From 053ad71b424232c5db283dbe70fb9094b2942c9b Mon Sep 17 00:00:00 2001
From: Norbert Podhorszki <pnorbert@ornl.gov>
Date: Wed, 1 Mar 2017 11:22:03 -0500
Subject: [PATCH] Simplify C++ code of HeatTransfer
---
examples/heatTransfer/HeatTransfer.cpp | 132 ++++++++++++-------------
examples/heatTransfer/HeatTransfer.h | 12 +--
examples/heatTransfer/IO.h | 4 +-
examples/heatTransfer/IO_adios1.cpp | 26 ++---
examples/heatTransfer/IO_adios2.cpp | 6 +-
examples/heatTransfer/IO_ascii.cpp | 26 ++---
examples/heatTransfer/IO_hdf5_a.cpp | 59 +++++++++++
examples/heatTransfer/Makefile | 10 +-
examples/heatTransfer/main.cpp | 88 ++++-------------
9 files changed, 188 insertions(+), 175 deletions(-)
create mode 100644 examples/heatTransfer/IO_hdf5_a.cpp
diff --git a/examples/heatTransfer/HeatTransfer.cpp b/examples/heatTransfer/HeatTransfer.cpp
index 473a5e000..970f7d2f1 100644
--- a/examples/heatTransfer/HeatTransfer.cpp
+++ b/examples/heatTransfer/HeatTransfer.cpp
@@ -20,17 +20,17 @@
#include "HeatTransfer.h"
-HeatTransfer::HeatTransfer( std::shared_ptr<Settings> settings )
+HeatTransfer::HeatTransfer( const Settings& settings )
: m_s{settings}
{
- m_T1 = new double*[ m_s->ndx+2 ];
- 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++)
+ m_T1 = new double*[ m_s.ndx+2 ];
+ 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++)
{
- m_T1[i] = m_T1[i-1] + m_s->ndy+2;
- m_T2[i] = m_T2[i-1] + m_s->ndy+2;
+ m_T1[i] = m_T1[i-1] + m_s.ndy+2;
+ m_T2[i] = m_T2[i-1] + m_s.ndy+2;
}
m_TCurrent = m_T1;
m_TNext = m_T2;
@@ -49,20 +49,20 @@ 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++)
- m_T1[i][j] = m_s->rank;
+ for (int i = 0; i < m_s.ndx+2; i++)
+ for (int j = 0; j < m_s.ndy+2; j++)
+ m_T1[i][j] = m_s.rank;
}
else
{
- const double hx = 2.0 * 4.0*atan(1.0)/m_s->ndx;
- const double hy = 2.0 * 4.0*atan(1.0)/m_s->ndy;
+ const double hx = 2.0 * 4.0*atan(1.0)/m_s.ndx;
+ 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 (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 (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) +
@@ -74,7 +74,7 @@ void HeatTransfer::init(bool init_with_rank)
m_TNext = m_T2;
}
-void HeatTransfer::printT(std::string message, MPI_Comm comm)
+void HeatTransfer::printT(std::string message, MPI_Comm comm) const
{
int rank, size;
int tag = 1;
@@ -88,10 +88,10 @@ void HeatTransfer::printT(std::string message, MPI_Comm comm)
}
std::cout << "Rank " << rank << " " << message << std::endl;
- for (int i = 0; i < m_s->ndx+2; i++)
+ for (int i = 0; i < m_s.ndx+2; i++)
{
std::cout << " T[" << i << "][] = ";
- for (int j = 0; j < m_s->ndy+2; j++)
+ for (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( int i = 1; i <= m_s.ndx; ++i)
{
- for( int j = 1; j <= m_s->ndy; ++j)
+ for( int j = 1; j <= m_s.ndy; ++j)
{
m_TNext[i][j] =
omega/4*(m_TCurrent[i-1][j] +
@@ -133,89 +133,89 @@ void HeatTransfer::iterate()
void HeatTransfer::heatEdges()
{
// Heat the whole global edges
- if( m_s->posx==0 )
- for( int j = 0; j < m_s->ndy+2; ++j)
+ if( m_s.posx==0 )
+ for( 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)
- m_TCurrent[m_s->ndx+1][j]= edgetemp;
+ if( m_s.posx==m_s.npx-1 )
+ for( 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)
+ if (m_s.posy==0)
+ for( 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)
- m_TCurrent[i][m_s->ndy+1]= edgetemp;
+ if (m_s.posy==m_s.npy-1)
+ for( int i = 0; i < m_s.ndx+2; ++i)
+ m_TCurrent[i][m_s.ndy+1]= edgetemp;
}
void HeatTransfer::exchange( MPI_Comm comm )
{
// Exchange ghost cells, in the order left-right-up-down
- double * send_x = new double[m_s->ndx+2];
- double * recv_x = new double[m_s->ndx+2];
+ double * send_x = new double[m_s.ndx+2];
+ double * recv_x = new double[m_s.ndx+2];
// send to left + receive from right
int tag = 1;
MPI_Status status;
- if( m_s->rank_left >= 0 )
+ 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)
+ 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)
send_x[i] = m_TCurrent[i][1];
- MPI_Send(send_x, m_s->ndx+2, MPI_REAL8, m_s->rank_left, tag, comm);
+ MPI_Send(send_x, m_s.ndx+2, MPI_REAL8, m_s.rank_left, tag, comm);
}
- if( m_s->rank_right >= 0 )
+ if( m_s.rank_right >= 0 )
{
- 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)
- m_TCurrent[i][m_s->ndy+1] = recv_x[i];
+ 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)
+ m_TCurrent[i][m_s.ndy+1] = recv_x[i];
}
// send to right + receive from left
tag = 2;
- if( m_s->rank_right >= 0 )
+ 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)
- 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);
+ 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)
+ 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);
}
- if( m_s->rank_left >= 0 )
+ if( m_s.rank_left >= 0 )
{
- 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)
+ 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)
m_TCurrent[i][0] = recv_x[i];
}
// send down + receive from above
tag = 3;
- if( m_s->rank_down >= 0 )
+ if( m_s.rank_down >= 0 )
{
- std::cout << "Rank " << m_s->rank << " send down to rank " << m_s->rank_down << std::endl;
- MPI_Send(m_TCurrent[m_s->ndx], m_s->ndy+2, MPI_REAL8, m_s->rank_down, tag, comm);
+ std::cout << "Rank " << m_s.rank << " send down to rank " << m_s.rank_down << std::endl;
+ MPI_Send(m_TCurrent[m_s.ndx], m_s.ndy+2, MPI_REAL8, m_s.rank_down, tag, comm);
}
- if ( m_s->rank_up >= 0 )
+ if ( m_s.rank_up >= 0 )
{
- std::cout << "Rank " << m_s->rank << " receive from above from rank " << m_s->rank_up << std::endl;
- MPI_Recv(m_TCurrent[0], m_s->ndy+2, MPI_REAL8, m_s->rank_up, tag, comm, &status);
+ std::cout << "Rank " << m_s.rank << " receive from above from rank " << m_s.rank_up << std::endl;
+ MPI_Recv(m_TCurrent[0], m_s.ndy+2, MPI_REAL8, m_s.rank_up, tag, comm, &status);
}
// send up + receive from below
tag = 4;
- if( m_s->rank_up >= 0 )
+ if( m_s.rank_up >= 0 )
{
- std::cout << "Rank " << m_s->rank << " send up to rank " << m_s->rank_up << std::endl;
- MPI_Send(m_TCurrent[1], m_s->ndy+2, MPI_REAL8, m_s->rank_up, tag, comm);
+ std::cout << "Rank " << m_s.rank << " send up to rank " << m_s.rank_up << std::endl;
+ MPI_Send(m_TCurrent[1], m_s.ndy+2, MPI_REAL8, m_s.rank_up, tag, comm);
}
- if ( m_s->rank_down >= 0 )
+ if ( m_s.rank_down >= 0 )
{
- std::cout << "Rank " << m_s->rank << " receive from below from rank " << m_s->rank_down << std::endl;
- MPI_Recv(m_TCurrent[m_s->ndx+1], m_s->ndy+2, MPI_REAL8, m_s->rank_down, tag, comm, &status);
+ std::cout << "Rank " << m_s.rank << " receive from below from rank " << m_s.rank_down << std::endl;
+ MPI_Recv(m_TCurrent[m_s.ndx+1], m_s.ndy+2, MPI_REAL8, m_s.rank_down, tag, comm, &status);
}
delete[] send_x;
@@ -227,12 +227,12 @@ void HeatTransfer::exchange( MPI_Comm comm )
* into a separate contiguous vector and returns it.
* @return A vector with ndx*ndy elements
*/
-std::vector<double> HeatTransfer::data_noghost()
+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 )
+ std::vector<double>d( m_s.ndx * m_s.ndy );
+ for( 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));
+ std::memcpy( &d[(i-1)*m_s.ndy], m_TCurrent[i]+1, m_s.ndy*sizeof(double));
}
return d;
}
diff --git a/examples/heatTransfer/HeatTransfer.h b/examples/heatTransfer/HeatTransfer.h
index 4fd2feff8..09589e8ae 100644
--- a/examples/heatTransfer/HeatTransfer.h
+++ b/examples/heatTransfer/HeatTransfer.h
@@ -16,7 +16,7 @@
class HeatTransfer
{
public:
- HeatTransfer( std::shared_ptr<Settings> settings ); // Create two 2D arrays with ghost cells to compute
+ HeatTransfer( const Settings& settings ); // Create two 2D arrays with ghost cells to compute
~HeatTransfer();
void init(bool init_with_rank); // set up array values with either rank or real demo values
void iterate(); // one local calculation step
@@ -24,13 +24,13 @@ public:
void exchange( MPI_Comm comm ); // send updates to neighbors
// return a single value at index i,j. 0 <= i <= ndx+2, 0 <= j <= ndy+2
- double T( int i, int j) {return m_TCurrent[i][j];};
+ double T( int i, int j) const {return m_TCurrent[i][j];};
// return (1D) pointer to current T data, ndx+2 * ndy+2 elements
- const double *data() {return m_TCurrent[0];};
+ double *data() const {return m_TCurrent[0];};
// return (1D) pointer to current T data without ghost cells, ndx*ndy elements
- std::vector<double> data_noghost();
+ std::vector<double> data_noghost() const;
- void printT(std::string message, MPI_Comm comm); // debug: print local TCurrent on stdout
+ void printT(std::string message, MPI_Comm comm) const; // debug: print local TCurrent on stdout
private:
const double edgetemp = 3.0; // temperature at the edges of the global plate
@@ -39,7 +39,7 @@ private:
double **m_T2; // another 2D array
double **m_TCurrent; // pointer to T1 or T2
double **m_TNext; // pointer to T2 or T1
- std::shared_ptr<Settings> m_s;
+ const Settings& m_s;
void switchCurrentNext(); // switch the current array with the next array
};
diff --git a/examples/heatTransfer/IO.h b/examples/heatTransfer/IO.h
index 542112f1c..789a4482b 100644
--- a/examples/heatTransfer/IO.h
+++ b/examples/heatTransfer/IO.h
@@ -16,9 +16,9 @@ class IO
{
public:
- IO( std::shared_ptr<Settings> s, MPI_Comm comm );
+ IO( const Settings& s, MPI_Comm comm );
~IO();
- void write( int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Settings> s, MPI_Comm comm );
+ void write( int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm );
private:
std::string m_outputfilename;
diff --git a/examples/heatTransfer/IO_adios1.cpp b/examples/heatTransfer/IO_adios1.cpp
index 3cd170581..8d3a4a9e4 100644
--- a/examples/heatTransfer/IO_adios1.cpp
+++ b/examples/heatTransfer/IO_adios1.cpp
@@ -15,10 +15,10 @@
static int64_t group;
static int rank_saved;
-IO::IO( std::shared_ptr<Settings> s, MPI_Comm comm )
+IO::IO( const Settings& s, MPI_Comm comm )
{
- rank_saved = s->rank;
- m_outputfilename = s->outputfile + ".bp";
+ rank_saved = s.rank;
+ m_outputfilename = s.outputfile + ".bp";
adios_init_noxml( comm );
adios_declare_group( &group, "heat", "", adios_stat_default );
adios_select_method( group, "MPI", "", "" );
@@ -26,9 +26,9 @@ IO::IO( std::shared_ptr<Settings> s, MPI_Comm comm )
adios_define_var( group, "gndx", "", adios_integer, "", "", "");
adios_define_var( group, "gndy", "", adios_integer, "", "", "");
- std::string ldims( std::to_string( s->ndx ) + "," + std::to_string( s->ndy ));
- std::string gdims( std::to_string( s->gndx ) + "," + std::to_string( s->gndy ));
- std::string offs( std::to_string( s->offsx ) + "," + std::to_string( s->offsy ));
+ std::string ldims( std::to_string( s.ndx ) + "," + std::to_string( s.ndy ));
+ std::string gdims( std::to_string( s.gndx ) + "," + std::to_string( s.gndy ));
+ std::string offs( std::to_string( s.offsx ) + "," + std::to_string( s.offsy ));
uint64_t T_id;
T_id = adios_define_var( group, "T", "", adios_double,
ldims.c_str(), gdims.c_str(), offs.c_str() );
@@ -42,7 +42,7 @@ IO::~IO()
adios_finalize(rank_saved);
}
-void IO::write( int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Settings> s, MPI_Comm comm )
+void IO::write( int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm )
{
char mode[2] = "w";
if (step > 0)
@@ -56,17 +56,17 @@ void IO::write( int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Sett
int64_t f;
adios_open( &f, "heat", m_outputfilename.c_str(), mode, comm);
- adios_write( f, "gndx", &s->gndx);
- adios_write( f, "gndy", &s->gndy);
- adios_write( f, "T", ht->data_noghost().data() );
+ adios_write( f, "gndx", &s.gndx);
+ adios_write( f, "gndy", &s.gndy);
+ adios_write( f, "T", ht.data_noghost().data() );
adios_close( f );
MPI_Barrier( comm );
double total_time = MPI_Wtime() - time_start;
- uint64_t adios_totalsize = 2*sizeof(int) + 2*s->ndx*s->ndy*sizeof(double);
- uint64_t sizeMB = adios_totalsize * s->nproc/1024/1024/1024; // size in MB
+ uint64_t adios_totalsize = 2*sizeof(int) + 2*s.ndx*s.ndy*sizeof(double);
+ uint64_t sizeMB = adios_totalsize * s.nproc/1024/1024/1024; // size in MB
uint64_t mbs = sizeMB/total_time;
- if (s->rank==0)
+ if (s.rank==0)
std::cout << "Step " << step << ": " << m_outputfilename
<< " " << sizeMB << " " << total_time << "" << mbs << std::endl;
}
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index c6f3615b4..d2e5618aa 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/examples/heatTransfer/IO_adios2.cpp
@@ -8,16 +8,16 @@
#include "IO.h"
-IO::IO( std::shared_ptr<Settings> s, MPI_Comm comm )
+IO::IO( const Settings& s, MPI_Comm comm )
{
- m_outputfilename = s->outputfile + ".bp";
+ m_outputfilename = s.outputfile + ".bp";
}
IO::~IO()
{
}
-void IO::write(int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Settings> s, MPI_Comm comm )
+void IO::write(int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm )
{
}
diff --git a/examples/heatTransfer/IO_ascii.cpp b/examples/heatTransfer/IO_ascii.cpp
index 4ab36749b..01bd6d2ed 100644
--- a/examples/heatTransfer/IO_ascii.cpp
+++ b/examples/heatTransfer/IO_ascii.cpp
@@ -14,9 +14,9 @@
static std::ofstream of;
static std::streambuf *buf;
-IO::IO( std::shared_ptr<Settings> s, MPI_Comm comm )
+IO::IO( const Settings& s, MPI_Comm comm )
{
- m_outputfilename = s->outputfile;
+ m_outputfilename = s.outputfile;
if (m_outputfilename == "cout")
{
@@ -40,19 +40,19 @@ IO::~IO()
}
}
-void IO::write( int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Settings> s, MPI_Comm comm)
+void IO::write( int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm)
{
std::ostream out(buf);
if( step == 0)
{
- out << "rank=" << s->rank
- << " size=" << s->ndx << "x" << s->ndy
- << " offsets=" << s->offsx << ":" << s->offsy
+ out << "rank=" << s.rank
+ << " size=" << s.ndx << "x" << s.ndy
+ << " offsets=" << s.offsx << ":" << s.offsy
<< " step=" << step << std::endl;
- out << " time row columns " << s->offsy << "..." << s->offsy+s->ndy-1 << std::endl;
+ out << " time row columns " << s.offsy << "..." << s.offsy+s.ndy-1 << std::endl;
out << " ";
- for (int j = 1; j <= s->ndy; ++j) {
- out << std::setw(9) << s->offsy+j-1;
+ for (int j = 1; j <= s.ndy; ++j) {
+ out << std::setw(9) << s.offsy+j-1;
}
out << "\n--------------------------------------------------------------\n";
}
@@ -61,12 +61,12 @@ void IO::write( int step, std::shared_ptr<HeatTransfer> ht, std::shared_ptr<Sett
out << std::endl;
}
- for (int i = 1; i <= s->ndx; ++i)
+ for (int i = 1; i <= s.ndx; ++i)
{
- out << std::setw(5) << step << std::setw(5) << s->offsx+i-1;
- for (int j = 1; j <= s->ndy; ++j)
+ out << std::setw(5) << step << std::setw(5) << s.offsx+i-1;
+ for (int j = 1; j <= s.ndy; ++j)
{
- out << std::setw(9) << ht->T(i,j);
+ out << std::setw(9) << ht.T(i,j);
}
out << std::endl;
}
diff --git a/examples/heatTransfer/IO_hdf5_a.cpp b/examples/heatTransfer/IO_hdf5_a.cpp
new file mode 100644
index 000000000..387260628
--- /dev/null
+++ b/examples/heatTransfer/IO_hdf5_a.cpp
@@ -0,0 +1,59 @@
+/*
+ * IO_hdf5_a.cpp
+ *
+ * Write output with sequential HDF5, one file per process, one separate set per timestep
+ *
+ * Created on: Feb 2017
+ * Author: Norbert Podhorszki
+ */
+
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <string>
+
+#include "IO.h"
+#include "hdf5.h"
+
+
+IO::IO( const Settings& s, MPI_Comm comm )
+:m_outputfilename{s.outputfile}
+{
+}
+
+IO::~IO()
+{
+}
+
+void IO::write( int step, const HeatTransfer& ht, const Settings& s, MPI_Comm comm)
+{
+ std::string rs = std::to_string(s.rank);
+ std::string ts = std::to_string(step);
+ std::string fname = s.outputfile + "." + rs + "." + ts + ".h5";
+
+ // for time measurements, let's synchronize the processes
+ MPI_Barrier( comm );
+ double time_start = MPI_Wtime();
+
+ hsize_t dims[2] = {static_cast<hsize_t>(s.ndx), static_cast<hsize_t>(s.ndy)};
+
+ hid_t space = H5Screate_simple( 2, dims, NULL );
+ hid_t file = H5Fcreate( fname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
+ hid_t dset = H5Dcreate( file, "T", H5T_NATIVE_DOUBLE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
+
+ H5Dwrite( dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, ht.data_noghost().data());
+
+ H5Dclose( dset );
+ H5Sclose( space );
+ H5Fclose( file );
+
+ MPI_Barrier( comm );
+ double total_time = MPI_Wtime() - time_start;
+ uint64_t adios_totalsize = 2*sizeof(int) + 2*s.ndx*s.ndy*sizeof(double);
+ uint64_t sizeMB = adios_totalsize * s.nproc/1024/1024/1024; // size in MB
+ uint64_t mbs = sizeMB/total_time;
+ if (s.rank==0)
+ std::cout << "Step " << step << ": " << m_outputfilename
+ << " " << sizeMB << " " << total_time << "" << mbs << std::endl;
+}
+
diff --git a/examples/heatTransfer/Makefile b/examples/heatTransfer/Makefile
index 1d8b8c5ac..ca8361a41 100644
--- a/examples/heatTransfer/Makefile
+++ b/examples/heatTransfer/Makefile
@@ -19,6 +19,11 @@ ADIOS1_DIR=/opt/adios/1.11
#ADIOS2 LOCATION
ADIOS2_DIR=../..
+# SEQUENTIAL HDF5 LOCATION
+HDF5_DIR=/opt/hdf5-1.8.17
+HDF5_INCLUDE=-I$(HDF5_DIR)/include
+HDF5_LIB=$(HDF5_DIR)/lib/libhdf5.la
+
#
# SHOULD NOT NEED TO CHANGE ANYTHING BELOW
#
@@ -47,6 +52,9 @@ help: default
ascii: main.cpp HeatTransfer.cpp Settings.cpp IO_ascii.cpp
$(MPICC) $(CFLAGS) -o heatTransfer_ascii $^ $(LDFLAGS)
+hdf5_a: main.cpp HeatTransfer.cpp Settings.cpp IO_hdf5_a.cpp
+ libtool --mode=link --tag=CC $(MPICC) $(CFLAGS) $(HDF5_INCLUDE) -o heatTransfer_hdf5_a $^ $(HDF5_LIB) $(LDFLAGS)
+
adios1: main.cpp HeatTransfer.cpp Settings.cpp IO_adios1.cpp
$(MPICC) $(CFLAGS) $(ADIOS1_INCLUDE) -o heatTransfer_adios1 $^ $(ADIOS1_LIB) $(LDFLAGS)
@@ -54,5 +62,5 @@ adios2: main.cpp HeatTransfer.cpp Settings.cpp IO_adios2.cpp
$(MPICC) $(CFLAGS) $(ADIOS2_INCLUDE) -o heatTransfer_adios2 $^ $(ADIOS2_LIB) $(LDFLAGS)
clean:
- rm -f heatTransfer_ascii heatTransfer_adios1 heatTransfer_adios2
+ rm -f heatTransfer_ascii heatTransfer_hdf5_a heatTransfer_adios1 heatTransfer_adios2
diff --git a/examples/heatTransfer/main.cpp b/examples/heatTransfer/main.cpp
index c4978446b..f000dbd18 100644
--- a/examples/heatTransfer/main.cpp
+++ b/examples/heatTransfer/main.cpp
@@ -57,28 +57,28 @@ int main( int argc, char* argv [] )
try
{
double timeStart = MPI_Wtime();
- std::shared_ptr<Settings> settings( new Settings( argc, argv, rank, nproc ));
- std::shared_ptr<HeatTransfer> ht( new HeatTransfer( settings ));
- std::shared_ptr<IO> io( new IO( settings, mpiHeatTransferComm ));
-
- ht->init(true);
- ht->printT("Initialized T:", mpiHeatTransferComm);
- ht->heatEdges();
- //ht->exchange( mpiHeatTransferComm );
- ht->printT("Heated T:", mpiHeatTransferComm);
- io->write( 0, ht, settings, mpiHeatTransferComm );
-
- for( int t = 1; t <= settings->steps; ++t )
+ Settings settings( argc, argv, rank, nproc );
+ HeatTransfer ht( settings );
+ IO io( settings, mpiHeatTransferComm );
+
+ ht.init(true);
+ ht.printT("Initialized T:", mpiHeatTransferComm);
+ ht.heatEdges();
+ //ht.exchange( mpiHeatTransferComm );
+ ht.printT("Heated T:", mpiHeatTransferComm);
+ io.write( 0, ht, settings, mpiHeatTransferComm );
+
+ for( int t = 1; t <= settings.steps; ++t )
{
if( rank == 0 )
std::cout << "Step " << t << ":\n";
- for( int iter = 1; iter <= settings->iterations; ++iter )
+ for( int iter = 1; iter <= settings.iterations; ++iter )
{
- ht->iterate();
- ht->exchange( mpiHeatTransferComm );
- ht->heatEdges();
+ ht.iterate();
+ ht.exchange( mpiHeatTransferComm );
+ ht.heatEdges();
}
- io->write( t, ht, settings, mpiHeatTransferComm );
+ io.write( t, ht, settings, mpiHeatTransferComm );
}
MPI_Barrier( mpiHeatTransferComm );
@@ -107,57 +107,3 @@ int main( int argc, char* argv [] )
return 0;
}
-
-/*std::unique_ptr<Settings> ProcessArguments( int argc, char* argv [], int rank, int nproc )
-{
- auto s = std::unique_ptr<Settings>( new Settings );
-
- if (argc < 8)
- {
- throw std::invalid_argument( "Not enough arguments" );
- }
-
- s->outputfile = argv[1];
- s->npx = convertToInt("N", argv[2]);
- s->npy = convertToInt("M", argv[3]);
- s->ndx = convertToInt("nx", argv[4]);
- s->ndy = convertToInt("ny", argv[5]);
- s->steps = convertToInt("steps", argv[6]);
- s->iterations = convertToInt("iterations", argv[7]);
-
- if( s->npx * s->npy != nproc )
- {
- throw std::invalid_argument( "N*M must equal the number of processes" );
- }
-
- // calculate global array size and the local offsets in that global space
- s->gndx = s->npx * s->ndx;
- s->gndy = s->npy * s->ndy;
- s->posx = rank % s->npx;
- s->posy = rank / s->npx;
- s->offsx = s->posx * s->ndx;
- s->offsy = s->posy * s->ndy;
-
- // determine neighbors
- if( s->posx == 0 )
- s->rank_left = -1;
- else
- s->rank_left = rank-1;
-
- if( s->posx == s->npx-1 )
- s->rank_right = -1;
- else
- s->rank_right = rank+1;
-
- if( s->posy == 0 )
- s->rank_up = -1;
- else
- s->rank_up = rank - s->npx;
-
- if( s->posy == s->npy-1 )
- s->rank_down = -1;
- else
- s->rank_down = rank + s->npx;
-
- return s;
-}*/
--
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