diff --git a/buildBP.sh b/buildBP.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1da55d54d515cf4f8448e69297e89e79150ea609
--- /dev/null
+++ b/buildBP.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+
+# buildTest.sh for BP Writer example
+# Created on: Feb 9, 2017
+# Author: wfg
+# Recommended: do a "make clean" the first time
+
+MPICOMPILER=mpic++
+
+if [ "$(uname)" == "Darwin" ]; then
+ CCOMPILER=clang++
+elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
+ CCOMPILER=g++
+fi
+echo "######################################################################################"
+echo "Start building ADIOS ./lib/libadios.a ./libadios_nompi.a"
+echo "######################################################################################"
+echo
+make -j4 CC=$CCOMPILER MPICC=$MPICOMPILER #build the ./lib/libadios.a and ./libadios_nompi.a
+echo
+echo "#################################################################"
+echo "Building BPWriter example"
+echo "#################################################################"
+make -j4 -C ./examples/hello/bpWriter CC=$CCOMPILER MPICC=$MPICOMPILER
+#make -j4 -C ./examples/hello/bpReader CC=$CCOMPILER MPICC=$MPICOMPILER
+echo
+echo
+echo
+echo "#################################################################"
+echo "Running nompi.exe example"
+echo "#################################################################"
+echo
+echo
+echo "#################################################################"
+echo "BP writer"
+echo "#################################################################"
+./examples/hello/bpWriter/helloBPWriter_nompi.exe
+echo "DONE...check for myDoubles_nompi.bp directory"
+
+echo "#################################################################"
+echo "BP reader..not ready yet"
+echo "#################################################################"
+#./examples/hello/bpWriter/helloBPReader.exe
+echo
+echo
+echo "#################################################################"
+echo "To run mpi version with 4 mpi processes: "
+echo "mpirun -n 4 ./examples/hello/bpWriter/helloBPWriter.exe"
+echo "mpirun -n 4 ./examples/hello/bpReader/helloBPReader.exe"
+echo "END"
+echo "################################################################"
diff --git a/examples/hello/bpReader/Makefile b/examples/hello/bpReader/Makefile
index b63e867e402f007f5e7d78eb9bb6241b778968cb..b5705da1c7f7e406623c9aafd9380d3dc94ead07 100644
--- a/examples/hello/bpReader/Makefile
+++ b/examples/hello/bpReader/Makefile
@@ -2,7 +2,7 @@
# Created on: Oct 4, 2016
# Author: wfg
-BASE_NAME=helloWriter
+BASE_NAME=helloBPReader
#COMPILERS
CC=g++
diff --git a/examples/hello/bpReader/helloBPReader.cpp b/examples/hello/bpReader/helloBPReader.cpp
index 6bb1ef383a39ec044c7feffac6047381cd857ba3..bb1bc35d9134b8fbe4bf5131aea99ff820e7a31c 100644
--- a/examples/hello/bpReader/helloBPReader.cpp
+++ b/examples/hello/bpReader/helloBPReader.cpp
@@ -28,16 +28,15 @@ int main( int argc, char* argv [] )
try
{
//Define method for engine creation, it is basically straight-forward parameters
- adios::Method& bpWriterSettings = adios.DeclareMethod( "SingleFile" ); //default method type is BPWriter
- bpWriterSettings.AddTransport( "File" ); //uses default POSIX library
+ adios::Method& bpReaderSettings = adios.DeclareMethod( "SingleFile" ); //default method type is BPWriter
+ bpReaderSettings.AddTransport( "File" ); //uses default POSIX library
//Create engine smart pointer due to polymorphism,
//Open returns a smart pointer to Engine containing the Derived class Writer
- auto bpWriter = adios.Open( "myDoubles.bp", "r", bpWriterSettings );
-
- if( bpWriter == nullptr )
- throw std::ios_base::failure( "ERROR: couldn't create bpWriter at Open\n" );
+ auto bpReader = adios.Open( "myDoubles_nompi.bp", "r", bpReaderSettings );
+ if( bpReader == nullptr )
+ throw std::ios_base::failure( "ERROR: couldn't create bpReader at Open\n" );
}
catch( std::invalid_argument& e )
diff --git a/examples/hello/bpReader/helloBPReader_nompi.cpp b/examples/hello/bpReader/helloBPReader_nompi.cpp
index b15518a2e1a4323f123047a83f36431e848b1c56..b5e437deabafc50c5e8ec80c7d0010fb10bb6f27 100644
--- a/examples/hello/bpReader/helloBPReader_nompi.cpp
+++ b/examples/hello/bpReader/helloBPReader_nompi.cpp
@@ -16,28 +16,18 @@ int main( int argc, char* argv [] )
const bool adiosDebug = true;
adios::ADIOS adios( adiosDebug );
- //Application variable
- std::vector<double> myDoubles = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
- const std::size_t Nx = myDoubles.size();
-
try
{
- //Define variable and local size
- auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", adios::Dims{Nx} );
-
- //Define method for engine creation, it is basically straight-forward parameters
- adios::Method& bpWriterSettings = adios.DeclareMethod( "SinglePOSIXFile" ); //default method type is Writer
- bpWriterSettings.AddTransport( "File", "have_metadata_file=yes" );
-
- //Create engine smart pointer due to polymorphism,
- //Open returns a smart pointer to Engine containing the Derived class Writer
- auto bpWriter = adios.Open( "myDoubles_nompi.bp", "w", bpWriterSettings );
+ //Define method for engine creation, it is basically straight-forward parameters
+ adios::Method& bpReaderSettings = adios.DeclareMethod( "SingleFile" ); //default method type is BPWriter/BPReader
+ bpReaderSettings.AddTransport( "File" ); //uses default POSIX library
- if( bpWriter == nullptr )
- throw std::ios_base::failure( "ERROR: couldn't create bpWriter at Open\n" );
+ //Create engine smart pointer due to polymorphism,
+ //Open returns a smart pointer to Engine containing the Derived class Writer
+ auto bpReader = adios.Open( "myDoubles.bp", "r", bpReaderSettings );
- bpWriter->Write<double>( ioMyDoubles, myDoubles.data() ); // Base class Engine own the Write<T> that will call overloaded Write from Derived
- bpWriter->Close( );
+ if( bpReader == nullptr )
+ throw std::ios_base::failure( "ERROR: couldn't create bpReader at Open\n" );
}
catch( std::invalid_argument& e )
{
diff --git a/include/ADIOS.h b/include/ADIOS.h
index c21977d78d999564fef88ebbb4e7c7ce8227a996..e0e4e19bff15d9b1f97a61438559a4d907efe677 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -11,7 +11,7 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <string>
#include <vector>
-#include <memory> //shared_ptr
+#include <memory> //std::shared_ptr
#include <ostream>
#include <set>
#include <map>
@@ -134,7 +134,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param name must be unique
* @param type supported type : "Writer" (default), "DataMan"...future: "Sirius"
*/
- Method& DeclareMethod( const std::string methodName, const std::string type = "BPWriter" );
+ Method& DeclareMethod( const std::string methodName, const std::string type = "" );
/**
diff --git a/include/core/Method.h b/include/core/Method.h
index 1decbd7aac2511d23145e055d78393d4fbca8403..84ed0f95ecc7ff13fa97f971f083c07f4f760aff 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -34,7 +34,7 @@ public:
/**
* Constructor
- * @param type must be an engine type, default = SingleBP
+ * @param type must be an engine type
*/
Method( const std::string type, const bool debugMode = false );
diff --git a/include/format/BP1.h b/include/format/BP1.h
index 1696c143b89073b894790b59a0f2d5aef080852c..cfccc7d47f543e1e432eea561ec5349130498d74 100644
--- a/include/format/BP1.h
+++ b/include/format/BP1.h
@@ -24,6 +24,7 @@ namespace adios
namespace format
{
+
/**
* Struct that tracks metadata indices in bp format
*/
diff --git a/include/format/BP1Writer.h b/include/format/BP1Writer.h
index 32bb42e3e40d95d8ce23a2115c521c9c494027db..e618b11d06c538e251961c62a56cd5dd7a663895 100644
--- a/include/format/BP1Writer.h
+++ b/include/format/BP1Writer.h
@@ -39,7 +39,7 @@ public:
unsigned int m_Cores = 1; ///< number of cores for thread operations in large array (min,max)
unsigned int m_Verbosity = 0; ///< statistics verbosity, can change if redefined in Engine method.
float m_GrowthFactor = 1.5; ///< memory growth factor, can change if redefined in Engine method.
- const std::uint8_t m_Version = 3;
+ const std::uint8_t m_Version = 3; ///< BP format version
/**
* Calculates the Process Index size in bytes according to the BP format, including list of method with no parameters (for now)
@@ -230,14 +230,16 @@ public:
/**
- * Function that collects metadata (if first close) and writes to a single transport
- * @param metadataSet
- * @param capsule
- * @param transport
- * @param isFirstClose
+ * Function that sets metadata (if first close) and writes to a single transport
+ * @param metadataSet current rank metadata set
+ * @param capsule contains data and metadata buffers
+ * @param transport does a write after data and metadata is setup
+ * @param isFirstClose true: metadata has been set and aggregated
+ * @param haveMetadata true: attach metadata buffer to each data buffer and do a transport write
+ * @param haveTiming true: add timing.log file
*/
- void Close( BP1MetadataSet& metadataSet, Capsule& capsule, Transport& transport, bool& isFirstClose ) const noexcept;
-
+ void Close( BP1MetadataSet& metadataSet, Capsule& capsule, Transport& transport, bool& isFirstClose,
+ const bool haveMetadata = true, const bool haveTiming = false ) const noexcept;
private:
diff --git a/src/engine/bp/BPReader.cpp b/src/engine/bp/BPReader.cpp
index c893d00478f9c31701f39145f12364a343d161e7..dd6481a2aaeecc6acfb99e60152055c7880b7b4e 100644
--- a/src/engine/bp/BPReader.cpp
+++ b/src/engine/bp/BPReader.cpp
@@ -135,20 +135,20 @@ void BPReader::InitTransports( ) //maybe move this?
if( itLibrary == parameters.end() || itLibrary->second == "POSIX" ) //use default POSIX
{
auto file = std::make_shared<transport::FD>( m_MPIComm, m_DebugMode );
- //m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
+ //m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
}
else if( itLibrary->second == "FILE*" || itLibrary->second == "stdio.h" )
{
auto file = std::make_shared<transport::FP>( m_MPIComm, m_DebugMode );
- //m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
+ //m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
}
else if( itLibrary->second == "fstream" || itLibrary->second == "std::fstream" )
{
auto file = std::make_shared<transport::FStream>( m_MPIComm, m_DebugMode );
- //m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
+ //m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
}
else if( itLibrary->second == "MPI-IO" )
diff --git a/src/format/BP1Writer.cpp b/src/format/BP1Writer.cpp
index fbbd68c3dac422ca3dc10fc770eece3230169604..a4ac52cf81ad29bd66c9807b8ad19bba28ebf722 100644
--- a/src/format/BP1Writer.cpp
+++ b/src/format/BP1Writer.cpp
@@ -93,21 +93,28 @@ void BP1Writer::WriteProcessGroupIndex( const bool isFortran, const std::string
}
-void BP1Writer::Close( BP1MetadataSet& metadataSet, Capsule& capsule,
- Transport& transport, bool& isFirstClose ) const noexcept
+void BP1Writer::Close( BP1MetadataSet& metadataSet, Capsule& capsule, Transport& transport, bool& isFirstClose,
+ const bool haveMetadata, const bool haveTiming ) const noexcept
{
if( isFirstClose == true )
{
- FlattenMetadata( metadataSet, capsule ); //now capsule
+ FlattenMetadata( metadataSet, capsule );
isFirstClose = false;
}
//implementing N-to-N for now, no aggregation
transport.Write( capsule.GetData(), capsule.m_DataPosition );
- transport.Write( capsule.GetMetadata(), capsule.GetMetadataSize() ); //we can improve this by copying metadata to data
+
+ if( haveMetadata == true )
+ transport.Write( capsule.GetMetadata(), capsule.GetMetadataSize() ); //we can improve this by copying metadata to data
+
+ //here accumulate in metadata file
+
transport.Close();
}
+
+//PRIVATE FUNCTIONS
void BP1Writer::WriteProcessGroupIndexCommon( const bool isFortran, const std::string name, const unsigned int processID,
const std::string timeStepName, const unsigned int timeStep,
const std::vector<int>& methodIDs,