From 449b86ce7f270e6ee92c08f07374129d34e4f9f7 Mon Sep 17 00:00:00 2001
From: wfg <wfg@pc0098504.ornl.gov>
Date: Mon, 9 Jan 2017 17:33:05 -0500
Subject: [PATCH] Testing non-XML hello SingleBP Engine
This version compiles.
Tested with 2 write APIs:
under examples/hello/singleBP
helloSingleBP.cpp -> using ADIOS single manager class from ADIOS.h
helloSingleBP.cpp -> using ADIOS objects from ADIOS_OO.h
both generate a .bp file using a POSIX transport
To do:
Test compilation in other platforms/compilers
Add coverage test cases
Add the NULL transport (does nothing)
Work on SingleBP engine to generate bp format
XML config file support (to be defined)
---
Makefile | 2 +-
Makefile.libs | 4 +-
examples/dataman/datamanNoXML.cpp | 96 --------
examples/hello/Makefile | 2 +-
examples/hello/helloADIOS.cpp | 49 ----
examples/hello/helloADIOS_C.c | 36 ---
examples/hello/helloADIOS_nompi.cpp | 30 ---
examples/hello/helloFStream.cpp | 79 -------
examples/hello/helloFStreamNoXML.cpp | 95 --------
examples/hello/singleBP/Makefile | 35 +++
examples/hello/singleBP/helloSingleBP.cpp | 89 ++++++++
examples/hello/singleBP/helloSingleBP_OOP.cpp | 86 +++++++
include/ADIOS.h | 10 +-
include/ADIOS_OOP.h | 20 ++
include/capsule/Heap.h | 13 +-
include/capsule/ShmSystemV.h | 11 +-
include/core/Capsule.h | 8 +-
include/core/Engine.h | 79 ++++---
include/core/Group.h | 23 +-
include/core/Method.h | 12 +-
include/core/Transform.h | 4 +-
include/core/Transport.h | 4 +-
include/core/Variable.h | 12 +-
include/engine/SingleBP.h | 19 +-
include/functions/capsuleTemplates.h | 138 +++++------
include/transform/{BZIP2.h => BZip2.h} | 7 +-
include/transport/MPIFile.h | 2 +-
src/ADIOS.cpp | 55 +++--
src/capsule/Heap.cpp | 8 +-
src/capsule/ShmSystemV.cpp | 55 +++--
src/core/Engine.cpp | 138 +++--------
src/core/Group.cpp | 45 ++--
src/engine/SingleBP.cpp | 214 +++++++++++++++---
src/functions/adiosFunctions.cpp | 2 +-
src/transform/{BZIP2.cpp => BZip2.cpp} | 8 +-
src/transport/FStream.cpp | 4 +-
src/transport/File.cpp | 2 +
src/transport/POSIX.cpp | 25 +-
38 files changed, 774 insertions(+), 747 deletions(-)
delete mode 100644 examples/dataman/datamanNoXML.cpp
delete mode 100644 examples/hello/helloADIOS.cpp
delete mode 100644 examples/hello/helloADIOS_C.c
delete mode 100644 examples/hello/helloADIOS_nompi.cpp
delete mode 100644 examples/hello/helloFStream.cpp
delete mode 100644 examples/hello/helloFStreamNoXML.cpp
create mode 100644 examples/hello/singleBP/Makefile
create mode 100644 examples/hello/singleBP/helloSingleBP.cpp
create mode 100644 examples/hello/singleBP/helloSingleBP_OOP.cpp
create mode 100644 include/ADIOS_OOP.h
rename include/transform/{BZIP2.h => BZip2.h} (86%)
rename src/transform/{BZIP2.cpp => BZip2.cpp} (75%)
diff --git a/Makefile b/Makefile
index 43b8bf1e3..74d6e6e0b 100644
--- a/Makefile
+++ b/Makefile
@@ -20,7 +20,7 @@ ARFLAGS:=rcs
HFiles:=$(shell find ./include -type f -name "*.h")
CPPFiles:=$(shell find ./src -type f -name "*.cpp")
INC:=-I./include
-VPATH = ./src ./src/core ./src/functions ./src/transform ./src/transport
+VPATH = ./src ./src/core ./src/functions ./src/engine ./src/capsule ./src/transform ./src/transport
#SEPARATE EXTERNAL LIBRARIES HANDLING in Makefile.libs
export $(HFiles) $(CPPFiles) $(CFLAGS) $(LIBS)
diff --git a/Makefile.libs b/Makefile.libs
index 5e075454b..22bfe3668 100644
--- a/Makefile.libs
+++ b/Makefile.libs
@@ -1,6 +1,6 @@
#Language API
-LANGUAGE_INC:=./include/public
-LANGUAGE_SRC:=./src/public
+LANGUAGE_INC:=./include
+LANGUAGE_SRC:=./src
ifeq ($(C_API),yes)
else
diff --git a/examples/dataman/datamanNoXML.cpp b/examples/dataman/datamanNoXML.cpp
deleted file mode 100644
index 8935049c1..000000000
--- a/examples/dataman/datamanNoXML.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
- * datamanNoXML.cpp: Example for DataMan Transport usage also using POSIX as additional transport
- * Writes a single char array (myChars) and its size (myCharsSize)
- *
- * Created on: Nov 15, 2016
- * Author: wfg
- */
-
-#ifdef HAVE_MPI
- #include <mpi.h>
-#else
- #include "mpidummy.h"
- using adios::MPI_Init;
- using adios::MPI_Comm_rank;
-#endif
-
-#include "ADIOS.h"
-
-
-int main( int argc, char* argv [] )
-{
- MPI_Init( &argc, &argv );
- int rank;
- MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-
- 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 each with value '1'
-
- //ADIOS init here, non-XML, debug mode is ON
- adios::ADIOS adios( MPI_COMM_WORLD, true );
-
- //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
-
- //Define method or engine
-
- //Open stream using two transports, DataMan is default, POSIX is an additional one
- const std::string streamTCP( "TCP.bp" );
- const unsigned int tcpHandle = adios.Open( streamTCP, "w", "SingleBP" ); //here open a stream called TCPStream for writing (w or write), name is the same as stream
- adios.AddTransport( , "write", "POSIX", "name=TCP.bp" ); //add POSIX transport with .bp name
- adios.SetMaxBufferSize( streamTCP, 1000000000 ); // Setting max Buffer size to 1Gb
-
- //Writing
- adios.SetCurrentGroup( streamTCP, groupTCP ); //no need to add group field in Write
- adios.Write( streamTCP, "myCharsSize", &myCharsSize );
- adios.Write( streamTCP, "myChars", &myChars[0] ); //getting the underlying char*
-
- //Close
- adios.Close( streamTCP ); // Flush to all transports, DataMan and POSIX
- }
- catch( std::bad_alloc& e )
- {
- if( rank == 0 )
- {
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::invalid_argument& e )
- {
- if( rank == 0 )
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::ios_base::failure& e )
- {
- if( rank == 0 )
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::exception& e )
- {
- if( rank == 0 )
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize( );
-
- return 0;
-}
-
-
-
diff --git a/examples/hello/Makefile b/examples/hello/Makefile
index 159aa3084..62588a062 100644
--- a/examples/hello/Makefile
+++ b/examples/hello/Makefile
@@ -3,7 +3,7 @@
# Author: wfg
-BASE_NAME=helloFStream
+BASE_NAME=helloADIOSNoXML_OOP
TOOL_DIR=/usr/bin
diff --git a/examples/hello/helloADIOS.cpp b/examples/hello/helloADIOS.cpp
deleted file mode 100644
index d17d59272..000000000
--- a/examples/hello/helloADIOS.cpp
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * helloMPI.cpp
- *
- * Created on: Oct 4, 2016
- * Author: wfg
- */
-
-
-
-#include <stdexcept>
-#include <mpi.h>
-#include <iostream>
-#include <fstream>
-#include <string>
-
-#include "../../include/ADIOS.h"
-
-
-int main( int argc, char* argv [] )
-{
- MPI_Init( &argc, &argv );
- int rank;
- MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-
- adios::ADIOS adios;
-
- try
- {
- //testing with CPOSIXMPI
- adios = adios::ADIOS( "writer.xml", MPI_COMM_WORLD, true ); //debug mode
-
- //Get Monitor info
- std::ofstream logStream( "info_" + std::to_string(rank) + ".log" );
- adios.MonitorGroups( logStream );
- }
- catch( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
- {
- if( rank == 0 )
- {
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Barrier( MPI_COMM_WORLD );
- MPI_Finalize( );
-
-
- return 0;
-}
diff --git a/examples/hello/helloADIOS_C.c b/examples/hello/helloADIOS_C.c
deleted file mode 100644
index 28af80107..000000000
--- a/examples/hello/helloADIOS_C.c
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * helloADIOS_C.cpp
- *
- * Created on: Oct 31, 2016
- * Author: wfg
- */
-
-#ifdef HAVE_MPI
- #include <mpi.h>
-#else
- #include "../../include/mpidummy.h"
-#endif
-
-#include "../../include/ADIOS_C.h"
-
-
-
-int main( int argc, char* argv [] )
-{
- MPI_Init( &argc, &argv );
- int rank;
- MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-
-
-
-
-
-
-
-
-
- MPI_Finalize( );
-
-
- return 0;
-}
diff --git a/examples/hello/helloADIOS_nompi.cpp b/examples/hello/helloADIOS_nompi.cpp
deleted file mode 100644
index 4109656f6..000000000
--- a/examples/hello/helloADIOS_nompi.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * helloADIOS_nompi.cpp
- *
- * Created on: Oct 4, 2016
- * Author: wfg
- */
-
-
-#include <stdexcept>
-#include <iostream>
-
-#include "../../include/ADIOS.h"
-
-
-int main( int argc, char* argv [] )
-{
- try
- {
- adios::ADIOS adios( "writer2Groups.xml", true ); //testing with CPOSIXNoMPI
- adios.MonitorGroups( std::cout );
- std::cout << "Finished initializing ADIOS\n";
- }
- catch( std::exception& e )
- {
- std::cout << e.what() << "\n";
- }
-
- return 0;
-}
-
diff --git a/examples/hello/helloFStream.cpp b/examples/hello/helloFStream.cpp
deleted file mode 100644
index 04d588b76..000000000
--- a/examples/hello/helloFStream.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * helloFStream.cpp
- *
- * Created on: Oct 24, 2016
- * Author: wfg
- */
-
-
-#include <stdexcept>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <numeric>
-
-#ifdef HAVE_MPI
- #include <mpi.h>
-#else
- #include "../../include/mpidummy.h"
-#endif
-
-#include "../../include/ADIOS.h"
-
-
-int main( int argc, char* argv [] )
-{
- MPI_Init( &argc, &argv );
- int rank;
- MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-
- try
- {
- unsigned int size = 10;
- std::vector<int> numbers( size, 1 );
-
- adios::ADIOS adios( "numbers.xml", MPI_COMM_WORLD, true ); //xml file, MPI Comm, debug mode
- adios.Open( "numbers.bp", "write", "FStream" );// open a file stream transport for writing to file numbers.bp
- adios.SetCurrentGroup( "numbers.bp", "Vector" );// Write will look for variables in the Vector group defined in numbers.xml
- adios.Write( "numbers.bp", "size", &size ); //writes size
- adios.Write( "numbers.bp", "numbers", &numbers[0] ); //writes vector numbers
- adios.Close( "numbers.bp" ); //flush and closes numbers.bp now containing size and numbers
- }
- catch( std::bad_alloc& e )
- {
- if( rank == 0 )
- {
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::invalid_argument& e )
- {
- if( rank == 0 )
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::ios_base::failure& e )
- {
- if( rank == 0 )
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::exception& e )
- {
- if( rank == 0 )
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
-
- MPI_Finalize( );
-
- return 0;
-}
diff --git a/examples/hello/helloFStreamNoXML.cpp b/examples/hello/helloFStreamNoXML.cpp
deleted file mode 100644
index 70f1181fe..000000000
--- a/examples/hello/helloFStreamNoXML.cpp
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
-/*
- * helloFStreamNoXML.cpp
- *
- * Created on: Dec 2, 2016
- * Author: wfg
- */
-
-#include <stdexcept>
-#include <iostream>
-#include <fstream>
-#include <string>
-
-#ifdef HAVE_MPI
- #include <mpi.h>
-#else
- #include "../../include/mpidummy.h"
-#endif
-
-#include "../../include/ADIOS.h"
-
-
-int main( int argc, char* argv [] )
-{
- MPI_Init( &argc, &argv );
- int rank;
- MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-
- try
- {
- unsigned int size = 10;
- std::vector<int> numbers( size, 1 );
-
- adios::ADIOS adios( MPI_COMM_WORLD, true ); //MPI Comm, debug mode
-
- const std::string group( "Vector" );
- adios.DeclareGroup( group );
- adios.DefineVariable( group, "size", "unsigned int" );
- adios.DefineVariable( group, "numbers", "int", "size" );
- adios.DefineAttribute( group, "description", "string", "1 to 10" );
-
- const std::string file( "numbers.bp" );
- adios.Open( file, "write", "FStream" );// open a file stream transport for writing to file numbers.bp
- adios.SetCurrentGroup( file, group );// Write will look for variables in the Vector group defined in numbers.xml
- adios.Write( file, "size", &size ); //writes size
- adios.Write( file, "numbers", &numbers[0] ); //writes vector numbers
- adios.Close( file ); //flush and closes numbers.bp now containing size and numbers
- }
- catch( std::bad_alloc& e )
- {
- if( rank == 0 )
- {
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::invalid_argument& e )
- {
- if( rank == 0 )
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::ios_base::failure& e )
- {
- if( rank == 0 )
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch( std::exception& e )
- {
- if( rank == 0 )
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
-
- MPI_Finalize( );
-
- return 0;
-}
- * helloFStreamNoXML.cpp
- *
- * Created on: Dec 2, 2016
- * Author: wfg
- */
-
-
-
-
diff --git a/examples/hello/singleBP/Makefile b/examples/hello/singleBP/Makefile
new file mode 100644
index 000000000..96edd8f1d
--- /dev/null
+++ b/examples/hello/singleBP/Makefile
@@ -0,0 +1,35 @@
+# Makefile for testing purposes, will build libadios.a
+# Created on: Oct 4, 2016
+# Author: wfg
+
+
+BASE_NAME=helloSingleBP_OOP
+
+TOOL_DIR=/usr/bin
+
+CC=$(TOOL_DIR)/g++ # Compiling with mpicc for now
+MPICC=$(TOOL_DIR)/mpic++
+AR=$(TOOL_DIR)/ar
+
+#ADIOS LOCATION
+ADIOS_DIR=../../..
+ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
+ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
+
+ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
+
+
+#FLAGS
+CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
+
+all: mpi
+
+mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
+ $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME)_mpi $(ADIOS_LIB)
+
+nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
+ $(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME)_nompi $(ADIOS_NOMPI_LIB)
+
+clean:
+ rm *_mpi; rm *_nompi
+
diff --git a/examples/hello/singleBP/helloSingleBP.cpp b/examples/hello/singleBP/helloSingleBP.cpp
new file mode 100644
index 000000000..35815996a
--- /dev/null
+++ b/examples/hello/singleBP/helloSingleBP.cpp
@@ -0,0 +1,89 @@
+/*
+ * helloADIOSNoXML_OOP.cpp
+ *
+ * Created on: Jan 9, 2017
+ * Author: wfg
+ */
+
+#include <vector>
+#include <iostream>
+
+#ifdef HAVE_MPI
+ #include <mpi.h>
+#else
+ #include "mpidummy.h"
+ using adios::MPI_Init;
+ using adios::MPI_Comm_rank;
+ using adios::MPI_Finalize;
+#endif
+
+
+#include "ADIOS.h"
+
+
+int main( int argc, char* argv [] )
+{
+ MPI_Init( &argc, &argv );
+ int rank;
+ MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+ const bool adiosDebug = true;
+
+ //Application variable
+ std::vector<double> myInts = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ int myIntsSize = 10;
+
+ try
+ {
+ //Define group and variables
+ adios::ADIOS adios( MPI_COMM_WORLD, adiosDebug );
+ const std::string groupName( "ints" );
+ adios.DeclareGroup( groupName );
+ adios.DefineVariable( groupName, "myIntsSize", "int" );
+ adios.DefineVariable( groupName, "myInts", "double", "myIntsSize" );
+
+ //Define method
+ const std::string methodName( "singleBP" );
+ adios.DeclareMethod( methodName, "singleBP" );
+ adios.AddCapsule( methodName, "buffer=Heap" );
+ adios.AddTransport( methodName, "transport=POSIX" );
+
+ //Create engine handler and Write
+ int handler = adios.Open( "myInts.bp", "w", methodName );
+ adios.SetDefaultGroup( handler, groupName );
+ adios.Write( handler, "myIntsSize", &myIntsSize );
+ adios.Write( handler, "myInts", &myInts.front() );
+ adios.Close( handler );
+ }
+ catch( std::invalid_argument& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::ios_base::failure& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::exception& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+
+ MPI_Finalize( );
+
+ return 0;
+
+}
+
+
+
diff --git a/examples/hello/singleBP/helloSingleBP_OOP.cpp b/examples/hello/singleBP/helloSingleBP_OOP.cpp
new file mode 100644
index 000000000..1e4c5ffdc
--- /dev/null
+++ b/examples/hello/singleBP/helloSingleBP_OOP.cpp
@@ -0,0 +1,86 @@
+/*
+ * helloADIOSNoXML_OOP.cpp
+ *
+ * Created on: Jan 9, 2017
+ * Author: wfg
+ */
+
+#include <vector>
+#include <iostream>
+
+#ifdef HAVE_MPI
+ #include <mpi.h>
+#else
+ #include "mpidummy.h"
+ using adios::MPI_Init;
+ using adios::MPI_Comm_rank;
+ using adios::MPI_Finalize;
+#endif
+
+
+#include "ADIOS_OOP.h"
+
+
+int main( int argc, char* argv [] )
+{
+ MPI_Init( &argc, &argv );
+ int rank;
+ MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+ const bool adiosDebug = true;
+
+ //Application variable
+ std::vector<double> myInts = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ int myIntsSize = 10;
+
+ try
+ {
+ //Define group and variables
+ adios::Group groupInts( adiosDebug );
+ groupInts.DefineVariable( "myIntsSize", "int" ); //define size as scalar
+ groupInts.DefineVariable( "myInts", "double", "myIntsSize" ); //define variable with associate size
+
+ //Define method
+ adios::Method single;
+ single.AddCapsule( "buffer=Heap" );
+ single.AddTransport( "transport=POSIX" );
+
+ //Create engine and Write
+ adios::engine::SingleBP engine( "myInts.bp", "w", MPI_COMM_WORLD, single, adiosDebug );
+ engine.SetDefaultGroup( groupInts );
+ engine.Write( "myIntsSize", &myIntsSize );
+ engine.Write( "myInts", &myInts.front() );
+ engine.Close( );
+ }
+ catch( std::invalid_argument& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::ios_base::failure& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::exception& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+
+ MPI_Finalize( );
+
+ return 0;
+
+}
+
+
+
diff --git a/include/ADIOS.h b/include/ADIOS.h
index b60c71b52..04c92fda0 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -24,9 +24,9 @@
#include "mpidummy.h"
#endif
+#include "core/Engine.h"
#include "core/Group.h"
#include "core/Method.h"
-#include "core/Engine.h"
#include "core/Support.h"
@@ -129,7 +129,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param name
* @param type
*/
- void DeclareMethod( const std::string methodName, const std::string type );
+ void DeclareMethod( const std::string methodName, const std::string type = "SingleBP" );
/**
* Add a capsule type to method name defined from DeclareMethod
@@ -143,7 +143,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
if( m_DebugMode == true )
CheckMethod( itMethod, methodName, " from call to AddBuffer\n" );
- itMethod->second.AddCapsule( args );
+ itMethod->second.AddCapsule( args... );
}
/**
@@ -158,7 +158,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
if( m_DebugMode == true )
CheckMethod( itMethod, methodName, " from call to AddTransport\n" );
- itMethod->second.AddTransport( args );
+ itMethod->second.AddTransport( args... );
}
/**
@@ -198,7 +198,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param streamName unique name
* @param groupName default group from which variables will be used
*/
- void SetGroup( const unsigned int handler, const std::string groupName );
+ void SetDefaultGroup( const unsigned int handler, const std::string groupName );
template<class T>
diff --git a/include/ADIOS_OOP.h b/include/ADIOS_OOP.h
new file mode 100644
index 000000000..988e327de
--- /dev/null
+++ b/include/ADIOS_OOP.h
@@ -0,0 +1,20 @@
+/*
+ * ADIOS_OOP.h
+ *
+ * Created on: Jan 9, 2017
+ * Author: wfg
+ */
+
+#ifndef ADIOS_OOP_H_
+#define ADIOS_OOP_H_
+
+
+#include "core/Group.h"
+#include "core/Method.h"
+
+//TRANSFORMS
+#include "engine/SingleBP.h"
+#include "transform/BZip2.h"
+
+
+#endif /* ADIOS_OOP_H_ */
diff --git a/include/capsule/Heap.h b/include/capsule/Heap.h
index b5085d125..d16d04df3 100644
--- a/include/capsule/Heap.h
+++ b/include/capsule/Heap.h
@@ -27,15 +27,16 @@ public:
* Unique constructor
* @param accessMode read, write or append
* @param rankMPI MPI rank
- * @param dataSize maximum data size set by user
- * @param metadataSize maximum metadata size set by user
+ * @param debugMode true: extra checks, slower
+ * @param cores threaded operations
*/
- Heap( const std::string accessMode, const int rankMPI, const bool debugMode = false, const unsigned int cores = 1 );
+ Heap( const std::string accessMode, const int rankMPI, const bool debugMode = false,
+ const unsigned int cores = 1 );
~Heap( );
- char* GetData( ) const;
- char* GetMetadata( ) const;
+ char* GetData( );
+ char* GetMetadata( );
const std::size_t GetDataSize( ) const;
const std::size_t GetMetadataSize( ) const;
@@ -77,8 +78,6 @@ private:
std::vector<char> m_Data; ///< data buffer allocated using the STL in heap memory, default size = 16 Mb
std::vector<char> m_Metadata; ///< metadata buffer allocated using the STL in heap memory, default size = 100 Kb
- const size_t m_MaxDataSize; ///< maximum data size set by user
- const size_t m_MaxMetadataSize; ///< maximum metadata size set by user
};
diff --git a/include/capsule/ShmSystemV.h b/include/capsule/ShmSystemV.h
index 7b2046a8f..c7e1f2c6c 100644
--- a/include/capsule/ShmSystemV.h
+++ b/include/capsule/ShmSystemV.h
@@ -26,14 +26,17 @@ public:
* @param pathName used to create the key as a unique identifier
* @param dataSize size of allocated memory segment for data
* @param metadataSize size of allocated memory segment for metadata
+ * @param debugMode true: extra checks, slower
+ * @param cores threaded operations
*/
ShmSystemV( const std::string accessMode, const int rankMPI, const std::string pathName,
- const size_t dataSize, const size_t metadataSize, const unsigned int cores = 1 );
+ const size_t dataSize, const size_t metadataSize,
+ const bool debugMode = false, const unsigned int cores = 1 );
~ShmSystemV( );
- char* GetData( ) const; ///< return the pointer to the raw data buffer
- char* GetMetadata( ) const; ///< return the pointer to the raw metadata buffer
+ char* GetData( ); ///< return the pointer to the raw data buffer
+ char* GetMetadata( ); ///< return the pointer to the raw metadata buffer
const std::size_t GetDataSize( ) const; ///< get current data buffer size
const std::size_t GetMetadataSize( ) const; ///< get current metadata buffer size
@@ -78,6 +81,8 @@ private:
const size_t m_MetadataSize; ///< size of the allocated shared memory segment
key_t m_MetadataKey; ///< key associated with the metadata buffer, created with ftok
int m_MetadataShmID; ///< metadata shared memory buffer id
+
+ void CheckShm( ) const; ///< checks if all shared memory allocations are correct, throws std::bad_alloc, called from constructor if debug mode is true
};
} //end namespace
diff --git a/include/core/Capsule.h b/include/core/Capsule.h
index 9f72f064a..ac3bf4b4b 100644
--- a/include/core/Capsule.h
+++ b/include/core/Capsule.h
@@ -40,8 +40,8 @@ public:
virtual ~Capsule( );
- virtual char* GetData( ) const = 0; ///< return the pointer to the raw data buffer
- virtual char* GetMetadata( ) const = 0; ///< return the pointer to the raw metadata buffer
+ virtual char* GetData( ) = 0; ///< return the pointer to the raw data buffer
+ virtual char* GetMetadata( ) = 0; ///< return the pointer to the raw metadata buffer
virtual const std::size_t GetDataSize( ) const = 0; ///< get current data buffer size
virtual const std::size_t GetMetadataSize( ) const = 0; ///< get current metadata buffer size
@@ -84,9 +84,9 @@ public:
virtual void WriteMetadata( const std::size_t first, const long double* metadata, const std::size_t size ) = 0;
-private:
+protected:
- const int m_RankMPI; ///< current MPI rank
+ const int m_RankMPI = 0; ///< current MPI rank
const bool m_DebugMode = false; ///< true: extra checks
const unsigned int m_Cores = 1; ///< number of cores for threaded operations
diff --git a/include/core/Engine.h b/include/core/Engine.h
index b7e2bcd96..208736cba 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -65,10 +65,13 @@ public:
* @param method
*/
Engine( const std::string engineType, const std::string name, const std::string accessMode,
- MPI_Comm mpiComm, const Method& method, const bool debugMode, const unsigned int cores );
+ MPI_Comm mpiComm, const Method& method, const bool debugMode = false, const unsigned int cores = 1,
+ const std::string endMessage = "" );
virtual ~Engine( );
+ void SetDefaultGroup( Group& group );
+
/**
* @brief Write functions can be overridden by derived classes. Base class behavior is to:
* 1) Write to Variable values (m_Values) in a group
@@ -78,33 +81,33 @@ public:
* @param variableName
* @param values coming from user app
*/
- virtual void Write( Group& group, const std::string variableName, const char* values );
- virtual void Write( Group& group, const std::string variableName, const unsigned char* values );
- virtual void Write( Group& group, const std::string variableName, const short* values );
- virtual void Write( Group& group, const std::string variableName, const unsigned short* values );
- virtual void Write( Group& group, const std::string variableName, const int* values );
- virtual void Write( Group& group, const std::string variableName, const unsigned int* values );
- virtual void Write( Group& group, const std::string variableName, const long int* values );
- virtual void Write( Group& group, const std::string variableName, const unsigned long int* values );
- virtual void Write( Group& group, const std::string variableName, const long long int* values );
- virtual void Write( Group& group, const std::string variableName, const unsigned long long int* values );
- virtual void Write( Group& group, const std::string variableName, const float* values );
- virtual void Write( Group& group, const std::string variableName, const double* values );
- virtual void Write( Group& group, const std::string variableName, const long double* values );
-
- virtual void Write( const std::string variableName, const char* values );
- virtual void Write( const std::string variableName, const unsigned char* values );
- virtual void Write( const std::string variableName, const short* values );
- virtual void Write( const std::string variableName, const unsigned short* values );
- virtual void Write( const std::string variableName, const int* values );
- virtual void Write( const std::string variableName, const unsigned int* values );
- virtual void Write( const std::string variableName, const long int* values );
- virtual void Write( const std::string variableName, const unsigned long int* values );
- virtual void Write( const std::string variableName, const long long int* values );
- virtual void Write( const std::string variableName, const unsigned long long int* values );
- virtual void Write( const std::string variableName, const float* values );
- virtual void Write( const std::string variableName, const double* values );
- virtual void Write( const std::string variableName, const long double* values );
+ virtual void Write( Group& group, const std::string variableName, const char* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const unsigned char* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const short* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const unsigned short* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const unsigned int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const long int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const unsigned long int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const long long int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const unsigned long long int* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const float* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const double* values ) = 0;
+ virtual void Write( Group& group, const std::string variableName, const long double* values ) = 0;
+
+ virtual void Write( const std::string variableName, const char* values ) = 0;
+ virtual void Write( const std::string variableName, const unsigned char* values ) = 0;
+ virtual void Write( const std::string variableName, const short* values ) = 0;
+ virtual void Write( const std::string variableName, const unsigned short* values ) = 0;
+ virtual void Write( const std::string variableName, const int* values ) = 0;
+ virtual void Write( const std::string variableName, const unsigned int* values ) = 0;
+ virtual void Write( const std::string variableName, const long int* values ) = 0;
+ virtual void Write( const std::string variableName, const unsigned long int* values ) = 0;
+ virtual void Write( const std::string variableName, const long long int* values ) = 0;
+ virtual void Write( const std::string variableName, const unsigned long long int* values ) = 0;
+ virtual void Write( const std::string variableName, const float* values ) = 0;
+ virtual void Write( const std::string variableName, const double* values ) = 0;
+ virtual void Write( const std::string variableName, const long double* values ) = 0;
virtual void Close( int transportIndex = -1 ); ///< Closes a particular transport
@@ -115,10 +118,11 @@ protected:
std::vector< std::shared_ptr<Transport> > m_Transports; ///< transports managed
const bool m_DebugMode = false; ///< true: additional checks, false: by-pass checks
unsigned int m_Cores = 1;
+ const std::string m_EndMessage; ///< added to exceptions to improve debugging
- virtual void Init( ); ///< Initialize m_Capsules and m_Transports, called from constructor
- virtual void InitCapsules( ); ///< Initialize transports from Method, called from Init in constructor.
- virtual void InitTransports( ); ///< Initialize transports from Method, called from Init in constructor.
+ virtual void Init( ) = 0; ///< Initialize m_Capsules and m_Transports, called from constructor
+ virtual void InitCapsules( ) = 0; ///< Initialize transports from Method, called from Init in constructor.
+ virtual void InitTransports( ) = 0; ///< Initialize transports from Method, called from Init in constructor.
/**
* Performs preliminary checks before writing a variable. Throws an exception if checks fail.
@@ -133,6 +137,19 @@ protected:
const std::set<std::string>& types,
const std::string hint ) const;
+ /**
+ * Used to verify parameters in m_Method containers
+ * @param itParam iterator to a certain parameter
+ * @param parameters map of parameters, from m_Method
+ * @param parameterName used if exception is thrown to provide debugging information
+ * @param hint used if exception is thrown to provide debugging information
+ */
+ void CheckParameter( const std::map<std::string, std::string>::const_iterator itParam,
+ const std::map<std::string, std::string>& parameters,
+ const std::string parameterName,
+ const std::string hint ) const;
+
+
std::string GetName( const std::vector<std::string>& arguments ) const; //might move this to adiosFunctions
};
diff --git a/include/core/Group.h b/include/core/Group.h
index 4d470880d..72b27220f 100644
--- a/include/core/Group.h
+++ b/include/core/Group.h
@@ -38,9 +38,9 @@ namespace adios
class Group
{
-public:
+ friend class Engine;
- std::set< std::string > m_WrittenVariables; ///< set of variables whose T* values have been set with Write (no nullptr)
+public:
/**
* Empty constructor
@@ -72,21 +72,22 @@ public:
* @param dimensionsCSV comma separated variable local dimensions (e.g. "Nx,Ny,Nz")
* @param globalDimensionsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
* @param globalOffsetsCSV comma separated variable global dimensions (e.g. "gNx,gNy,gNz"), if globalOffsetsCSV is also empty variable is local
- * @param transform pointer reference to a Transform object, default = nullptr
- * @param parameter corresponding parameter used by Transform to do operations
+ * @param transforms collection of Transform objects applied to this variable, sequence matters, default is empty
+ * @param parameters corresponding parameter used by a Transform object in transforms (index should match), default is empty
*/
void DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV = "",
const std::string globalDimensionsCSV = "", const std::string globalOffsetsCSV = "",
- const Transform* transform = nullptr, const short parameter = -1 );
+ const std::vector<Transform*> transforms = std::vector<Transform*>(),
+ const std::vector<int> parameters = std::vector<int>() );
/**
* Sets a variable transform contained in ADIOS Transforms (single container for all groups and variables)
* @param variableName variable to be assigned a transformation
* @param transform corresponding transform object, non-const as a pointer is created and pushed to a vector
- * @param parameter optional parameter interpreted by the corresponding Transform
+ * @param parameter optional parameter interpreted by the corresponding Transform, default = -1
*/
- void AddTransform( const std::string variableName, Transform& transform, const short parameter = -1 );
+ void AddTransform( const std::string variableName, Transform& transform, const int parameter = -1 );
/**
* Define a new attribute
@@ -112,9 +113,13 @@ public:
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:
+
+ std::set< std::string > m_WrittenVariables; ///< set of variables whose T* values have been set with Write (no nullptr)
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
+ 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 Variable
std::vector< Variable<char> > m_Char; ///< Key: variable name, Value: variable of type char
std::vector< Variable<unsigned char> > m_UChar; ///< Key: variable name, Value: variable of type unsigned char
@@ -156,7 +161,7 @@ public:
* @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;
*/
- const short SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept;
+ const int SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept;
/**
diff --git a/include/core/Method.h b/include/core/Method.h
index 1c38e3525..2a9551c1e 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -26,35 +26,33 @@ public:
const std::string m_Type = "SingleBP"; ///< Method type
const bool m_DebugMode = false; ///< true: on, throws exceptions and do additional checks, false: off, faster, but unsafe
+ std::vector< std::map<std::string, std::string> > m_CapsuleParameters; ///< each is a separate Transport containing their own parameters
+ std::vector< std::map<std::string, std::string> > m_TransportParameters; ///< each is a separate Transport containing their own parameters
/**
* Unique constructor, must have a type
* @param type must be an engine type, default = SingleBP
*/
- Method( const std::string type = "SingleBP", const bool debugMode = false );
+ Method( const std::string type = "", const bool debugMode = false );
~Method( );
template< class ...Args>
void AddCapsule( Args... args )
{
- std::vector<std::string> parameters = { args };
+ std::vector<std::string> parameters = { args... };
AddCapsuleParameters( parameters );
}
template< class ...Args>
void AddTransport( Args... args )
{
- std::vector<std::string> parameters = { args };
+ std::vector<std::string> parameters = { args... };
AddTransportParameters( parameters );
}
-
private:
- std::vector< std::map<std::string, std::string> > m_CapsuleParameters; ///< each is a separate Transport containing their own parameters
- std::vector< std::map<std::string, std::string> > m_TransportParameters; ///< each is a separate Transport containing their own parameters
-
void AddCapsuleParameters( const std::vector<std::string>& parameters );
void AddTransportParameters( const std::vector<std::string>& parameters );
diff --git a/include/core/Transform.h b/include/core/Transform.h
index 6737a160d..e664fb574 100644
--- a/include/core/Transform.h
+++ b/include/core/Transform.h
@@ -11,10 +11,9 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <string>
+#include <vector>
/// \endcond
-#include "core/Variable.h"
-
namespace adios
{
@@ -33,7 +32,6 @@ public:
/**
* Initialize parent method
* @param method zlib, bzip2, szip
- * @param variable
*/
Transform( const std::string method );
diff --git a/include/core/Transport.h b/include/core/Transport.h
index 4a0451c7f..fa98eb15b 100644
--- a/include/core/Transport.h
+++ b/include/core/Transport.h
@@ -30,8 +30,8 @@ class Transport
public:
const std::string m_Type; ///< transport type from derived class
- const std::string m_Name; ///< from Open
- const std::string m_AccessMode; ///< from Open
+ std::string m_Name; ///< from Open
+ std::string m_AccessMode; ///< from Open
#ifdef HAVE_MPI
MPI_Comm m_MPIComm = NULL; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
diff --git a/include/core/Variable.h b/include/core/Variable.h
index fbbf72b1f..cc822d136 100644
--- a/include/core/Variable.h
+++ b/include/core/Variable.h
@@ -13,7 +13,7 @@
#include <vector>
/// \endcond
-#include "Transform.h"
+#include "core/Transform.h"
namespace adios
{
@@ -21,14 +21,14 @@ namespace adios
* @param Base (parent) class for template derived (child) class CVariable. Required to put CVariable objects in STL containers.
*/
template< class T >
-class Variable
+struct Variable
{
- const std::string DimensionsCSV; ///< comma separated list for variables to search for local dimensions
- const T* Values; ///< pointer to values passed from user in ADIOS Write
- const unsigned short GlobalBoundsIndex; ///< if global > 0, index corresponds to global-bounds in m_GlobalBounds in CGroup, if local then = -1
+ std::string DimensionsCSV; ///< comma separated list for variables to search for local dimensions
+ T* Values; ///< pointer to values passed from user in ADIOS Write
+ int GlobalBoundsIndex; ///< if global > 0, index corresponds to global-bounds in m_GlobalBounds in CGroup, if local then = -1
std::vector< Transform* > Transforms; ///< associated transforms, sequence determines application order, e.g. first Transforms[0] then Transforms[1]. Pointer used as reference (no memory management).
- std::vector< short > Parameters; ///< additional optional parameter understood by the corresponding Transform in Transforms vector
+ std::vector< int > Parameters; ///< additional optional parameter understood by the corresponding Transform in Transforms vector
};
diff --git a/include/engine/SingleBP.h b/include/engine/SingleBP.h
index cebbed5e2..52706956b 100644
--- a/include/engine/SingleBP.h
+++ b/include/engine/SingleBP.h
@@ -13,6 +13,8 @@
namespace adios
{
+namespace engine
+{
class SingleBP : public Engine
@@ -47,6 +49,19 @@ public:
void Write( Group& group, const std::string variableName, const double* values );
void Write( Group& group, const std::string variableName, const long double* values );
+ void Write( const std::string variableName, const char* values );
+ void Write( const std::string variableName, const unsigned char* values );
+ void Write( const std::string variableName, const short* values );
+ void Write( const std::string variableName, const unsigned short* values );
+ void Write( const std::string variableName, const int* values );
+ void Write( const std::string variableName, const unsigned int* values );
+ void Write( const std::string variableName, const long int* values );
+ void Write( const std::string variableName, const unsigned long int* values );
+ void Write( const std::string variableName, const long long int* values );
+ void Write( const std::string variableName, const unsigned long long int* values );
+ void Write( const std::string variableName, const float* values );
+ void Write( const std::string variableName, const double* values );
+ void Write( const std::string variableName, const long double* values );
private:
@@ -62,8 +77,8 @@ private:
-
-} //end namespace
+} //end namespace engine
+} //end namespace adios
#endif /* SINGLEBP_H_ */
diff --git a/include/functions/capsuleTemplates.h b/include/functions/capsuleTemplates.h
index 6a29acceb..802c12244 100644
--- a/include/functions/capsuleTemplates.h
+++ b/include/functions/capsuleTemplates.h
@@ -30,7 +30,7 @@ namespace adios
* @param max
*/
template<class T>
-void GetMinMax( const T* values, const size_t size, T& min, T& max )
+void GetMinMax( const T* values, const size_t size, T& min, T& max, const unsigned int cores = 1 )
{
min = values[0];
max = values[0];
@@ -93,74 +93,74 @@ void MemcpyThreads( T* destination, const U* source, std::size_t count, const un
* @param maxBufferSize
* @param buffer
*/
-template<class T>
-void WriteToBuffer( const T* data, const size_t size,
- std::vector< std::shared_ptr<Transport> >& transports,
- const size_t maxBufferSize, std::vector<char>& buffer )
-{
- auto lf_TransportsWrite = []( const int transportIndex, std::vector< std::shared_ptr<Transport> >& transports,
- std::vector<char>& buffer )
- {
- if( transportIndex == -1 ) // all transports
- {
- for( auto& transport : transports )
- transport->Write( buffer );
- }
- else
- transports[ transportIndex ]->Write( buffer );
- };
-
- //FUNCTION starts here
- const size_t dataBytes = size * sizeof( T ); //size of data in bytes
-
- //check for DataMan transport
- if( transportIndex == -1 ) // all transports
- {
- for( auto& transport : transports )
- {
- if( transport->m_Method == "DataMan" ) //DataMan needs all the information
- buffer.resize( dataBytes ); //resize buffer to fit all data
- }
- }
- else //just one transport
- {
- if( transports[transportIndex]->m_Method == "DataMan" )
- buffer.resize( dataBytes ); //resize buffer to fit all data
- }
-
- if( dataBytes <= buffer.size() ) // dataBytes < buffer.size()
- {
- buffer.resize( dataBytes ); //this resize shouldn't change capacity or call realloc
- MemcpyThreads( &buffer[0], data, dataBytes, 1 ); //copy memory in threaded fashion, need to test with size, serial for now
- lf_TransportsWrite( transportIndex, transports, buffer );
- return;
- }
-
- if( buffer.size() < dataBytes && dataBytes <= maxBufferSize ) // buffer.size() < dataBytes < maxBufferSize
- {
- buffer.resize( dataBytes );
- MemcpyThreads( &buffer[0], data, dataBytes, 1 ); //copy memory in threaded fashion, need to test with size, serial for now
- lf_TransportsWrite( transportIndex, transports, buffer );
- return;
- }
-
- // dataBytes > maxBufferSize == buffer.size() split the variable in buffer buckets
- buffer.resize( maxBufferSize ); //resize to maxBufferSize, this might call realloc
- const size_t buckets = dataBytes / maxBufferSize + 1;
- const size_t remainder = dataBytes % maxBufferSize;
-
- for( unsigned int bucket = 0; buckets < buckets; ++bucket )
- {
- const size_t dataOffset = bucket * maxBufferSize / sizeof( T );
-
- if( bucket == buckets-1 )
- MemcpyThreads( &buffer[0], data[dataOffset], remainder, 1 );
- else
- MemcpyThreads( &buffer[0], data[dataOffset], maxBufferSize, 1 );
-
- lf_TransportsWrite( transportIndex, transports, buffer );
- }
-}
+//template<class T>
+//void WriteToBuffer( const T* data, const size_t size,
+// std::vector< std::shared_ptr<Transport> >& transports,
+// const size_t maxBufferSize, std::vector<char>& buffer )
+//{
+// auto lf_TransportsWrite = []( const int transportIndex, std::vector< std::shared_ptr<Transport> >& transports,
+// std::vector<char>& buffer )
+// {
+// if( transportIndex == -1 ) // all transports
+// {
+// for( auto& transport : transports )
+// transport->Write( buffer );
+// }
+// else
+// transports[ transportIndex ]->Write( buffer );
+// };
+//
+// //FUNCTION starts here
+// const size_t dataBytes = size * sizeof( T ); //size of data in bytes
+//
+// //check for DataMan transport
+// if( transportIndex == -1 ) // all transports
+// {
+// for( auto& transport : transports )
+// {
+// if( transport->m_Method == "DataMan" ) //DataMan needs all the information
+// buffer.resize( dataBytes ); //resize buffer to fit all data
+// }
+// }
+// else //just one transport
+// {
+// if( transports[transportIndex]->m_Method == "DataMan" )
+// buffer.resize( dataBytes ); //resize buffer to fit all data
+// }
+//
+// if( dataBytes <= buffer.size() ) // dataBytes < buffer.size()
+// {
+// buffer.resize( dataBytes ); //this resize shouldn't change capacity or call realloc
+// MemcpyThreads( &buffer[0], data, dataBytes, 1 ); //copy memory in threaded fashion, need to test with size, serial for now
+// lf_TransportsWrite( transportIndex, transports, buffer );
+// return;
+// }
+//
+// if( buffer.size() < dataBytes && dataBytes <= maxBufferSize ) // buffer.size() < dataBytes < maxBufferSize
+// {
+// buffer.resize( dataBytes );
+// MemcpyThreads( &buffer[0], data, dataBytes, 1 ); //copy memory in threaded fashion, need to test with size, serial for now
+// lf_TransportsWrite( transportIndex, transports, buffer );
+// return;
+// }
+//
+// // dataBytes > maxBufferSize == buffer.size() split the variable in buffer buckets
+// buffer.resize( maxBufferSize ); //resize to maxBufferSize, this might call realloc
+// const size_t buckets = dataBytes / maxBufferSize + 1;
+// const size_t remainder = dataBytes % maxBufferSize;
+//
+// for( unsigned int bucket = 0; buckets < buckets; ++bucket )
+// {
+// const size_t dataOffset = bucket * maxBufferSize / sizeof( T );
+//
+// if( bucket == buckets-1 )
+// MemcpyThreads( &buffer[0], data[dataOffset], remainder, 1 );
+// else
+// MemcpyThreads( &buffer[0], data[dataOffset], maxBufferSize, 1 );
+//
+// lf_TransportsWrite( transportIndex, transports, buffer );
+// }
+//}
diff --git a/include/transform/BZIP2.h b/include/transform/BZip2.h
similarity index 86%
rename from include/transform/BZIP2.h
rename to include/transform/BZip2.h
index 43799e306..2f2daffc5 100644
--- a/include/transform/BZIP2.h
+++ b/include/transform/BZip2.h
@@ -1,5 +1,5 @@
/*
- * BZIP2.h
+ * BZip2.h
*
* Created on: Oct 17, 2016
* Author: wfg
@@ -14,6 +14,8 @@
namespace adios
{
+namespace transform
+{
class BZIP2 : public Transform
@@ -36,7 +38,8 @@ public:
};
-} //end namespace
+} //end namespace transform
+} //end namespace adios
diff --git a/include/transport/MPIFile.h b/include/transport/MPIFile.h
index 89d22765c..57389b334 100644
--- a/include/transport/MPIFile.h
+++ b/include/transport/MPIFile.h
@@ -22,7 +22,7 @@ class MPIFile : public Transport
public:
- MPIFile( MPI_Comm mpiComm, const bool debugMode, const std::vector<std::string>& arguments );
+ MPIFile( MPI_Comm mpiComm, const bool debugMode );
~MPIFile( );
diff --git a/src/ADIOS.cpp b/src/ADIOS.cpp
index b9b8df803..8b650933c 100644
--- a/src/ADIOS.cpp
+++ b/src/ADIOS.cpp
@@ -15,6 +15,8 @@
#include "ADIOS.h"
#include "functions/adiosFunctions.h"
+//Engine
+#include "engine/SingleBP.h"
namespace adios
{
@@ -67,22 +69,33 @@ void ADIOS::DeclareGroup( const std::string groupName )
throw std::invalid_argument( "ERROR: group " + groupName + " already exist, from call to DeclareGroup\n" );
}
- m_Groups.emplace( groupName, Group( m_HostLanguage, m_DebugMode ) );
+ m_Groups.emplace( groupName, Group( m_DebugMode ) );
}
-void ADIOS::SetGroup( const unsigned int handler, const std::string groupName )
+void ADIOS::SetDefaultGroup( const unsigned int handler, const std::string groupName )
{
auto itEngine = m_Engines.find( handler );
auto itGroup = m_Groups.find( groupName );
if( m_DebugMode == true )
{
- CheckEngine( itEngine, handler, " in call to SetGroup.\n" );
- CheckGroup( itGroup, groupName, " in call to SetGroup.\n" );
+ CheckEngine( itEngine, handler, " in call to SetDefaultGroup.\n" );
+ CheckGroup( itGroup, groupName, " in call to SetDefaultGroup.\n" );
}
- itEngine->second->m_Group = &( itGroup->second );
+ itEngine->second->SetDefaultGroup( itGroup->second );
+}
+
+
+void ADIOS::DeclareMethod( const std::string methodName, const std::string type )
+{
+ if( m_DebugMode == true )
+ {
+ if( m_Methods.count( methodName ) == 1 )
+ throw std::invalid_argument( "ERROR: method " + methodName + " already declared, from DeclareMethod\n" );
+ }
+ m_Methods.emplace( methodName, Method( type, m_DebugMode ) );
}
@@ -100,24 +113,38 @@ const unsigned int ADIOS::Open( const std::string name, const std::string access
}
++m_EngineCounter;
+ const std::string type( itMethod->second.m_Type );
- if( methodName == "SingleBP" )
+ if( type == "SingleBP" || type == "singleBP" || type == "singlebp" )
{
- m_Engines[ m_EngineCounter ] = std::make_shared<SingleBP>( name, accessMode, mpiComm, itMethod->second, cores );
+ m_Engines.emplace( m_EngineCounter, std::make_shared<engine::SingleBP>( name, accessMode, mpiComm, itMethod->second, cores ) );
}
- else if( methodName == "SIRIUS" )
+// else if( type == "SIRIUS" )
+// {
+// //here must complete
+// }
+// else if( type == "DataMan" )
+// {
+// //here must complete
+// }
+ else
{
- //here must complete
- }
- else if( methodName == "DataMan" )
- {
- //here must complete
+ if( m_DebugMode == true )
+ throw std::invalid_argument( "ERROR: type " + type + " not supported for method " + methodName + ", in call to Open\n" );
}
return m_EngineCounter;
}
+const unsigned int ADIOS::Open( const std::string streamName, const std::string accessMode, const std::string methodName,
+ const unsigned int cores )
+{
+ return Open( streamName, accessMode, m_MPIComm, methodName, cores );
+}
+
+
+
void ADIOS::Close( const unsigned int handler, const int transportIndex ) //close stream
{
auto itEngine = m_Engines.find( handler );
@@ -203,7 +230,7 @@ void ADIOS::CheckEngine( std::unordered_map< unsigned int, std::shared_ptr<Engin
const unsigned int handle, const std::string hint ) const
{
if( itEngine == m_Engines.end() )
- throw std::invalid_argument( "ERROR: stream (or file) from handle " + handle + " not created with Open , " + hint + "\n" );
+ throw std::invalid_argument( "ERROR: stream (or file) from handle " + std::to_string( handle ) + " not created with Open , " + hint + "\n" );
}
diff --git a/src/capsule/Heap.cpp b/src/capsule/Heap.cpp
index c858a4c4a..7706601ad 100644
--- a/src/capsule/Heap.cpp
+++ b/src/capsule/Heap.cpp
@@ -26,15 +26,15 @@ Heap::~Heap( )
{ }
-char* Heap::GetData( ) const
+char* Heap::GetData( )
{
- return m_Data.front();
+ return &m_Data.front();
}
-char* Heap::GetMetadata( ) const
+char* Heap::GetMetadata( )
{
- return m_Metadata.front();
+ return &m_Metadata.front();
}
diff --git a/src/capsule/ShmSystemV.cpp b/src/capsule/ShmSystemV.cpp
index 1b0bdfbc9..0ed5cef2b 100644
--- a/src/capsule/ShmSystemV.cpp
+++ b/src/capsule/ShmSystemV.cpp
@@ -7,7 +7,10 @@
#include <sys/shm.h>
+#include <ios> //std::ios_base::failure
+
#include "capsule/ShmSystemV.h"
+#include "functions/capsuleTemplates.h"
namespace adios
@@ -15,8 +18,9 @@ namespace adios
ShmSystemV::ShmSystemV( const std::string accessMode, const int rankMPI, const std::string pathName,
- const size_t dataSize, const size_t metadataSize, const unsigned int cores ):
- Capsule( "ShmSystemV", accessMode, rankMPI, cores ),
+ const size_t dataSize, const size_t metadataSize,
+ const bool debugMode, const unsigned int cores ):
+ Capsule( "ShmSystemV", accessMode, rankMPI, debugMode, cores ),
m_DataSize{ dataSize },
m_MetadataSize{ metadataSize }
{
@@ -24,30 +28,17 @@ ShmSystemV::ShmSystemV( const std::string accessMode, const int rankMPI, const s
const std::string dataPath( pathName + "/adios.shm.data." + std::to_string( m_RankMPI ) );
m_DataKey = ftok( dataPath.c_str(), m_RankMPI+1 );
m_DataShmID = shmget( m_DataKey, m_DataSize, IPC_CREAT | 0666 );
-
- if( m_DataShmID < 0)
- throw std::ios_base::failure( "ERROR: Failed to create data shm segment of size " + m_DataSize +
- " from call to ShmSystemV constructor\n" );
-
m_Data = (char*)shmat( m_DataShmID, NULL, 0 );
- if( m_Data == nullptr )
- throw std::ios_base::failure( "ERROR: Failed to attach to data shm segment of size " + m_DataSize +
- " from call to ShmSystemV constructor\n" );
// Metadata Shared memory sector
const std::string metadataPath( pathName + "/adios.shm.metadata." + std::to_string( m_RankMPI ) );
m_MetadataKey = ftok( metadataPath.c_str(), m_RankMPI+1 ); //2nd field must be greater than zero and unique
m_MetadataShmID = shmget( m_MetadataKey, m_MetadataSize, IPC_CREAT | 0666 );
-
- if( m_DataShmID < 0)
- throw std::ios_base::failure( "ERROR: Failed to create metadata shm segment of size " + m_MetadataSize +
- " from call to ShmSystemV constructor\n" );
-
m_Metadata = (char*)shmat( m_MetadataShmID, NULL, 0 );
- if( m_Metadata == nullptr )
- throw std::ios_base::failure( "ERROR: Failed to attach to metadata shm segment of size " + m_MetadataSize +
- " from call to ShmSystemV constructor\n" );
+
+ if( m_DebugMode == true )
+ CheckShm( );
}
@@ -55,13 +46,13 @@ ShmSystemV::~ShmSystemV( )
{ }
-char* ShmSystemV::GetData( ) const
+char* ShmSystemV::GetData( )
{
return m_Data;
}
-char* ShmSystemV::GetMetadata( ) const
+char* ShmSystemV::GetMetadata( )
{
return m_Metadata;
}
@@ -78,7 +69,6 @@ const std::size_t ShmSystemV::GetMetadataSize( ) const
return m_MetadataSize;
}
-
//WriteData functions
void ShmSystemV::WriteData( const std::size_t first, const char* data, const std::size_t size )
{
@@ -212,5 +202,28 @@ void ShmSystemV::WriteMetadata( const std::size_t first, const long double* meta
}
+void ShmSystemV::CheckShm( ) const
+{
+ if( m_DataShmID < 0)
+ throw std::ios_base::failure( "ERROR: Failed to create data shm segment of size " + std::to_string( m_DataSize ) +
+ " from call to ShmSystemV constructor\n" );
+
+ if( m_Data == nullptr )
+ throw std::ios_base::failure( "ERROR: Failed to attach to data shm segment of size " + std::to_string( m_DataSize ) +
+ " and id " + std::to_string( m_DataShmID ) +
+ ", from call to ShmSystemV constructor\n" );
+
+ if( m_DataShmID < 0)
+ throw std::ios_base::failure( "ERROR: Failed to create metadata shm segment of size " + std::to_string( m_MetadataSize ) +
+ " from call to ShmSystemV constructor\n" );
+
+
+ if( m_Metadata == nullptr )
+ throw std::ios_base::failure( "ERROR: Failed to attach to metadata shm segment of size " + std::to_string( m_MetadataSize ) +
+ " and id " + std::to_string( m_MetadataShmID ) +
+ " from call to ShmSystemV constructor\n" );
+}
+
+
} //end namespace
diff --git a/src/core/Engine.cpp b/src/core/Engine.cpp
index fea99e02f..90d5cd98c 100644
--- a/src/core/Engine.cpp
+++ b/src/core/Engine.cpp
@@ -7,7 +7,8 @@
#include "core/Engine.h"
-#include "functions/engineTemplates.h"
+#include "core/Support.h"
+#include "functions/adiosFunctions.h"
namespace adios
@@ -16,14 +17,15 @@ namespace adios
Engine::Engine( const std::string engineType, const std::string name, const std::string accessMode,
const MPI_Comm mpiComm, const Method& method,
- const bool debugMode, const unsigned int cores ):
+ const bool debugMode, const unsigned int cores, const std::string endMessage ):
+ m_MPIComm{ mpiComm },
m_EngineType{ engineType },
m_Name{ name },
m_AccessMode{ accessMode },
- m_Method{ &method },
- m_MPIComm{ mpiComm },
+ m_Method{ method },
m_DebugMode{ debugMode },
- m_Cores{ cores }
+ m_Cores{ cores },
+ m_EndMessage{ endMessage }
{
MPI_Comm_rank( m_MPIComm, &m_RankMPI );
MPI_Comm_size( m_MPIComm, &m_SizeMPI );
@@ -33,104 +35,12 @@ Engine::Engine( const std::string engineType, const std::string name, const std:
Engine::~Engine( )
{ }
-
-void Engine::Init( )
-{ }
-
-
-void Engine::InitCapsules( )
-{ }
-
-
-void Engine::InitTransports( )
-{ }
-
-
-//WRITE Functions
-void Engine::Write( Group& group, const std::string variableName, const char* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("char"), " from call to Write char*" );
- WriteToCapsules( group, group.m_Char[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const unsigned char* values )
+void Engine::SetDefaultGroup( Group& group )
{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("unsigned char"), " from call to Write unsigned char*" );
- WriteToCapsules( group, group.m_UChar[index], values, m_Capsules, m_Transports );
+ m_Group = &group;
}
-
-void Engine::Write( Group& group, const std::string variableName, const short* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("short"), " from call to Write short*" );
- WriteToCapsules( group, group.m_Short[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const unsigned short* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("unsigned short"), " from call to Write unsigned short*" );
- WriteToCapsules( group, group.m_UShort[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("int"), " from call to Write int*" );
- WriteToCapsules( group, group.m_Int[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const unsigned int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("unsigned int"), " from call to Write unsigned int*" );
- WriteToCapsules( group, group.m_UInt[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const long int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("long int"), " from call to Write long int*" );
- WriteToCapsules( group, group.m_LInt[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const unsigned long int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("unsigned long int"), " from call to Write unsigned long int*" );
- WriteToCapsules( group, group.m_ULInt[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const long long int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("long long int"), " from call to Write long long int*" );
- WriteToCapsules( group, group.m_LLInt[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const unsigned long long int* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("unsigned long long int"), " from call to Write unsigned long long int*" );
- WriteToCapsules( group, group.m_ULLInt[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const float* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("float"), " from call to Write float*" );
- WriteToCapsules( group, group.m_Float[index], values, m_Capsules, m_Transports );
-}
-
-
-void Engine::Write( Group& group, const std::string variableName, const double* values )
-{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("double"), " from call to Write double*" );
- WriteToCapsules( group, group.m_Double[index], values, m_Capsules, m_Transports );
-}
-
-
+//PROTECTED
const unsigned int Engine::PreSetVariable( Group& group, const std::string variableName,
const std::set<std::string>& types,
const std::string hint ) const
@@ -142,7 +52,7 @@ const unsigned int Engine::PreSetVariable( Group& group, const std::string varia
if( itVariable == group.m_Variables.end() )
throw std::invalid_argument( "ERROR: variable " + variableName + " doesn't exist " + hint + ".\n" );
- if( IsTypeAlias( itVariable->first, types ) == false )
+ if( IsTypeAlias( itVariable->second.first, types ) == false )
throw std::invalid_argument( "ERROR: type in variable " + variableName + " doesn't match " + hint + ".\n" );
}
@@ -165,8 +75,29 @@ void Engine::Close( int transportIndex )
}
}
+void Engine::Init( )
+{ }
+
+
+void Engine::InitCapsules( )
+{ }
+
+
+void Engine::InitTransports( )
+{ }
+
+
+void Engine::CheckParameter( const std::map<std::string, std::string>::const_iterator itParam,
+ const std::map<std::string, std::string>& parameters,
+ const std::string parameterName,
+ const std::string hint ) const
+{
+ if( itParam == parameters.end() )
+ throw std::invalid_argument( "ERROR: parameter name " + parameterName + " not found " + hint );
+}
+
+
-//PROTECTED
std::string Engine::GetName( const std::vector<std::string>& arguments ) const
{
bool isNameFound = false;
@@ -194,6 +125,3 @@ std::string Engine::GetName( const std::vector<std::string>& arguments ) const
} //end namespace
-
-
-
diff --git a/src/core/Group.cpp b/src/core/Group.cpp
index 7602abb60..21164d622 100644
--- a/src/core/Group.cpp
+++ b/src/core/Group.cpp
@@ -19,11 +19,15 @@
namespace adios
{
-
Group::Group( )
{ }
+Group::Group( const bool debugMode ):
+ m_DebugMode{ debugMode }
+{ }
+
+
Group::Group( const std::string& xmlGroup, std::vector< std::shared_ptr<Transform> >& transforms, const bool debugMode ):
m_DebugMode{ debugMode }
{
@@ -38,7 +42,7 @@ Group::~Group( )
void Group::DefineVariable( const std::string variableName, const std::string type,
const std::string dimensionsCSV,
const std::string globalDimensionsCSV, const std::string globalOffsetsCSV,
- const Transform* transform, const short parameter )
+ std::vector<Transform*> transforms, std::vector<int> parameters )
{
if( m_DebugMode == true )
{
@@ -46,71 +50,71 @@ void Group::DefineVariable( const std::string variableName, const std::string ty
throw std::invalid_argument( "ERROR: variable " + variableName + " already exists, in call to DefineVariable\n" );
}
- short globalBoundsIndex = SetGlobalBounds( globalDimensionsCSV, globalOffsetsCSV );
+ const int globalBoundsIndex = SetGlobalBounds( globalDimensionsCSV, globalOffsetsCSV );
if( IsTypeAlias( type, Support::DatatypesAliases.at("char") ) == true )
{
- m_Char.push_back( Variable<char>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_Char.push_back( Variable<char>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_Char.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("unsigned char") ) == true )
{
- m_UChar.push_back( Variable<unsigned char>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_UChar.push_back( Variable<unsigned char>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_UChar.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("short") ) == true )
{
- m_Short.push_back( Variable<short>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_Short.push_back( Variable<short>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_Short.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("unsigned short") ) == true )
{
- m_UShort.push_back( Variable<unsigned short>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_UShort.push_back( Variable<unsigned short>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_UShort.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("int") ) == true )
{
- m_Int.push_back( Variable<int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_Int.push_back( Variable<int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_Int.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("unsigned int") ) == true )
{
- m_UInt.push_back( Variable<unsigned int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_UInt.push_back( Variable<unsigned int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_UInt.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("long int") ) == true )
{
- m_LInt.push_back( Variable<long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_LInt.push_back( Variable<long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_LInt.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("unsigned long int") ) == true )
{
- m_ULInt.push_back( Variable<unsigned long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_ULInt.push_back( Variable<unsigned long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_ULInt.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("long long int") ) == true )
{
- m_LLInt.push_back( Variable<long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_LLInt.push_back( Variable<long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_LLInt.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("unsigned long long int") ) == true )
{
- m_ULLInt.push_back( Variable<unsigned long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_ULLInt.push_back( Variable<unsigned long long int>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_ULLInt.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("float") ) == true )
{
- m_Float.push_back( Variable<float>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_Float.push_back( Variable<float>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_Float.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("double") ) == true )
{
- m_Double.push_back( Variable<double>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_Double.push_back( Variable<double>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_Double.size()-1 );
}
else if( IsTypeAlias( type, Support::DatatypesAliases.at("long double") ) == true )
{
- m_LDouble.push_back( Variable<long double>{ dimensionsCSV, nullptr, globalBoundsIndex, transform, parameter } );
+ m_LDouble.push_back( Variable<long double>{ dimensionsCSV, nullptr, globalBoundsIndex, transforms, parameters } );
m_Variables[variableName] = std::make_pair( type, m_LDouble.size()-1 );
}
else
@@ -123,7 +127,7 @@ void Group::DefineVariable( const std::string variableName, const std::string ty
}
-void Group::AddTransform( const std::string variableName, Transform& transform, const short parameter )
+void Group::AddTransform( const std::string variableName, Transform& transform, const int parameter )
{
auto itVariable = m_Variables.find( variableName );
@@ -203,7 +207,7 @@ void Group::DefineAttribute( const std::string attributeName, const std::string
{
auto lf_GetTypeID = []( const std::string type, const bool debugMode ) -> const char
{
- char typeID;
+ char typeID = '\0';
if( type == "string" )
typeID = '0';
else if( type == "numeric" )
@@ -211,7 +215,8 @@ void Group::DefineAttribute( const std::string attributeName, const std::string
else
{
if( debugMode == true )
- throw std::invalid_argument( "ERROR: type " + type + " must be string or numeric, in call to DefineAttribute\n" );
+ throw std::invalid_argument( "ERROR: type " + type + " must be string or numeric, "
+ " in call to DefineAttribute\n" );
}
return typeID;
@@ -423,7 +428,7 @@ void Group::ParseXMLGroup( const std::string& xmlGroup, std::vector< std::shared
}
-const short Group::SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept
+const int Group::SetGlobalBounds( const std::string globalDimensionsCSV, const std::string globalOffsetsCSV ) noexcept
{
if( globalDimensionsCSV.empty() || globalOffsetsCSV.empty() )
return -1;
diff --git a/src/engine/SingleBP.cpp b/src/engine/SingleBP.cpp
index a1e750b75..fdb47ff15 100644
--- a/src/engine/SingleBP.cpp
+++ b/src/engine/SingleBP.cpp
@@ -4,7 +4,11 @@
* Created on: Dec 19, 2016
* Author: wfg
*/
+
+#include <iostream>
+
#include "engine/SingleBP.h"
+#include "core/Support.h"
//supported capsules
#include "capsule/Heap.h"
@@ -12,15 +16,18 @@
//supported transports
#include "transport/POSIX.h"
#include "transport/FStream.h"
+#include "transport/File.h"
namespace adios
{
+namespace engine
+{
SingleBP::SingleBP( const std::string streamName, const std::string accessMode, const MPI_Comm mpiComm,
const Method& method, const bool debugMode, const unsigned int cores ):
- Engine( "SingleBP", streamName, accessMode, mpiComm, method, debugMode, cores )
+ Engine( "SingleBP", streamName, accessMode, mpiComm, method, debugMode, cores, " SingleBP constructor (or call to ADIOS Open).\n" )
{
Init( );
}
@@ -37,10 +44,138 @@ void SingleBP::Init( )
}
+void SingleBP::Write( Group& group, const std::string variableName, const char* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const unsigned char* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const short* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const unsigned short* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const unsigned int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const long int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const unsigned long int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const long long int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const unsigned long long int* values )
+{
+
+}
+
+void SingleBP::Write( Group& group, const std::string variableName, const float* values )
+{
+
+}
+
void SingleBP::Write( Group& group, const std::string variableName, const double* values )
{
- auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("double"), " from call to Write double*" );
+ //auto index = PreSetVariable( group, variableName, Support::DatatypesAliases.at("double"), " from call to Write double*" );
+}
+
+
+void SingleBP::Write( Group& group, const std::string variableName, const long double* values )
+{
+
+}
+
+
+void SingleBP::Write( const std::string variableName, const char* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const unsigned char* values )
+{
+
+}
+void SingleBP::Write( const std::string variableName, const short* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const unsigned short* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const int* values )
+{
+ auto index = PreSetVariable( *m_Group, variableName, Support::DatatypesAliases.at("int"), " from call to Write int*" );
+ std::cout << "Hello from SingleBP Write integer with index " << index << "\n";
+}
+
+void SingleBP::Write( const std::string variableName, const unsigned int* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const long int* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const unsigned long int* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const long long int* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const unsigned long long int* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const float* values )
+{
+
+}
+
+void SingleBP::Write( const std::string variableName, const double* values )
+{
+ auto index = PreSetVariable( *m_Group, variableName, Support::DatatypesAliases.at("double"), " from call to Write double*" );
+ std::cout << "Hello from SingleBP Write double with index " << index << "\n";
+}
+
+
+void SingleBP::Write( const std::string variableName, const long double* values )
+{
}
@@ -51,14 +186,21 @@ void SingleBP::InitCapsules( )
{
if( m_Method.m_CapsuleParameters.size() > 1 )
{
- throw std::invalid_argument( "ERROR: SingleBP engine only allows one heap buffer, from SingleBP constructor in Open.\n" );
+ throw std::invalid_argument( "ERROR: SingleBP engine only allows one heap buffer, in " + m_Name +
+ m_EndMessage );
}
else if( m_Method.m_CapsuleParameters.size() == 1 )
{
- if( m_Method.m_CapsuleParameters[0].at("type") != "Heap" )
- throw std::invalid_argument( "ERROR: SingleBP doesn't support Capsule of type " + + ", from SingleBP constructor in Open.\n" );
- }
+ auto itType = m_Method.m_CapsuleParameters[0].find( "buffer" );
+
+ if( m_DebugMode == true )
+ CheckParameter( itType, m_Method.m_CapsuleParameters[0], " capsule buffer",
+ ", in " + m_Name + m_EndMessage );
+ if( !( itType->second == "Heap" || itType->second == "HEAP" ) )
+ throw std::invalid_argument( "ERROR: SingleBP doesn't support Capsule of buffer type " +
+ itType->second + " in " + m_Name + m_EndMessage );
+ }
}
//Create single capsule of type heap
m_Capsules.push_back( std::make_shared<Heap>( m_AccessMode, m_RankMPI, m_Cores ) );
@@ -70,50 +212,68 @@ void SingleBP::InitTransports( )
{
std::set< std::string > transportStreamNames; //used to check for name conflict between transports
+ const unsigned int transportsSize = m_Method.m_TransportParameters.size();
for( const auto& parameters : m_Method.m_TransportParameters )
{
- const std::string transport = parameters.at("type");
- const std::string name = parameters.at("name");
+ auto itTransport = parameters.find( "transport" );
+ if( m_DebugMode == true )
+ CheckParameter( itTransport, parameters, "transport", ", in " + m_Name + m_EndMessage );
+
- if( transport == "POSIX" )
+ if( itTransport->second == "POSIX" )
{
m_Transports.push_back( std::make_shared<POSIX>( m_MPIComm, m_DebugMode ) );
}
- else if( transport == "File" )
+ else if( itTransport->second == "File" )
{
- m_Transports.push_back( std::make_shared<FStream>( m_MPIComm, m_DebugMode ) );
-
+ m_Transports.push_back( std::make_shared<File>( m_MPIComm, m_DebugMode ) );
}
- else if( transport == "FStream" )
+ else if( itTransport->second == "FStream" )
{
m_Transports.push_back( std::make_shared<FStream>( m_MPIComm, m_DebugMode ) );
}
- else if( transport == "MPIFile" )
+ else if( itTransport->second == "MPIFile" )
{
- m_Transports.push_back( std::make_shared<FStream>( m_MPIComm, m_DebugMode ) );
+ //m_Transports.push_back( std::make_shared<MPIFile>( m_MPIComm, m_DebugMode ) );
}
else
{
if( m_DebugMode == true )
- throw std::invalid_argument( "ERROR: transport + " + transport + " not supported, in Engine constructor (or Open).\n" );
+ throw std::invalid_argument( "ERROR: transport + " + itTransport->second + " not supported, in " +
+ m_Name + m_EndMessage );
}
+ //name
+ if( transportsSize > 1 )
+ {
+ auto itName = parameters.find( "name" ); //first check name
+ if( m_DebugMode == true )
+ CheckParameter( itName, parameters, "name", " in transport " + itTransport->second +
+ ", in " + m_Name + m_EndMessage );
- m_Transports.back()->Open( name, m_AccessMode );
- }
-}
-
-
-
-
-
-
-
+ m_Transports.back()->Open( itName->second, m_AccessMode );
+ }
+ else if( transportsSize == 1 )
+ {
+ auto itName = parameters.find( "name" );
+ if( itName == parameters.end() ) //take streamName
+ m_Transports.back()->Open( m_Name, m_AccessMode );
+ else
+ m_Transports.back()->Open( m_Name, m_AccessMode );
+ }
+ else if( transportsSize == 0 )
+ {
+ if( m_DebugMode == true )
+ throw std::invalid_argument( "ERROR: transport not defined for engine " + m_Name + m_EndMessage );
+ }
+ }
+}
-} //end namespace
+} //end namespace engine
+} //end namespace adios
diff --git a/src/functions/adiosFunctions.cpp b/src/functions/adiosFunctions.cpp
index 05bcb0d6f..67e089599 100644
--- a/src/functions/adiosFunctions.cpp
+++ b/src/functions/adiosFunctions.cpp
@@ -269,7 +269,7 @@ void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm, const b
throw std::invalid_argument( "ERROR: group " + groupName + " defined twice.\n" );
}
- groups.emplace( groupName, Group( hostLanguage, xmlGroup, transforms, debugMode ) );
+ groups.emplace( groupName, Group( xmlGroup, transforms, debugMode ) );
currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size() );
currentPosition = 0;
diff --git a/src/transform/BZIP2.cpp b/src/transform/BZip2.cpp
similarity index 75%
rename from src/transform/BZIP2.cpp
rename to src/transform/BZip2.cpp
index 2d42b7ba1..36c3bde0b 100644
--- a/src/transform/BZIP2.cpp
+++ b/src/transform/BZip2.cpp
@@ -7,12 +7,14 @@
-#include "transform/BZIP2.h"
+#include "../../include/transform/BZip2.h"
namespace adios
{
+namespace transform
+{
BZIP2::BZIP2( ):
@@ -37,7 +39,7 @@ void BZIP2::Decompress( const std::vector<char>& bufferIn, std::vector<char>& bu
}
-
-} //end namespace
+} //end namespace transform
+} //end namespace adios
diff --git a/src/transport/FStream.cpp b/src/transport/FStream.cpp
index 08dde2e02..5c0e2ec68 100644
--- a/src/transport/FStream.cpp
+++ b/src/transport/FStream.cpp
@@ -18,9 +18,7 @@ namespace adios
FStream::FStream( MPI_Comm mpiComm, const bool debugMode ):
Transport( "FStream", mpiComm, debugMode )
-{
- Init( arguments );
-}
+{ }
FStream::~FStream( )
diff --git a/src/transport/File.cpp b/src/transport/File.cpp
index d259e1249..ed8a4796f 100644
--- a/src/transport/File.cpp
+++ b/src/transport/File.cpp
@@ -5,6 +5,8 @@
* Author: wfg
*/
+#include <ios> //std::ios_base::failure
+
#include "transport/File.h"
diff --git a/src/transport/POSIX.cpp b/src/transport/POSIX.cpp
index 2bea6189c..78834a31d 100644
--- a/src/transport/POSIX.cpp
+++ b/src/transport/POSIX.cpp
@@ -1,14 +1,18 @@
/*
- * POSIXMPI.cpp
+ * POSIX.cpp
*
* Created on: Oct 6, 2016
* Author: wfg
*/
-#include <fcntl.h>
-#include <sys/types.h>
-#include <sys/stat.h>
+#include <fcntl.h> //open
+#include <sys/types.h> //open
+#include <sys/stat.h> //open
+#include <stddef.h> // write output
+#include <unistd.h> // write, close
+
+#include <ios> //std::ios_base::failure
#include "transport/POSIX.h"
@@ -51,13 +55,19 @@ void POSIX::Open( const std::string name, const std::string accessMode )
void POSIX::Write( const char* buffer, std::size_t size )
{
- int status = write( m_FileDescriptor, buffer, size );
+ auto writtenSize = write( m_FileDescriptor, buffer, size );
if( m_DebugMode == true )
{
- if( status == -1 )
+ if( writtenSize == -1 )
throw std::ios_base::failure( "ERROR: couldn't write to file " + m_Name +
", in call to POSIX write\n" );
+
+ if( static_cast<std::size_t>( writtenSize ) != size )
+ throw std::ios_base::failure( "ERROR: written size + " + std::to_string( writtenSize ) +
+ " is not equal to intended size " +
+ std::to_string( size ) + " in file " + m_Name +
+ ", in call to POSIX write\n" );
}
}
@@ -75,7 +85,4 @@ void POSIX::Close( )
}
-
-
-
}//end namespace
--
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