diff --git a/examples/heatTransfer/HeatTransfer.cpp b/examples/heatTransfer/HeatTransfer.cpp
index 970f7d2f10911c3fa4309a4eb9bb977f1f183fb9..fd6d84f6c0a4b77449f34587238a19859dd3d960 100644
--- a/examples/heatTransfer/HeatTransfer.cpp
+++ b/examples/heatTransfer/HeatTransfer.cpp
@@ -27,7 +27,7 @@ HeatTransfer::HeatTransfer( const Settings& settings )
m_T1[0] = new double[ (m_s.ndx+2) * (m_s.ndy+2) ];
m_T2 = new double*[ m_s.ndx+2 ];
m_T2[0] = new double[ (m_s.ndx+2) * (m_s.ndy+2) ];
- for (int i = 1; i < m_s.ndx+2; i++)
+ for (unsigned int i = 1; i < m_s.ndx+2; i++)
{
m_T1[i] = m_T1[i-1] + m_s.ndy+2;
m_T2[i] = m_T2[i-1] + m_s.ndy+2;
@@ -49,8 +49,8 @@ void HeatTransfer::init(bool init_with_rank)
{
if (init_with_rank)
{
- for (int i = 0; i < m_s.ndx+2; i++)
- for (int j = 0; j < m_s.ndy+2; j++)
+ for (unsigned int i = 0; i < m_s.ndx+2; i++)
+ for (unsigned int j = 0; j < m_s.ndy+2; j++)
m_T1[i][j] = m_s.rank;
}
else
@@ -59,10 +59,10 @@ void HeatTransfer::init(bool init_with_rank)
const double hy = 2.0 * 4.0*atan(1.0)/m_s.ndy;
double x, y;
- for (int i = 0; i < m_s.ndx+2; i++)
+ for (unsigned int i = 0; i < m_s.ndx+2; i++)
{
x = 0.0 + hx*(i-1);
- for (int j = 0; j < m_s.ndy+2; j++)
+ for (unsigned int j = 0; j < m_s.ndy+2; j++)
{
y = 0.0 + hy*(j-1);
m_T1[i][j] = cos(8*x) + cos(6*x) - cos(4*x) + cos(2*x) - cos(x) +
@@ -88,10 +88,10 @@ void HeatTransfer::printT(std::string message, MPI_Comm comm) const
}
std::cout << "Rank " << rank << " " << message << std::endl;
- for (int i = 0; i < m_s.ndx+2; i++)
+ for (unsigned int i = 0; i < m_s.ndx+2; i++)
{
std::cout << " T[" << i << "][] = ";
- for (int j = 0; j < m_s.ndy+2; j++)
+ for (unsigned int j = 0; j < m_s.ndy+2; j++)
{
std::cout << std::setw(6) << m_TCurrent[i][j];
}
@@ -115,9 +115,9 @@ void HeatTransfer::switchCurrentNext()
void HeatTransfer::iterate()
{
- for( int i = 1; i <= m_s.ndx; ++i)
+ for( unsigned int i = 1; i <= m_s.ndx; ++i)
{
- for( int j = 1; j <= m_s.ndy; ++j)
+ for( unsigned int j = 1; j <= m_s.ndy; ++j)
{
m_TNext[i][j] =
omega/4*(m_TCurrent[i-1][j] +
@@ -134,19 +134,19 @@ void HeatTransfer::heatEdges()
{
// Heat the whole global edges
if( m_s.posx==0 )
- for( int j = 0; j < m_s.ndy+2; ++j)
+ for( unsigned int j = 0; j < m_s.ndy+2; ++j)
m_TCurrent[0][j]= edgetemp;
if( m_s.posx==m_s.npx-1 )
- for( int j = 0; j < m_s.ndy+2; ++j)
+ for( unsigned int j = 0; j < m_s.ndy+2; ++j)
m_TCurrent[m_s.ndx+1][j]= edgetemp;
if (m_s.posy==0)
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
m_TCurrent[i][0]= edgetemp;
if (m_s.posy==m_s.npy-1)
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
m_TCurrent[i][m_s.ndy+1]= edgetemp;
}
@@ -163,7 +163,7 @@ void HeatTransfer::exchange( MPI_Comm comm )
if( m_s.rank_left >= 0 )
{
std::cout << "Rank " << m_s.rank << " send left to rank " << m_s.rank_left << std::endl;
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
send_x[i] = m_TCurrent[i][1];
MPI_Send(send_x, m_s.ndx+2, MPI_REAL8, m_s.rank_left, tag, comm);
}
@@ -171,7 +171,7 @@ void HeatTransfer::exchange( MPI_Comm comm )
{
std::cout << "Rank " << m_s.rank << " receive from right from rank " << m_s.rank_right << std::endl;
MPI_Recv(recv_x, m_s.ndx+2, MPI_REAL8, m_s.rank_right, tag, comm, &status);
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
m_TCurrent[i][m_s.ndy+1] = recv_x[i];
}
@@ -180,7 +180,7 @@ void HeatTransfer::exchange( MPI_Comm comm )
if( m_s.rank_right >= 0 )
{
std::cout << "Rank " << m_s.rank << " send right to rank " << m_s.rank_right << std::endl;
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
send_x[i] = m_TCurrent[i][m_s.ndy];
MPI_Send(send_x, m_s.ndx+2, MPI_REAL8, m_s.rank_right, tag, comm);
}
@@ -188,7 +188,7 @@ void HeatTransfer::exchange( MPI_Comm comm )
{
std::cout << "Rank " << m_s.rank << " receive from left from rank " << m_s.rank_left << std::endl;
MPI_Recv(recv_x, m_s.ndx+2, MPI_REAL8, m_s.rank_left, tag, comm, &status);
- for( int i = 0; i < m_s.ndx+2; ++i)
+ for( unsigned int i = 0; i < m_s.ndx+2; ++i)
m_TCurrent[i][0] = recv_x[i];
}
@@ -230,7 +230,7 @@ void HeatTransfer::exchange( MPI_Comm comm )
std::vector<double> HeatTransfer::data_noghost() const
{
std::vector<double>d( m_s.ndx * m_s.ndy );
- for( int i = 1; i <= m_s.ndx; ++i )
+ for( unsigned int i = 1; i <= m_s.ndx; ++i )
{
std::memcpy( &d[(i-1)*m_s.ndy], m_TCurrent[i]+1, m_s.ndy*sizeof(double));
}
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index d2e5618aab1d17aa7e120448f399facc90f3156e..8290337c874c3443fd4c7b68a081b0cccf229cd0 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/examples/heatTransfer/IO_adios2.cpp
@@ -6,18 +6,91 @@
*/
#include "IO.h"
+#include "ADIOS_CPP.h"
+#include <string>
+
+static int rank_saved;
+adios::ADIOS * ad = nullptr;
+std::shared_ptr<adios::Engine> bpWriter;
+adios::Variable<double> * varT = nullptr;
IO::IO( const Settings& s, MPI_Comm comm )
{
+ rank_saved = s.rank;
m_outputfilename = s.outputfile + ".bp";
+ ad = new adios::ADIOS( "adios2.xml", comm, adios::INFO );
+
+ //Define method for engine creation
+ // 1. Get method def from config file or define new one
+
+ adios::Method& bpWriterSettings = ad->DeclareMethod( "output" );
+ if( ! bpWriterSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ bpWriterSettings.SetEngine( "BP" ); // BP is the default engine
+ bpWriterSettings.SetAvailableCores( 2); // no threading for data processing (except for staging)
+ bpWriterSettings.AddTransport( "File", "lucky=yes" ); // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.SetParameters("have_metadata_file","yes" ); // Passing parameters to the engine
+ bpWriterSettings.SetParameters( "Aggregation", std::to_string((s.nproc+1)/2) ); // number of aggregators
+ }
+
+
+ // define T as 2D global array
+ varT = &ad->DefineVariable<double>(
+ "T",
+ {s.gndx,s.gndy}, // Global dimensions
+ {s.ndx,s.ndy}, // local size, could be defined later using SetSelection()
+ {s.offsx,s.offsy} // offset of the local array in the global space
+ );
+
+
+ //add transform to variable
+ //adios::Transform tr = adios::transform::BZIP2( );
+ //varT.AddTransform( tr, "" );
+ // varT.AddTransform( tr,"accuracy=0.001" ); // for ZFP
+
+ bpWriter = ad->Open( m_outputfilename, "w", comm, bpWriterSettings, adios::COLLECTIVE_IO);
+
+ if( bpWriter == nullptr )
+ throw std::ios_base::failure( "ERROR: failed to open ADIOS bpWriter\n" );
+
+
}
IO::~IO()
{
+ bpWriter->Close();
+ delete ad;
+}
+
+void /*IO::*/old_style_write(int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm )
+{
+ bpWriter->Write<double>( *varT, ht.data_noghost().data());
+ bpWriter->Advance( );
}
void IO::write(int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm )
{
+ /* This selection is redundant and not required, since we defined
+ * the selection already in DefineVariable(). It is here just as an example.
+ */
+ // Make a selection to describe the local dimensions of the variable we write and
+ // its offsets in the global spaces. This could have been done in adios.DefineVariable()
+ adios::Selection sel = adios.SelectionBoundingBox( {s.ndx,s.ndy}, {s.offsx,s.offsy} ); // local dims and offsets; both as list
+ var2D.SetSelection( sel );
+
+ /* Select the area that we want to write from the data pointer we pass to the writer.
+ Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
+ Engine will copy this bounding box from the data pointer into the output buffer.
+ Size of the bounding box should match the "space" selection which was given above.
+ Default memspace is always the full selection.
+ */
+ adios::Selection memspace = adios.SelectionBoundingBox( {s.ndx,s.ndy}, {1,1} );
+ var2D.SetMemorySelection( memspace );
+
+ bpWriter->Write<double>( *varT, ht.data());
+ bpWriter->Advance( );
}
diff --git a/examples/heatTransfer/Settings.cpp b/examples/heatTransfer/Settings.cpp
index 6cd14307dab7f0dee79990db7d2fa97620c1b032..8910cbc838a084511d8142eaaffd3a3480f2419d 100644
--- a/examples/heatTransfer/Settings.cpp
+++ b/examples/heatTransfer/Settings.cpp
@@ -13,7 +13,7 @@
#include "Settings.h"
-static int convertToInt( std::string varName, char *arg )
+static unsigned int convertToUint( std::string varName, char *arg )
{
char *end;
int retval = std::strtoll( arg, &end, 10);
@@ -22,26 +22,32 @@ static int convertToInt( std::string varName, char *arg )
throw std::invalid_argument( "Invalid value given for " + varName + ": "
+ std::string(arg) );
}
- return retval;
+ if( retval < 0 )
+ {
+ throw std::invalid_argument( "Negative value given for " + varName + ": "
+ + std::string(arg) );
+ }
+ return (unsigned int) retval;
}
Settings::Settings( int argc, char* argv [], int rank, int nproc )
-: rank{rank}, nproc{nproc}
+: rank{rank}
{
if (argc < 8)
{
throw std::invalid_argument( "Not enough arguments" );
}
+ this->nproc = (unsigned int) nproc;
outputfile = argv[1];
- npx = convertToInt("N", argv[2]);
- npy = convertToInt("M", argv[3]);
- ndx = convertToInt("nx", argv[4]);
- ndy = convertToInt("ny", argv[5]);
- steps = convertToInt("steps", argv[6]);
- iterations = convertToInt("iterations", argv[7]);
-
- if( npx * npy != nproc )
+ npx = convertToUint("N", argv[2]);
+ npy = convertToUint("M", argv[3]);
+ ndx = convertToUint("nx", argv[4]);
+ ndy = convertToUint("ny", argv[5]);
+ steps = convertToUint("steps", argv[6]);
+ iterations = convertToUint("iterations", argv[7]);
+
+ if( npx * npy != this->nproc )
{
throw std::invalid_argument( "N*M must equal the number of processes" );
}
diff --git a/examples/heatTransfer/Settings.h b/examples/heatTransfer/Settings.h
index 0db8b28d9cea08666a6448ef8289d6610eb79956..26ec50e18b270dc8945fd6df242116de89536931 100644
--- a/examples/heatTransfer/Settings.h
+++ b/examples/heatTransfer/Settings.h
@@ -16,27 +16,27 @@ class Settings
public:
// user arguments
std::string outputfile;
- int npx; // Number of processes in X (slow) dimension
- int npy; // Number of processes in Y (fast) dimension
- int ndx; // Local array size in X dimension per process
- int ndy; // Local array size in y dimension per process
- int steps; // Number of output steps
- int iterations; // Number of computing iterations between steps
+ unsigned int npx; // Number of processes in X (slow) dimension
+ unsigned int npy; // Number of processes in Y (fast) dimension
+ unsigned int ndx; // Local array size in X dimension per process
+ unsigned int ndy; // Local array size in y dimension per process
+ unsigned int steps; // Number of output steps
+ unsigned int iterations; // Number of computing iterations between steps
// calculated values from those arguments and number of processes
- int gndx; // Global array size in slow dimension
- int gndy; // Global array size in fast dimension
+ unsigned int gndx; // Global array size in slow dimension
+ unsigned int gndy; // Global array size in fast dimension
// X dim positions: rank 0, npx, 2npx... are in the same X position
// Y dim positions: npx number of consecutive processes belong to one row (npx columns)
- int posx; // Position of this process in X dimension
- int posy; // Position of this process in Y dimension
- int offsx; // Offset of local array in X dimension on this process
- int offsy; // Offset of local array in Y dimension on this process
+ unsigned int posx; // Position of this process in X dimension
+ unsigned int posy; // Position of this process in Y dimension
+ unsigned int offsx; // Offset of local array in X dimension on this process
+ unsigned int offsy; // Offset of local array in Y dimension on this process
int rank; // MPI rank
- int nproc; // number of processors
+ unsigned int nproc; // number of processors
- // neighbours by their MPI ranks
+ // neighbors by their MPI ranks, -1 if there is no such neighbor
int rank_left;
int rank_right;
int rank_up;
diff --git a/examples/heatTransfer/main.cpp b/examples/heatTransfer/main.cpp
index f000dbd185b571308480bf3cef303ee7f5804741..22fd919cefd2338b3bd79d8df3ef8ec81d7cd8a6 100644
--- a/examples/heatTransfer/main.cpp
+++ b/examples/heatTransfer/main.cpp
@@ -68,11 +68,11 @@ int main( int argc, char* argv [] )
ht.printT("Heated T:", mpiHeatTransferComm);
io.write( 0, ht, settings, mpiHeatTransferComm );
- for( int t = 1; t <= settings.steps; ++t )
+ for( unsigned int t = 1; t <= settings.steps; ++t )
{
if( rank == 0 )
std::cout << "Step " << t << ":\n";
- for( int iter = 1; iter <= settings.iterations; ++iter )
+ for( unsigned int iter = 1; iter <= settings.iterations; ++iter )
{
ht.iterate();
ht.exchange( mpiHeatTransferComm );