diff --git a/examples/hello/writer/helloWriter.cpp b/examples/hello/writer/helloWriter.cpp
index 57dc41ad8b44f0753345f3a83144d681f903376b..9667b3ae484d563344e62e75aced778aa644aa6b 100644
--- a/examples/hello/writer/helloWriter.cpp
+++ b/examples/hello/writer/helloWriter.cpp
@@ -32,7 +32,7 @@ int main( int argc, char* argv [] )
try
{
//Define variable and local size
- auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx} );
+ 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
diff --git a/examples/hello/writer/helloWriter_nompi.cpp b/examples/hello/writer/helloWriter_nompi.cpp
index 7ba6b4ffe90c227d6cbe72a82467293581cf36d2..7438715cc89fba5393db5bb19683995e383536d7 100644
--- a/examples/hello/writer/helloWriter_nompi.cpp
+++ b/examples/hello/writer/helloWriter_nompi.cpp
@@ -23,7 +23,7 @@ int main( int argc, char* argv [] )
try
{
//Define variable and local size
- auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx} );
+ 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
diff --git a/examples/solidfluid/Makefile b/examples/solidfluid/Makefile
index 00f97805631d729d763cc499c4326fd8f08df0d5..f4acbc65533602d220cafeae1af7c57ef486e3b3 100644
--- a/examples/solidfluid/Makefile
+++ b/examples/solidfluid/Makefile
@@ -4,12 +4,9 @@
BASE_NAME=solidfluid_write
-
-TOOL_DIR=/usr/bin
-CC=$(TOOL_DIR)/g++ # Compiling with mpicc for now
+CC=g++ # Compiling with mpicc for now
MPICC:=mpic++
-AR=$(TOOL_DIR)/ar
#ADIOS LOCATION
ADIOS_DIR=../..
@@ -22,15 +19,15 @@ ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
#FLAGS
CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
-all: mpi
+all: mpi nompi
mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
- $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME)_mpi $(ADIOS_LIB)
+ $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) -lpthread
nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
- $(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME)_nompi $(ADIOS_NOMPI_LIB)
+ $(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) -lpthread
clean:
- rm -f *_mpi *_nompi *.o
+ rm -f *.exe
rm -rf *.dSYM
diff --git a/examples/solidfluid/solidfluid_write.cpp b/examples/solidfluid/solidfluid_write.cpp
index 933a1c3fdc2bfaf61dbff696716c5f61a1e41531..293003b45837f255c61abf1abfab0142017d881c 100644
--- a/examples/solidfluid/solidfluid_write.cpp
+++ b/examples/solidfluid/solidfluid_write.cpp
@@ -1,5 +1,5 @@
/*
- * globalArrayXML.cpp
+ * solid fluid example
*
* Created on: Oct 31, 2016
* Author: pnorbert
@@ -12,7 +12,9 @@
#include <string>
#include <vector>
-#include "ADIOS_OOP.h"
+#include "ADIOS_CPP.h"
+
+using adiosFile = std::shared_ptr<adios::Engine>;
struct MYDATA {
@@ -27,23 +29,20 @@ MPI_Comm comm=MPI_COMM_WORLD;
int rank, size;
-void write_data (std::shared_ptr<adios::Engine> writer, struct MYDATA &data)
+void write_data( adiosFile writer, struct MYDATA &data )
{
writer->Write("NX", &data.NX);
writer->Write("rank", &rank);
writer->Write("size", &size);
writer->Write("temperature", data.t);
writer->Write("pressure", data.p.data());
- //writer->Flush();
+ //writer->Flush(); AdvanceStep()???
}
-void write_checkpoint (adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid)
+void write_checkpoint( adiosFile ckptfile, const struct MYDATA &solid, const struct MYDATA &fluid )
{
- try {
- // Open an output for a Group
- // a transport or an engine should be associated with the group
- auto ckptfile = adios.Open("checkpoint.bp","w",comm,"checkpoint");
-
+ try
+ {
ckptfile->Write ("solid/NX", &solid.NX);
ckptfile->Write ("solid/rank", &rank);
ckptfile->Write ("solid/size", &size);
@@ -55,14 +54,14 @@ void write_checkpoint (adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &
ckptfile->Write ("fluid/size", &size);
ckptfile->Write ("fluid/temperature", fluid.t);
ckptfile->Write ("fluid/pressure", fluid.p.data());
+ //ckptfile->AdvanceStep(); ??
- //ckptfile->Flush();
- ckptfile->Close(); // Should this do Write() if user misses or should we complain?
}
catch ( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
if( rank == 0 )
{
+ std::cout << "ERROR: caught an exception from write_checkpoint\n";
std::cout << e.what() << "\n";
}
}
@@ -114,24 +113,29 @@ int main( int argc, char* argv [] )
MPI_Comm_size (comm, &size);
solid.NX = N;
- solid.t = new double(N);
+ solid.t = new double[N];
solid.p = std::vector<double>(N);
fluid.NX = N;
- fluid.t = new double(N);
+ fluid.t = new double[N];
fluid.p = std::vector<double>(N);
try
{
// ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios( "solidfluid.xml", comm, true );
+ adios::ADIOS adios( comm, true );
+
+ adios::Method& fileSettings = adios.DeclareMethod( "Reusable" ); //default engine is BP writer
+ fileSettings.AddTransport( "POSIX", "have_metadata_file=no" );
// Open a file with a Method which has selected a group and a transport in the XML.
// "a" will append to an already existing file, "w" would create a new file
// Multiple writes to the same file work as append in this application run
// FIXME: how do we support Update to same step?
- auto solidfile = adios.Open("solid.bp", "a", comm, "solid");
+ auto solidfile = adios.Open( "solid.bp", "w", comm, fileSettings );
+
+
// "solid" is a method but incidentally also a group
// Constructor only creates an object and what is needed there but does not open a stream/file
// It can be used to initialize a staging connection if not declared before
@@ -144,30 +148,44 @@ int main( int argc, char* argv [] )
// "a" will append to an already existing file, "w" would create a new file
// Multiple writes to the same file work as append in this application run
// FIXME: how do we support Update to same step?
- auto fluidfile = adios.Open("fluid.bp", "a", comm, "fluid");
+ auto fluidfile = adios.Open("fluid.bp", "w", comm, fileSettings );
+
+ auto checkpointFile = adios.Open("checkpoint.bp", "w", comm, fileSettings );
//int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
// we do not open this here, but every time when needed in a function
// Another output not associated with a single group, so that we can mix variables to it
//adios:handle vizstream = adios.Open( "stream.bp", comm, "w", "STAGING", "options to staging method");
- auto vizstream = adios.Open("stream.bp", "w", comm, "groupless");
+ auto vizstream = adios.Open("stream.bp", "w", comm, fileSettings );
// This creates an empty group inside, and we can write all kinds of variables to it
//Get Monitor info
std::ofstream logStream( "info_" + std::to_string(rank) + ".log" );
- adios.MonitorGroups( logStream );
+ adios.MonitorVariables( logStream );
+
+ int checkPointSteps = 10;
+
for (int it = 1; it <= 100; it++)
{
compute (it, solid, fluid);
- write_data(solidfile, solid);
- write_data(fluidfile, fluid);
+ write_data( solidfile, solid );
+ write_data( fluidfile, fluid );
+
+ if (it%checkPointSteps == 0) {
+ write_checkpoint( checkpointFile, solid, fluid );
- if (it%10 == 0) {
- write_checkpoint (adios, solid, fluid);
+ MPI_Barrier( comm );
+ if( rank == 0 )
+ {
+ std::cout << "New checkpoint step, current = " << checkPointSteps << "\n";
+ std::cin >> checkPointSteps;
+ MPI_Bcast( &checkPointSteps, 1, MPI_INT, 0, comm );
+ }
+ MPI_Barrier( comm );
}
write_viz(vizstream, solid, fluid);
@@ -188,7 +206,7 @@ int main( int argc, char* argv [] )
{
if( rank == 0 )
{
- std::cout << "Error: " << e.what() << "\n";
+ std::cout << "ERROR: " << e.what() << "\n";
}
}
diff --git a/examples/solidfluid/solidfluid_write_nompi.cpp b/examples/solidfluid/solidfluid_write_nompi.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ec450fd9a13337582f2c9e5f87c5394e0ec55b58
--- /dev/null
+++ b/examples/solidfluid/solidfluid_write_nompi.cpp
@@ -0,0 +1,217 @@
+/*
+ * solid fluid example
+ *
+ * Created on: Oct 31, 2016
+ * Author: pnorbert
+ */
+
+#include <stdexcept>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <vector>
+
+#include "ADIOS_CPP.h"
+
+using adiosFile = std::shared_ptr<adios::Engine>;
+
+
+struct MYDATA {
+ int NX;
+ double *t;
+ std::vector<double> p;
+};
+
+const int N = 10;
+struct MYDATA solid, fluid;
+int rank = 0, size = 1;
+
+
+void set_io_variables( adios::ADIOS& adios, const std::string process )
+{
+ adios.DefineVariable<int>( process + "/NX" );
+ adios.DefineVariable<int>( process + "/rank" );
+ adios.DefineVariable<int>( process + "/size" );
+ adios.DefineVariable<double>( process + "/temperature", adios::Dims{N} );
+ adios.DefineVariable<double>( process + "/pressure", adios::Dims{N} );
+}
+
+
+void write_data( adiosFile writer, const std::string process, struct MYDATA &data)
+{
+ writer->Write( process + "/NX", &data.NX);
+ writer->Write( process + "/rank", &rank);
+ writer->Write( process + "/size", &size);
+ writer->Write( process + "/temperature", data.t );
+ writer->Write( process + "/pressure", data.p.data());
+ //writer->Flush(); AdvanceStep()???
+}
+
+
+void write_checkpoint( adiosFile ckptfile, const struct MYDATA &solid, const struct MYDATA &fluid )
+{
+ try
+ {
+ ckptfile->Write ("solid/NX", &solid.NX);
+ ckptfile->Write ("solid/rank", &rank);
+ ckptfile->Write ("solid/size", &size);
+ ckptfile->Write ("solid/temperature", solid.t);
+ ckptfile->Write ("solid/pressure", &solid.p[0]);
+
+ ckptfile->Write ("fluid/NX", &fluid.NX);
+ ckptfile->Write ("fluid/rank", &rank);
+ ckptfile->Write ("fluid/size", &size);
+ ckptfile->Write ("fluid/temperature", fluid.t);
+ ckptfile->Write ("fluid/pressure", fluid.p.data());
+ //ckptfile->AdvanceStep(); ??
+
+ }
+ catch ( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
+ {
+ if( rank == 0 )
+ {
+ std::cout << "ERROR: caught an exception from write_checkpoint\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+}
+
+void write_viz( adiosFile vizstream, struct MYDATA &solid, struct MYDATA &fluid )
+{
+ // This stream is not associated with a group, so we must say for each write which group to use
+ // The output variable is re-defined inside as <groupname>/<varname>, unless given as third string argument
+ // An array variable's dimension definitions are also re-defined with dimensions <groupname>/<dimensionvar>
+
+ //vizstream->Write ("solid", "NX", &solid.NX);
+ //vizstream->Write ("solid", "rank", &rank);
+ //vizstream->Write ("solid", "size", &size);
+
+ // write solid group's temperature simply as temperature, risking overloading the 'temperature' variable when
+ // reading from a file
+
+ //vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
+
+ //vizstream->Write ("fluid", "NX", &fluid.NX);
+ //vizstream->Write ("fluid", "rank", &rank);
+ //vizstream->Write ("fluid", "size", &size);
+
+ //vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
+
+ //vizstream->Flush(); // flushes all data to disk; required operation
+ //vizstream.AdvanceStep();
+}
+
+void compute (int it, struct MYDATA &solid, struct MYDATA &fluid)
+{
+ for (int i = 0; i < solid.NX; i++)
+ {
+ solid.t[i] = it*100.0 + rank*solid.NX + i;
+ solid.p[i] = it*1000.0 + rank*solid.NX + i;
+ }
+ for (int i = 0; i < fluid.NX; i++)
+ {
+ fluid.t[i] = it*200.0 + rank*fluid.NX + i;
+ fluid.p[i] = it*2000.0 + rank*fluid.NX + i;
+ }
+}
+
+int main( int argc, char* argv [] )
+{
+ solid.NX = N;
+ solid.t = new double[N];
+ solid.p = std::vector<double>(N);
+
+ fluid.NX = N;
+ fluid.t = new double[N];
+ fluid.p = std::vector<double>(N);
+
+ try
+ {
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios( true );
+ set_io_variables( adios, "solid" );
+ set_io_variables( adios, "fluid" );
+
+ adios::Method& fileSettings = adios.DeclareMethod( "Reusable" ); //default engine is BP writer
+ fileSettings.AddTransport( "POSIX", "have_metadata_file=no" );
+
+ // Open a file with a Method which has selected a group and a transport in the XML.
+ // "a" will append to an already existing file, "w" would create a new file
+ // Multiple writes to the same file work as append in this application run
+ // FIXME: how do we support Update to same step?
+
+ auto solidfile = adios.Open( "solid.bp", "w", fileSettings );
+
+
+ // "solid" is a method but incidentally also a group
+ // Constructor only creates an object and what is needed there but does not open a stream/file
+ // It can be used to initialize a staging connection if not declared before
+ // FIXME: which argument can be post-poned into Open() instead of constructor?
+ //solidfile.Open("solid.bp");
+
+
+ // Open a file with a Method that has selected a group and an engine in the XML
+ // The transport method(s) are (must be) associated with the engines
+ // "a" will append to an already existing file, "w" would create a new file
+ // Multiple writes to the same file work as append in this application run
+ // FIXME: how do we support Update to same step?
+ auto fluidfile = adios.Open("fluid.bp", "w", fileSettings );
+
+ auto checkpointFile = adios.Open("checkpoint.bp", "w", fileSettings );
+
+ //int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
+ // we do not open this here, but every time when needed in a function
+
+ // Another output not associated with a single group, so that we can mix variables to it
+ //adios:handle vizstream = adios.Open( "stream.bp", comm, "w", "STAGING", "options to staging method");
+ auto vizstream = adios.Open("stream.bp", "w", fileSettings );
+
+ // This creates an empty group inside, and we can write all kinds of variables to it
+
+ //Get Monitor info
+ std::ofstream logStream( "info_nompi.log" );
+ adios.MonitorVariables( logStream );
+
+ int checkPointSteps = 10;
+
+
+ for (int it = 1; it <= 100; it++)
+ {
+ compute (it, solid, fluid);
+
+ write_data( solidfile, "solid", solid );
+ write_data( fluidfile, "fluid", fluid );
+
+ if (it%checkPointSteps == 0) {
+ write_checkpoint( checkpointFile, solid, fluid );
+
+ {
+ std::cout << "New checkpoint step, current = " << checkPointSteps << "\n";
+ std::cin >> checkPointSteps;
+ }
+
+ }
+
+ write_viz(vizstream, solid, fluid);
+
+ std::cout << "Timestep " << it << " written\n";
+ }
+
+ solidfile->Close();
+ fluidfile->Close();
+ vizstream->Close();
+ checkpointFile->Close();
+
+ // need barrier before we destroy the ADIOS object here automatically ...no!
+ std::cout << "Finalize adios\n";
+ }
+ catch( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
+ {
+ std::cout << e.what() << "\n";
+ }
+
+ delete[] solid.t;
+ delete[] fluid.t;
+
+ return 0;
+}
diff --git a/include/ADIOS.h b/include/ADIOS.h
index caaeb76a440594d2e4540c46965dce2e659ee444..001334b700a30ddfb2ec300672faa5e5e72db962 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -184,7 +184,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* Note that either the user closes this fileStream or it's closed at the end.
* @param logStream either std::cout standard output, or a std::ofstream file
*/
- void MonitorVariables( std::ostream& logStream ) const;
+ void MonitorVariables( std::ostream& logStream );
@@ -236,7 +236,7 @@ private: //no const to allow default empty and copy constructors
const std::string methodName, const std::string hint ) const;
template< class T >
- unsigned int GetVariableIndex( const std::string name ) const
+ unsigned int GetVariableIndex( const std::string name )
{
auto itVariable = m_Variables.find( name );
CheckVariableName( itVariable, name, "in call to GetVariable<" + GetType<T>() + ">" );
@@ -324,8 +324,8 @@ Variable<long int>& ADIOS::DefineVariable( const std::string name, const Dims di
template<> inline
-Variable<unsigned long int>& ADIOS::DefineVariable<unsigned long int>( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
+Variable<unsigned long int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
+ const Dims globalDimensions, const Dims globalOffsets )
{
CheckVariableInput( name, dimensions );
m_ULInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
@@ -438,7 +438,7 @@ Variable<double>& ADIOS::GetVariable( const std::string name )
{ return m_Double[ GetVariableIndex<double>(name) ]; }
template<> inline
-Variable<long double>& ADIOS::GetVariable<long double>( const std::string name )
+Variable<long double>& ADIOS::GetVariable( const std::string name )
{ return m_LDouble[ GetVariableIndex<long double>(name) ]; }
diff --git a/include/core/Engine.h b/include/core/Engine.h
index d2adc18e830e3092b60340f82d3faf8a00e35dcc..2255cbf9db60cd5d4fe0b4b40cc2d7017e26c39f 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -79,7 +79,7 @@ public:
* Write function that adds static checking on the variable to be passed by values
* It then calls its corresponding derived class virtual function
* This version uses m_Group to look for the variableName.
- * @param variableName name of variable to the written
+ * @param variable name of variable to the written
* @param values pointer passed from the application
*/
template< class T >
diff --git a/include/core/Variable.h b/include/core/Variable.h
index 1473a59791b93657b24e8ad2cbc86606eb380851..d413ea23fd668bd4751cbec0b294cefaa625c8ec 100644
--- a/include/core/Variable.h
+++ b/include/core/Variable.h
@@ -85,16 +85,21 @@ public:
void Monitor( std::ostream& logInfo ) const noexcept
{
- logInfo << "Hello from DataMan Write variable " << m_Name << "\n";
+ logInfo << "Variable: " << m_Name << "\n";
logInfo << "Type: " << m_Type << "\n";
logInfo << "Size: " << TotalSize() << " elements\n";
logInfo << "Payload: " << PayLoadSize() << " bytes\n";
- logInfo << "Values: \n";
- for( unsigned int i = 0; i < TotalSize(); ++i )
+ if( m_AppValues != nullptr )
{
- logInfo << m_AppValues[i] << " ";
+ logInfo << "Values (first 10): \n";
+ for( unsigned int i = 0; i < 100; ++i )
+ {
+ logInfo << m_AppValues[i] << " ";
+ }
+ logInfo << " ...";
}
+
logInfo << "\n";
}
diff --git a/src/ADIOS.cpp b/src/ADIOS.cpp
index 1020f05330b16aa9cd0958d6bee1a999dd72cc43..a5fd9a0f096c3cc7e50acb4c98e483c00ad2e478 100644
--- a/src/ADIOS.cpp
+++ b/src/ADIOS.cpp
@@ -149,14 +149,53 @@ std::shared_ptr<Engine> ADIOS::Open( const std::string name, const std::string a
}
-void ADIOS::MonitorVariables( std::ostream& logStream ) const
+void ADIOS::MonitorVariables( std::ostream& logStream )
{
logStream << "\tVariable \t Type\n";
for( auto& variablePair : m_Variables )
{
- logStream << "Variable:..." << variablePair.first << "\n";
- //variablePair.second.Monitor( logStream );
+ const std::string name( variablePair.first );
+ const std::string type( variablePair.second.first );
+
+ if( type == GetType<char>() )
+ GetVariable<char>( name ).Monitor( logStream );
+
+ else if( type == GetType<unsigned char>() )
+ GetVariable<unsigned char>( name ).Monitor( logStream );
+
+ else if( type == GetType<short>() )
+ GetVariable<short>( name ).Monitor( logStream );
+
+ else if( type == GetType<unsigned short>() )
+ GetVariable<unsigned short>( name ).Monitor( logStream );
+
+ else if( type == GetType<int>() )
+ GetVariable<int>( name ).Monitor( logStream );
+
+ else if( type == GetType<unsigned int>() )
+ GetVariable<unsigned int>( name ).Monitor( logStream );
+
+ else if( type == GetType<long int>() )
+ GetVariable<long int>( name ).Monitor( logStream );
+
+ else if( type == GetType<unsigned long int>() )
+ GetVariable<unsigned long int>( name ).Monitor( logStream );
+
+ else if( type == GetType<long long int>() )
+ GetVariable<long long int>( name ).Monitor( logStream );
+
+ else if( type == GetType<unsigned long long int>() )
+ GetVariable<unsigned long long int>( name ).Monitor( logStream );
+
+ else if( type == GetType<float>() )
+ GetVariable<float>( name ).Monitor( logStream );
+
+ else if( type == GetType<double>() )
+ GetVariable<double>( name ).Monitor( logStream );
+
+ else if( type == GetType<long double>() )
+ GetVariable<long double>( name ).Monitor( logStream );
}
}