include/CTransport.h
index 7f3c31d60..63de67c57 100644
--- a/include/CTransport.h
+++ b/include/CTransport.h
@@ -25,6 +25,8 @@ public:
const unsigned int m_Priority;
const unsigned int m_Iteration;
const bool m_IsUsingMPI;
+ std::string m_FileName;
+ std::string m_AccessMode;
CTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
bool isUsingMPI ):
@@ -37,7 +39,14 @@ public:
virtual ~CTransport( )
{ }
- virtual void Write( CVariable& variable ) = 0;
+
+ void Open( const std::string fileName, const std::string accessMode = "w" )
+ {
+ m_FileName = fileName;
+ m_AccessMode = accessMode;
+ }
+
+ virtual void Write( const CVariable& variable ) = 0;
};
diff --git a/include/CVariable.h b/include/CVariable.h
index a1960b17c..5344f3833 100644
--- a/include/CVariable.h
+++ b/include/CVariable.h
@@ -48,7 +48,7 @@ public:
template<class T, class U> void Set(const U& rhs);
-//protected:
+//protected: turned off for testing
bool m_IsGlobal = false;
std::string m_Type = "NONE"; ///< mandatory, double, float, unsigned integer, integer, etc.
std::vector<std::string> m_Dimensions = {"1"}; ///< if empty variable is a scalar, else N-dimensional variable
@@ -67,6 +67,7 @@ public:
/**
* Template constructor class required for putting CVariable objects as value in a STL map container
* @param isGlobal
+ * @param type
* @param dimensionsCSV
* @param transform
*/
@@ -77,8 +78,10 @@ public:
~CVariableTemplate( )
{ }
+ T* m_Value; // pointer or no pointer?
+
const T& Get() const { return m_Value; }
- T m_Value;
+
};
diff --git a/include/SSupport.h b/include/SSupport.h
index 5d4c06831..e07d4399d 100644
--- a/include/SSupport.h
+++ b/include/SSupport.h
@@ -15,9 +15,10 @@
namespace adios
{
-const std::string Version{"2.00"};
+const std::string c_Version{"2.00"};
-const std::set<std::string> HostLanguages {
+
+const std::set<std::string> c_HostLanguages {
"C",
"C++",
"Fortran",
@@ -25,7 +26,7 @@ const std::set<std::string> HostLanguages {
"Java"
};
-const std::set<std::string> TransportMethods {
+const std::set<std::string> c_Transports {
"NULL",
"POSIX",
"MPI",
@@ -39,14 +40,14 @@ const std::set<std::string> TransportMethods {
"ICEE"
};
-const std::set<std::string> Tranformations {
+const std::set<std::string> c_Transformations {
"none",
"identity",
"bzip2",
"isobar"
};
-const std::map<std::string, std::string> DataTypes {
+const std::map<std::string, std::string> c_DataTypes {
{ "unsigned integer", "unsigned int" },
{ "integer", "int" },
{ "real" , "float" },
@@ -55,17 +56,7 @@ const std::map<std::string, std::string> DataTypes {
};
-
-
-
-
-
-
-
-
-
-
-}
+} //end namespace
#endif /* SSUPPORT_H_ */
diff --git a/include/mpi/transport/CPOSIXMPI.h b/include/mpi/transport/CPOSIXMPI.h
index 3b337e032..db2977e7a 100644
--- a/include/mpi/transport/CPOSIXMPI.h
+++ b/include/mpi/transport/CPOSIXMPI.h
@@ -29,7 +29,7 @@ public:
~CPOSIXMPI( );
- void Write( CVariable& variable );
+ void Write( const CVariable& variable );
};
diff --git a/include/mpi/transport/CTransportMPI.h b/include/mpi/transport/CTransportMPI.h
index d70aeeb2d..77633cd74 100644
--- a/include/mpi/transport/CTransportMPI.h
+++ b/include/mpi/transport/CTransportMPI.h
@@ -32,7 +32,7 @@ public:
virtual ~CTransportMPI( )
{ }
- virtual void Write( CVariable& variable ) = 0;
+ virtual void Write( const CVariable& variable ) = 0;
};
diff --git a/include/nompi/transport/CPOSIXNoMPI.h b/include/nompi/transport/CPOSIXNoMPI.h
index e590b1419..4bd390f8f 100644
--- a/include/nompi/transport/CPOSIXNoMPI.h
+++ b/include/nompi/transport/CPOSIXNoMPI.h
@@ -27,7 +27,7 @@ public:
~CPOSIXNoMPI( );
- void Write( CVariable& variable );
+ void Write( const CVariable& variable );
};
diff --git a/include/nompi/transport/CTransportNoMPI.h b/include/nompi/transport/CTransportNoMPI.h
index f45caeb57..7e212bcdf 100644
--- a/include/nompi/transport/CTransportNoMPI.h
+++ b/include/nompi/transport/CTransportNoMPI.h
@@ -26,7 +26,7 @@ public:
virtual ~CTransportNoMPI( )
{ }
- virtual void Write( CVariable& variable ) = 0;
+ virtual void Write( const CVariable& variable ) = 0;
};
diff --git a/src/ADIOS.cpp b/src/ADIOS.cpp
index 0bba0cdf6..a2b55deba 100644
--- a/src/ADIOS.cpp
+++ b/src/ADIOS.cpp
@@ -62,41 +62,69 @@ void ADIOS::InitNoMPI( )
std::string xmlFileContent;
DumpFileToStream( m_XMLConfigFile, xmlFileContent ); //in ADIOSFunctions.h dumps all XML Config File to xmlFileContent
SetMembers( xmlFileContent, m_HostLanguage, m_Groups );
-
- //SetMembersFromXMLConfigFile( xmlFileContent, m_HostLanguage, m_Groups ); //in ADIOSFunctions.h sets m_HostLanguage and m_Groups
- //std::cout << "Finishing Initialization";
}
-#ifdef MPI_VERSION
+
+#ifdef HAVE_MPI
void ADIOS::InitMPI( )
{
- std::cout << "Just testing the InitMPI Function\n";
+ int rank;
+ MPI_Comm_rank( m_MPIComm, &rank );
+
+ int xmlFileContentSize; // common
+ std::string xmlFileContent;
+
+ if( rank == 0 )
+ {
+ std::string xmlFileContent;
+ DumpFileToStream( m_XMLConfigFile, xmlFileContent ); //in ADIOSFunctions.h dumps all XML Config File to xmlFileContent
+ xmlFileContentSize = m_XMLConfigFile.size( ) + 1; // add one for the null character
+
+ MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, m_MPIComm ); //broadcast size
+ MPI_Bcast( (char*)xmlFileContent.c_str(), xmlFileContentSize, MPI_CHAR, 0, m_MPIComm );
+
+ SetMembers( xmlFileContent, m_HostLanguage, m_Groups );
+ }
+ else
+ {
+ MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, m_MPIComm ); //broadcast size
+ char* xmlFileContentMPI = new char[ xmlFileContentSize ]; //allocate C char
+ MPI_Bcast( xmlFileContentMPI, xmlFileContentSize, MPI_CHAR, 0, m_MPIComm ); //receive from rank=0
+
+ xmlFileContent.assign( xmlFileContentMPI );
+ SetMembers( xmlFileContent, m_HostLanguage, m_Groups );
+ }
}
#endif
void ADIOS::Open( const std::string groupName, const std::string fileName, const std::string accessMode )
{
- //retrieve a group name from m_Groups
- std::cout << "Just testing the Open function\n";
+ m_Groups.at( groupName ).Open( fileName, accessMode );
}
template<class T> void ADIOS::Write( const std::string groupName, const std::string variableName, const T* values )
{
- std::cout << "Just testing the Write function\n";
+ m_Groups.at( groupName ).Write( variableName, values );
}
-void ADIOS::MonitorGroups( )
+void ADIOS::MonitorGroups( std::ostream& logStream ) const
{
for( auto& groupPair : m_Groups )
{
- std::cout << "Group:..." << groupPair.first << "\n";
- groupPair.second.MonitorGroup();
+ logStream << "Group:..." << groupPair.first << "\n";
+ groupPair.second.Monitor( logStream );
}
}
+void ADIOS::CheckGroup( const std::string groupName )
+{
+ auto it = m_Groups.find( groupName );
+ if( it == m_Groups.end() ) throw std::invalid_argument( "ERROR: group " + groupName + " not found\n" );
+}
+
} //end namespace
diff --git a/src/ADIOSFunctions.cpp b/src/ADIOSFunctions.cpp
index 73ca9ff20..e83428196 100644
--- a/src/ADIOSFunctions.cpp
+++ b/src/ADIOSFunctions.cpp
@@ -136,13 +136,14 @@ void SetMembers( const std::string& fileContent, std::string& hostLanguage, std:
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
- std::string configTag;
currentPosition = 0;
- GetSubString( "<", ">", currentContent, configTag, currentPosition );
- configTag = configTag.substr( 1, configTag.size() - 2 ); //eliminate < >
- std::vector< std::pair<const std::string, const std::string> > pairs;
- GetPairsFromTag( currentContent, configTag, pairs );
+ GetSubString( "<", ">", currentContent, tag, currentPosition );
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+ GetPairsFromTag( currentContent, tag, pairs );
for( auto& pair : pairs )
{
@@ -150,7 +151,7 @@ void SetMembers( const std::string& fileContent, std::string& hostLanguage, std:
}
//adios-group
- std::string xmlGroup( "Used for groups" );
+ std::string xmlGroup;
while( currentPosition != std::string::npos )
{
GetSubString("<adios-group ", "</adios-group>", currentContent, xmlGroup, currentPosition );
@@ -159,43 +160,147 @@ void SetMembers( const std::string& fileContent, std::string& hostLanguage, std:
std::string groupName;
CGroup group( xmlGroup, groupName );
groups[ groupName ] = group; //copy as it's a small object
- }
+ currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size() );
+ currentPosition = 0;
+ }
+ //transport
+ currentPosition = 0;
+ while( currentPosition != std::string::npos )
+ {
+ GetSubString( "<transport ", ">", currentContent, tag, currentPosition );
+ if( tag.empty() ) break;
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+ pairs.clear();
+ GetPairsFromTag( currentContent, tag, pairs );
+
+ std::string groupName, method, priorityStr, iterationStr;
+ for( auto& pair : pairs )
+ {
+ if( pair.first == "group" ) groupName = pair.second;
+ else if( pair.first == "method" ) method = pair.second;
+ else if( pair.first == "priority" ) priorityStr = pair.second;
+ else if( pair.first == "iteration" ) iterationStr = pair.second;
+ }
+ auto itGroup = groups.find( groupName );
+ if( itGroup == groups.end() ) //not found
+ {
+ continue;
+ }
- //transports tag
-// std::map< std::string, std::map<std::string,std::string> > groupsTransport;
-// std::string::size_type startTransport = currentContent.find("<transport ");
-//
-// while( startTransport != currentContent.npos )
-// {
-// std::string::size_type endTransport( currentContent.find( "</transport>") );
-// std::string::size_type endTag( currentContent.find('>', startTransport ) );
-//
-// const std::string transportTag( currentContent.substr( startTransport+1, endTag-startTransport-1 ) );
-// std::vector< std::pair<const std::string, const std::string> > transportPairs;
-// std::cout << "Transport tag..." << transportTag << "...\n";
-// GetPairsFromTag( currentContent, transportTag, transportPairs );
-//
-// for( auto& pair : pairs )
-// {
-// if( pair.first == "group" )
-// {
-//
-// }
-// }
-// const std::string transportContents( currentContent.substr( startTransport, endTransport-startTransport) );
-// std::cout << "Transport contents..." << transportContents << "...\n";
-//
-// currentContent.erase( startTransport, endTransport-startComment + 12 );
-// std::cout << "Current content..." << currentContent << "...\n";
-//
-// startTransport = currentContent.find( "<transport " );
-// }
+ //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 );
+
+ itGroup->second.SetTransport( method, (unsigned int)priority, (unsigned int)iteration );
+ }
}
+#ifdef HAVE_MPI
+void SetMembers( const std::string& fileContent, std::string& hostLanguage, std::map< std::string, CGroup >& groups,
+ const MPI_Comm mpiComm )
+{
+ //adios-config
+ std::string currentContent;
+ std::string::size_type currentPosition( 0 );
+ GetSubString( "<adios-config ", "</adios-config>", fileContent, currentContent, currentPosition );
+
+ //remove comment sections
+ std::string::size_type startComment ( currentContent.find( "<!--" ) );
+
+ while( startComment != currentContent.npos )
+ {
+ std::string::size_type endComment( currentContent.find( "-->") );
+ currentContent.erase( startComment, endComment-startComment+3 );
+ 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 );
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+ GetPairsFromTag( currentContent, tag, pairs );
+
+ for( auto& pair : pairs )
+ {
+ if( pair.first == "host-language" ) hostLanguage = pair.second;
+ }
+
+ //adios-group
+ std::string xmlGroup;
+ while( currentPosition != std::string::npos )
+ {
+ GetSubString("<adios-group ", "</adios-group>", currentContent, xmlGroup, currentPosition );
+ if( xmlGroup.empty() ) break;
+
+ std::string groupName;
+ CGroup group( xmlGroup, groupName );
+ groups[ groupName ] = group; //copy as it's a small object
+
+ currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size() );
+ currentPosition = 0;
+ }
+ //transport
+ currentPosition = 0;
+ while( currentPosition != std::string::npos )
+ {
+ GetSubString( "<transport ", ">", currentContent, tag, currentPosition );
+ if( tag.empty() ) break;
+ tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
+ pairs.clear();
+ GetPairsFromTag( currentContent, tag, pairs );
+
+ std::string groupName, method, priorityStr, iterationStr;
+ for( auto& pair : pairs )
+ {
+ if( pair.first == "group" ) groupName = pair.second;
+ else if( pair.first == "method" ) method = pair.second;
+ else if( pair.first == "priority" ) priorityStr = pair.second;
+ else if( pair.first == "iteration" ) iterationStr = pair.second;
+ }
+
+ auto itGroup = groups.find( groupName );
+ if( itGroup == groups.end() ) //not found
+ {
+ continue;
+ }
+
+ //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 );
+
+ itGroup->second.SetTransport( method, (unsigned int)priority, (unsigned int)iteration, mpiComm );
+ }
+}
+#endif
diff --git a/src/CGroup.cpp b/src/CGroup.cpp
index 31c5871f2..dcb47db68 100644
--- a/src/CGroup.cpp
+++ b/src/CGroup.cpp
@@ -9,6 +9,14 @@
#include "CGroup.h"
#include "ADIOSFunctions.h"
+#include "SSupport.h"
+
+//MPI transport methods
+#ifdef HAVE_MPI
+#include "mpi/transport/CPOSIXMPI.h"
+#endif
+
+#include "nompi/transport/CPOSIXNoMPI.h"
namespace adios
@@ -25,6 +33,12 @@ CGroup::CGroup( const std::string& xmlGroup, std::string& groupName )
CGroup::~CGroup( )
{ }
+void CGroup::Open( const std::string fileName, const std::string accessMode )
+{
+ m_IsOpen = true;
+ m_Transport->Open( fileName, accessMode );
+}
+
void CGroup::SetVariable( const std::string name, const bool isGlobal, const std::string type, const std::string dimensionsCSV,
const std::string transform )
@@ -73,17 +87,36 @@ void CGroup::SetGlobalBounds( const std::string dimensionsCSV, const std::string
}
}
-void CGroup::MonitorGroup( )
+void CGroup::SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration )
+{
+ CheckTransport( method );
+ if( m_ActiveTransport == "POSIX" ) m_Transport = std::make_shared<CPOSIXNoMPI>( method, priority, iteration );
+}
+
+#ifdef HAVE_MPI
+void CGroup::SetTransport( const std::string method, const unsigned int priority, const unsigned int iteration,
+ const MPI_Comm mpiComm )
+{
+ CheckTransport( method );
+ if( m_ActiveTransport == "POSIX" ) m_Transport = std::make_shared<CPOSIXMPI>( method, priority, iteration, mpiComm );
+}
+#endif
+
+
+//PRIVATE FUNCTIONS BELOW
+
+void CGroup::Monitor( std::ostream& logStream ) const
{
for( auto& variablePair : m_Variables )
{
- std::cout << "VarName:..." << variablePair.first << " Type:..." << variablePair.second->m_Type << "\n";
+ logStream << "VarName:..." << variablePair.first << " Type:..." << variablePair.second->m_Type << "\n";
}
- std::cout << "Transport Method Unique?: " << m_TransportMethod.unique() << "\n";
-
+ logStream << "Transport Method " << m_ActiveTransport << "\n";
+ logStream << std::ostream::boolalpha << "Transport Method Unique?: " << m_Transport.unique() << "\n";
}
+
void CGroup::ParseXMLGroup( const std::string& xmlGroup, std::string& groupName )
{
//get name
@@ -153,6 +186,16 @@ void CGroup::ParseXMLGroup( const std::string& xmlGroup, std::string& groupName
}
+void CGroup::CheckTransport( const std::string method )
+{
+ if( c_Transports.count( method ) == 0 )
+ 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
+ m_Transport.reset();
+
+ m_ActiveTransport = method;
+}
} //end namespace
diff --git a/src/mpi/transport/CPOSIXMPI.cpp b/src/mpi/transport/CPOSIXMPI.cpp
index 1d697f694..3670c4620 100644
--- a/src/mpi/transport/CPOSIXMPI.cpp
+++ b/src/mpi/transport/CPOSIXMPI.cpp
@@ -25,7 +25,7 @@ CPOSIXMPI::~CPOSIXMPI( )
{ }
-void CPOSIXMPI::Write( CVariable& variable )
+void CPOSIXMPI::Write( const CVariable& variable )
{
int rank;
MPI_Comm_rank( m_MPIComm, &rank );
diff --git a/src/nompi/transport/CPOSIXNoMPI.cpp b/src/nompi/transport/CPOSIXNoMPI.cpp
index 3bc5ed640..623e7d836 100644
--- a/src/nompi/transport/CPOSIXNoMPI.cpp
+++ b/src/nompi/transport/CPOSIXNoMPI.cpp
@@ -24,7 +24,7 @@ CPOSIXNoMPI::~CPOSIXNoMPI( )
{ }
-void Write( CVariable& variable )
+void CPOSIXNoMPI::Write( const CVariable& variable )
{
std::cout << "Just saying Hello from CPOSIXNoMPI Write\n";
}
--
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