diff --git a/Makefile b/Makefile
index ab0db8f0f1f613d200613c00cc159921b1689222..ea705d1d4e18a4eb215cd4dcc5b7fe35e7ccba2d 100644
--- a/Makefile
+++ b/Makefile
@@ -69,4 +69,4 @@ nompi: $(HFiles) $(OBJNoMPI)
$(CC) $(CFLAGS) $(INC) -DADIOS_NOMPI -o $@ $<
clean:
- rm ./bin/mpi/*.o ./bin/nompi/*.o ./lib/*.a ./lib/*.so
+ rm ./bin/mpi/*.o ./bin/nompi/*.o ./lib/*
diff --git a/bindings/python/test_hello.py b/bindings/python/test_hello.py
index cb28d2f1eec22f733dc39305cbf494a7888a9da4..db0b2c6ef927d13f671d37d451f2b86b5db8bf29 100644
--- a/bindings/python/test_hello.py
+++ b/bindings/python/test_hello.py
@@ -27,8 +27,8 @@ if( rank % 2 == 1 ): # odd ranks only
#Setup method and print summary
ioSettings = adios.DeclareMethod("adiosSettings", "BPFileWriter")
-ioSettings.SetParameters( max_buffer_size = '10000000' )
-ioSettings.AddTransport( 'File', have_metadata_file = 'yes', library = 'POSIX' ) # POSIX is default, just checking
+ioSettings.SetParameters( profile_units = 'mus' )
+ioSettings.AddTransport( 'File', have_metadata_file = 'no', profile_units = 'mus' ) # POSIX is default, just checking
#Start Engine
bpFileWriter = adios.Open( "file.bp", "w", ioSettings, None ) # Open files using N-to-N method, None means no new MPI communicator
diff --git a/examples/hello/bpWriter/helloBPWriter.cpp b/examples/hello/bpWriter/helloBPWriter.cpp
index 496bdeb3fdf1ec298e46d991efac9c887d3da81c..b962d524a1aa17e7fd6c125b93a9725eb9ade77a 100644
--- a/examples/hello/bpWriter/helloBPWriter.cpp
+++ b/examples/hello/bpWriter/helloBPWriter.cpp
@@ -54,7 +54,8 @@ int main( int argc, char* argv [] )
//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", "have_metadata_file=no" ); //uses default POSIX library
+ bpWriterSettings.SetParameters( "profile_units=mus" );
+ bpWriterSettings.AddTransport( "File", "profile_units=mus", "have_metadata_file=no" ); //uses default POSIX library
//Create engine smart pointer due to polymorphism,
//Open returns a smart pointer to Engine containing the Derived class Writer
diff --git a/examples/hello/bpWriter/helloBPWriter_nompi.cpp b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
index a06b1b06136b969c5962586894f50cf2fa2c7a1e..89eb754a1ae7f5f24ccc4b8041fabdcd5edee55d 100644
--- a/examples/hello/bpWriter/helloBPWriter_nompi.cpp
+++ b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
@@ -40,7 +40,8 @@ int main( int argc, char* argv [] )
//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" );
+ bpWriterSettings.SetParameters( "profile_units=mus" );
+ bpWriterSettings.AddTransport( "File", "have_metadata_file=yes", "profile_units=mus" );
//Create engine smart pointer due to polymorphism,
//Open returns a smart pointer to Engine containing the Derived class Writer
diff --git a/include/core/Transport.h b/include/core/Transport.h
index dc6409e6eb9ae9f8ad984cc038ee10d77dad8957..1c2c0d0bacec7fb76e4584ab5774723b0c0da8fd 100644
--- a/include/core/Transport.h
+++ b/include/core/Transport.h
@@ -78,7 +78,7 @@ public:
virtual void Close( ); ///< closes current transport and flushes everything, transport becomes unreachable
- virtual void InitProfiler( const Support::Resolutions resolution );
+ virtual void InitProfiler( const std::string accessMode, const Support::Resolutions resolution );
protected:
diff --git a/include/format/BP1.h b/include/format/BP1.h
index 2e551ecec359039b984a8f4ff3259bf0eaaa1b8d..10c28a28214f8bbb1e02616c45c5ab3da372eeca 100644
--- a/include/format/BP1.h
+++ b/include/format/BP1.h
@@ -65,6 +65,13 @@ class BP1
public:
+ /**
+ * Checks if input name has .bp extension and returns a .bp directory name
+ * @param name input (might or not have .bp)
+ * @return either name.bp (name has no .bp) or name (name has .bp extension)
+ */
+ std::string GetDirectoryName( const std::string name ) const noexcept;
+
/**
* Opens rank files in the following format:
* if transport.m_MPIComm different from MPI_Comm_SELF --> name.bp.dir/name.bp.rank
@@ -72,7 +79,7 @@ public:
* @param accessMode "write" "w", "r" "read", "append" "a"
* @param transport file I/O transport
*/
- void OpenRankFiles( const std::string name, const std::string accessMode, Transport& transport );
+ void OpenRankFiles( const std::string name, const std::string accessMode, Transport& transport ) const;
protected:
diff --git a/include/mpidummy.h b/include/mpidummy.h
index 619a50ad9d554b5d06f4eca0352942934dfe5fb8..865320755eb511d564c3968f7be7ce3e1f4f3c30 100644
--- a/include/mpidummy.h
+++ b/include/mpidummy.h
@@ -92,6 +92,8 @@ int MPI_Irecv( void *recvbuffer, int count, MPI_Datatype type, int source, int t
int MPI_Send( void *sendbuffer, int count, MPI_Datatype type, int destination, int tag, MPI_Comm comm );
int MPI_Isend( void *recvbuffer, int count, MPI_Datatype type, int source, int tag, MPI_Comm comm, MPI_Request* request );
+int MPI_Wait( MPI_Request* request, MPI_Status* status );
+
int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh);
int MPI_File_close(MPI_File *fh);
int MPI_File_get_size(MPI_File fh, MPI_Offset *size);
diff --git a/src/core/Transport.cpp b/src/core/Transport.cpp
index 81095c229661af8939a04b66da725fcbd30e6df7..4bbc1f7439e6f2db0e09859f16b0aecae7697bcb 100644
--- a/src/core/Transport.cpp
+++ b/src/core/Transport.cpp
@@ -37,17 +37,17 @@ void Transport::Close( )
{ }
-void Transport::InitProfiler( const Support::Resolutions resolution )
+void Transport::InitProfiler( const std::string accessMode, const Support::Resolutions resolution )
{
m_Profiler.m_Timers.emplace_back( "open", Support::Resolutions::mus );
- if( m_AccessMode == "w" || m_AccessMode == "write" )
+ if( accessMode == "w" || accessMode == "write" )
m_Profiler.m_Timers.emplace_back( "write", resolution );
- else if( m_AccessMode == "a" || m_AccessMode == "append" )
+ else if( accessMode == "a" || accessMode == "append" )
m_Profiler.m_Timers.emplace_back( "append", resolution );
- else if( m_AccessMode == "r" || m_AccessMode == "read" )
+ else if( accessMode == "r" || accessMode == "read" )
m_Profiler.m_Timers.emplace_back( "read", resolution );
m_Profiler.m_Timers.emplace_back( "close", Support::Resolutions::mus );
diff --git a/src/engine/bp/BPFileWriter.cpp b/src/engine/bp/BPFileWriter.cpp
index 85fce4ace4aac55d5a75c7b30a6ac040ed381cb4..d717e6d01d31f0554dd39cbf2d4984335464e7a4 100644
--- a/src/engine/bp/BPFileWriter.cpp
+++ b/src/engine/bp/BPFileWriter.cpp
@@ -34,6 +34,7 @@ BPFileWriter::~BPFileWriter( )
void BPFileWriter::Init( )
{
+ InitParameters( );
InitTransports( );
InitProcessGroup( );
}
@@ -177,8 +178,8 @@ void BPFileWriter::Close( const int transportIndex )
{
const std::string rankLog = m_BP1Writer.GetRankProfilingLog( m_RankMPI, m_MetadataSet, m_Transports );
-
-
+ const std::string fileName( m_BP1Writer.GetDirectoryName(m_Name) + "/profiling.log" );
+ m_BP1Aggregator.WriteProfilingLog( fileName, rankLog );
}
}
@@ -211,7 +212,7 @@ void BPFileWriter::InitParameters( )
throw std::invalid_argument( "ERROR: Method buffer_growth argument can't be less of equal than 1, in " + m_EndMessage + "\n" );
}
- m_MaxBufferSize = std::stoul( itMaxBufferSize->second ) * 1048576; //convert to bytes
+ m_MaxBufferSize = std::stoul( itMaxBufferSize->second ) * 1048576; //convert from MB to bytes
}
auto itVerbosity = m_Method.m_Parameters.find( "verbose" );
@@ -232,19 +233,19 @@ void BPFileWriter::InitParameters( )
auto& profiler = m_MetadataSet.Log;
if( itProfile->second == "mus" || itProfile->second == "microseconds" )
- profiler.m_Timers.emplace_back( "Buffering", Support::Resolutions::mus );
+ profiler.m_Timers.emplace_back( "buffering", Support::Resolutions::mus );
else if( itProfile->second == "ms" || itProfile->second == "milliseconds" )
- profiler.m_Timers.emplace_back( "Buffering", Support::Resolutions::ms );
+ profiler.m_Timers.emplace_back( "buffering", Support::Resolutions::ms );
else if( itProfile->second == "s" || itProfile->second == "seconds" )
- profiler.m_Timers.emplace_back( "Buffering", Support::Resolutions::s );
+ profiler.m_Timers.emplace_back( "buffering", Support::Resolutions::s );
else if( itProfile->second == "min" || itProfile->second == "minutes" )
- profiler.m_Timers.emplace_back( "Buffering", Support::Resolutions::m );
+ profiler.m_Timers.emplace_back( "buffering", Support::Resolutions::m );
else if( itProfile->second == "h" || itProfile->second == "hours" )
- profiler.m_Timers.emplace_back( "Buffering", Support::Resolutions::h );
+ profiler.m_Timers.emplace_back( "buffering", Support::Resolutions::h );
else
{
if( m_DebugMode == true )
@@ -270,6 +271,7 @@ void BPFileWriter::InitTransports( )
for( const auto& parameters : m_Method.m_TransportParameters )
{
auto itProfile = parameters.find( "profile_units" );
+ bool doProfiling = false;
Support::Resolutions resolution = Support::Resolutions::s; //default is seconds
if( itProfile != parameters.end() )
{
@@ -293,6 +295,7 @@ void BPFileWriter::InitTransports( )
if( m_DebugMode == true )
throw std::invalid_argument( "ERROR: Transport profile_units argument must be mus, ms, s, min or h " + m_EndMessage );
}
+ doProfiling = true;
}
auto itTransport = parameters.find( "transport" );
@@ -303,8 +306,8 @@ void BPFileWriter::InitTransports( )
if( itLibrary == parameters.end() || itLibrary->second == "POSIX" ) //use default POSIX
{
auto file = std::make_shared<transport::FileDescriptor>( m_MPIComm, m_DebugMode );
- if( parameters.count( "profile_units" ) == 1 )
- file->InitProfiler( resolution );
+ if( doProfiling == true )
+ file->InitProfiler( m_AccessMode, resolution );
m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
@@ -313,8 +316,8 @@ void BPFileWriter::InitTransports( )
else if( itLibrary->second == "FILE*" || itLibrary->second == "stdio" )
{
auto file = std::make_shared<transport::FilePointer>( m_MPIComm, m_DebugMode );
- if( parameters.count( "profile_units" ) == 1 )
- file->InitProfiler( resolution );
+ if( doProfiling == true )
+ file->InitProfiler( m_AccessMode, resolution );
m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
@@ -322,8 +325,9 @@ void BPFileWriter::InitTransports( )
else if( itLibrary->second == "fstream" || itLibrary->second == "std::fstream" )
{
auto file = std::make_shared<transport::FStream>( m_MPIComm, m_DebugMode );
- if( parameters.count( "profile_units" ) == 1 )
- file->InitProfiler( resolution );
+
+ if( doProfiling == true )
+ file->InitProfiler( m_AccessMode, resolution );
m_BP1Writer.OpenRankFiles( m_Name, m_AccessMode, *file );
m_Transports.push_back( std::move( file ) );
diff --git a/src/format/BP1.cpp b/src/format/BP1.cpp
index 2c28f28cbc995ce5c8ae49887d14524b5dcf3550..ddf74bb83bdc6a48e9a1dbbb6faffc677cadfc11 100644
--- a/src/format/BP1.cpp
+++ b/src/format/BP1.cpp
@@ -16,29 +16,29 @@ namespace format
{
-void BP1::OpenRankFiles( const std::string name, const std::string accessMode, Transport& file )
+std::string BP1::GetDirectoryName( const std::string name ) const noexcept
{
std::string directory;
- std::string baseName;
- if( name.find(".bp") == name.size()-3 ) //need to test
- {
- baseName = name.substr( 0, name.size()-3 );
+ if( name.find(".bp") == name.size()-3 )
directory = name;
- }
else
- {
- baseName = name;
directory = name + ".bp";
- }
+
+ return directory;
+}
+
+
+void BP1::OpenRankFiles( const std::string name, const std::string accessMode, Transport& file ) const
+{
+ const std::string directory = GetDirectoryName( name );
CreateDirectory( directory ); //creates a directory and sub-directories recursively
- std::string fileName( directory + "/" + baseName + ".bp." + std::to_string( file.m_RankMPI ) );
+ std::string fileName( directory + "/" + directory + "." + std::to_string( file.m_RankMPI ) );
file.Open( fileName, accessMode ); // opens a file transport under name.bp.dir/name.bp.rank reserve that location fro writing
}
-
std::vector<int> BP1::GetMethodIDs( const std::vector< std::shared_ptr<Transport> >& transports ) const noexcept
{
auto lf_GetMethodID = []( const std::string method ) -> int
diff --git a/src/format/BP1Aggregator.cpp b/src/format/BP1Aggregator.cpp
index bb2328ff305d4e1f7a7cc7bf328e29bbee2dcb64..9e38f378639453dcbe9abb60db66914740a59397 100644
--- a/src/format/BP1Aggregator.cpp
+++ b/src/format/BP1Aggregator.cpp
@@ -7,6 +7,8 @@
#include <vector>
#include <fstream>
+#include <iostream> // must be deleted
+#include <unistd.h> // must be deleted
#include "format/BP1Aggregator.h"
@@ -30,61 +32,61 @@ BP1Aggregator::~BP1Aggregator( )
{ }
-
void BP1Aggregator::WriteProfilingLog( const std::string fileName, const std::string& rankLog )
{
if( m_RankMPI == 0 )
{
- std::vector< std::vector<char> > rankLogs( m_SizeMPI - 1 ); //rankLogs from other processes
+ unsigned int sizeMPI = static_cast<unsigned int>( m_SizeMPI );
+ std::vector< std::vector<char> > rankLogs( sizeMPI - 1 ); //rankLogs from other processes
+ std::vector< int > rankLogsSizes( sizeMPI-1, -1 ); //init with -1
+ std::vector<MPI_Request> requests( sizeMPI );
+ std::vector<MPI_Status> statuses( sizeMPI );
//first receive sizes
- unsigned int sizeMPI = static_cast<unsigned int>( m_SizeMPI );
+ for( unsigned int i = 1; i < sizeMPI; ++i )
+ MPI_Irecv( &rankLogsSizes[i-1], 1, MPI_INT, i, 0, m_MPIComm, &requests[i] );
for( unsigned int i = 1; i < sizeMPI; ++i )
{
- int size = -1;
- MPI_Request request;
- MPI_Irecv( &size, 1, MPI_INT, i, 0, m_MPIComm, &request );
-
+ MPI_Wait( &requests[i], &statuses[i] );
if( m_DebugMode == true )
{
- if( size == -1 )
+ if( rankLogsSizes[i-1] == -1 )
throw std::runtime_error( "ERROR: couldn't get size from rank " + std::to_string(i) + ", in ADIOS aggregator for Profiling.log\n" );
- //here check request
}
- rankLogs[i-1].resize( size ); //allocate with zeros
+ rankLogs[i-1].resize( rankLogsSizes[i-1] ); //allocate with zeros
}
+
//receive rankLog from other ranks
for( unsigned int i = 1; i < sizeMPI; ++i )
- {
- int size = static_cast<int>( rankLogs[i-1].size() );
- MPI_Request request;
- MPI_Irecv( rankLogs[i-1].data(), size, MPI_CHAR, i, 0, m_MPIComm, &request );
+ MPI_Irecv( rankLogs[i-1].data(), rankLogsSizes[i-1], MPI_CHAR, i, 1, m_MPIComm, &requests[i] );
+
+ for( unsigned int i = 1; i < sizeMPI; ++i )
+ MPI_Wait( &requests[i], &statuses[i] );
- if( m_DebugMode == true )
- {
- //here check request
- }
- }
//write file
- std::string logFile( "log = { " + rankLog + "\n" );
+ std::string logFile( "log = { \n" );
+ logFile += rankLog + "\n";
for( unsigned int i = 1; i < sizeMPI; ++i )
{
- std::string rankLogStr( rankLogs[i-1].data() );
+ const std::string rankLogStr( rankLogs[i-1].data(), rankLogs[i-1].size() );
logFile += rankLogStr + "\n";
}
logFile += " }\n";
+ std::cout << logFile;
std::ofstream logStream( fileName );
logStream.write( logFile.c_str(), logFile.size() );
logStream.close();
}
else
{
- int size = static_cast<int>( rankLog.size() );
- MPI_Request request;
- MPI_Isend( &size, 1, MPI_INT, 0, 0, m_MPIComm, &request );
- MPI_Isend( const_cast<char*>( rankLog.c_str() ), size, MPI_CHAR, 0, 0, m_MPIComm, &request );
+ int rankLogSize = static_cast<int>( rankLog.size() );
+ MPI_Request requestSize;
+ MPI_Isend( &rankLogSize, 1, MPI_INT, 0, 0, m_MPIComm, &requestSize );
+
+ MPI_Request requestRankLog;
+ MPI_Isend( const_cast<char*>( rankLog.c_str() ), rankLogSize, MPI_CHAR, 0, 1, m_MPIComm, &requestRankLog );
}
}
diff --git a/src/format/BP1Writer.cpp b/src/format/BP1Writer.cpp
index 2ad022f860b346623c309e4e46702622251576fd..cb63d54fdbb1f82c2207a1731d18014de46b040b 100644
--- a/src/format/BP1Writer.cpp
+++ b/src/format/BP1Writer.cpp
@@ -7,6 +7,8 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <string>
+#include <iostream>
+#include <unistd.h> //sleep must be removed
/// \endcond
#include "format/BP1Writer.h"
@@ -103,8 +105,6 @@ void BP1Writer::WriteProcessGroupIndex( const bool isFortran, const std::string
void BP1Writer::Advance( BP1MetadataSet& metadataSet, capsule::STLVector& buffer )
{
FlattenData( metadataSet, buffer );
-
-
}
@@ -150,29 +150,33 @@ void BP1Writer::Close( BP1MetadataSet& metadataSet, capsule::STLVector& buffer,
std::string BP1Writer::GetRankProfilingLog( const int rank, const BP1MetadataSet& metadataSet,
const std::vector< std::shared_ptr<Transport> >& transports ) const noexcept
{
- auto lf_WriterTimer = []( const std::string name, const Timer& timer, std::string rankLog )
+ auto lf_WriterTimer = []( std::string& rankLog, const Timer& timer )
{
- rankLog += "'" + name + "_" + timer.GetUnits() + "': " + std::to_string( timer.ProcessTime ) + ", ";
+ rankLog += timer.Process + "_" + timer.GetUnits() + "': " + std::to_string( timer.ProcessTime ) + ", ";
};
//prepare string dictionary per rank
std::string rankLog( "'rank_" + std::to_string( rank ) + "': { " );
auto& profiler = metadataSet.Log;
- rankLog += "'totalBytes': " + std::to_string( profiler.m_TotalBytes[0] ) + ", ";
- lf_WriterTimer( "t_buffering", profiler.m_Timers[0], rankLog );
+ rankLog += "'bytes': " + std::to_string( profiler.m_TotalBytes[0] ) + ", ";
+ lf_WriterTimer( rankLog, profiler.m_Timers[0] );
for( unsigned int t = 0; t < transports.size(); ++t )
{
auto& timers = transports[t]->m_Profiler.m_Timers;
rankLog += "'transport_" + std::to_string(t) + "': { ";
- lf_WriterTimer( "t_open", timers[0], rankLog );
- lf_WriterTimer( "t_write", timers[1], rankLog );
- lf_WriterTimer( "t_close", timers[2], rankLog );
+ rankLog += "'lib:' " + transports[t]->m_Type + ", ";
+
+ for( unsigned int i = 0; i < 3; ++i )
+ lf_WriterTimer( rankLog, timers[i] );
+
rankLog += " }, ";
}
rankLog += "}, ";
+
+ //std::cout << rankLog << "\n";
return rankLog;
}
diff --git a/src/functions/adiosFunctions.cpp b/src/functions/adiosFunctions.cpp
index 2abe0c7c4ff22dddc680b660eb6654b1bdda0866..48fd527502fbb3cd041587d9c3434e1602bbd668 100644
--- a/src/functions/adiosFunctions.cpp
+++ b/src/functions/adiosFunctions.cpp
@@ -378,9 +378,7 @@ void CreateDirectory( const std::string fullPath ) noexcept
auto lf_Mkdir = []( const std::string directory, struct stat& st )
{
if ( stat( directory.c_str(), &st ) == -1 )
- {
mkdir( directory.c_str(), 0777 );
- }
};
auto directoryPosition = fullPath.find( "/" );
diff --git a/src/mpidummy.cpp b/src/mpidummy.cpp
index 52fd646e4c02b8cfe2c5e60099f1f0d5a0dd9f23..e58e1b817cdf2756be130428857f0c844079f0f4 100644
--- a/src/mpidummy.cpp
+++ b/src/mpidummy.cpp
@@ -177,6 +177,8 @@ int MPI_Send( void *sendbuffer, int count, MPI_Datatype type, int destination, i
int MPI_Isend( void *recvbuffer, int count, MPI_Datatype type, int source, int tag, MPI_Comm comm, MPI_Request* request )
{ return 0; }
+int MPI_Wait( MPI_Request* request, MPI_Status* status )
+{ return 0; }
int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh)
{