Updated heatTransfer write part: common handling filename argument; uses...

Updated heatTransfer write part: common handling filename argument; uses PutDeferred and skips PerformPuts

examples/heatTransfer/ReadMe.md

@@ -8,8 +8,8 @@ an application to the ADIOS2 library for its IO.
 1. write: illustrates the Write API as well as has implementations of other IO libraries
   
     * adios 1.x    
-    * hdf5
-    * phdf5
+    * hdf5 sequential, separate file per process per step
+    * phdf5 parallel, steps appended to the same one file
 
 2. read: illustrates the Read API that allows running the reader either as
 
@@ -38,7 +38,11 @@ Writer usage:  heatTransfer  config output  N  M   nx  ny   steps iterations
   steps:  the total number of steps to output
   iterations: one step consist of this many iterations
 
-$  mpirun -np 12 ./bin/heatTransfer_write_adios2 ../examples/heatTransfer/heat.xml  heat  4 3  5 10 10 10
+The ADIOS2 executable needs an XML config file to select the Engine used for the output. The engines are: BPFile, ADIOS1 and HDF5, the corresponding XML config files are in the examples/heatTransfer/ directory.
+
+The adios1, ph5 and hdf5 versions of the example do not use XML config files, so just type "none" for the config argument.
+
+$  mpirun -np 12 ./bin/heatTransfer_write_adios2 ../examples/heatTransfer/heat_bpfile.xml  heat  4 3  5 10 10 10
 
 
 2. Read the output step-by-step and print data into text files (data.<rank> per reader process)

examples/heatTransfer/write/CMakeLists.txt

@@ -14,15 +14,24 @@ if(ADIOS2_HAVE_MPI)
     adios2 MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
   )
 
-
+  add_executable(heatTransfer_write_ascii
+    main.cpp
+    HeatTransfer.cpp
+    Settings.cpp
+    IO_ascii.cpp
+  )
+  target_link_libraries(heatTransfer_write_ascii
+    MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
+  )
+  
   if(ADIOS2_HAVE_ADIOS1)
-    add_executable(heatTransfer_write_adios1
+    add_executable(heatTransfer_write_adios1.x
       main.cpp
       HeatTransfer.cpp
       Settings.cpp
-      IO_adios1.cpp
+      IO_adios1.x.cpp
     )
-    target_link_libraries(heatTransfer_write_adios1
+    target_link_libraries(heatTransfer_write_adios1.x
       adios1::adios MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
     )
   endif()

examples/heatTransfer/write/IO.h

@@ -26,6 +26,50 @@ public:
 
 private:
     std::string m_outputfilename;
+
+    // Generate a file name from the outputfile string and the arguments
+    // default is add suffix if not already there
+    // if rank and step is specified, it will create a unique file name for that
+    // rank and step
+    std::string MakeFilename(const std::string &outputfile,
+                             const std::string &suffix, int rank = -1,
+                             int step = -1)
+    {
+        std::string name;
+        int ss = outputfile.size();
+        if (rank == -1 && step == -1)
+        {
+            // add suffix if not present already
+            name = outputfile;
+            if ((ss > suffix.size()) &&
+                outputfile.find(suffix) != ss - suffix.size())
+            {
+                name += suffix;
+            }
+        }
+        else
+        {
+            // we need a unique name here
+            name = outputfile;
+            if ((ss > suffix.size()) &&
+                outputfile.find(suffix) == ss - suffix.size())
+            {
+                name = outputfile.substr(0, ss - suffix.size());
+            }
+            if (rank >= 0)
+            {
+                std::string rs = std::to_string(rank);
+                name += "." + rs;
+            }
+            if (step >= 0)
+            {
+                std::string ts = std::to_string(step);
+                name += "." + ts;
+            }
+            name += suffix;
+        }
+        return name;
+    }
 };
 
 #endif /* IO_H_ */

examples/heatTransfer/write/IO_adios1.cpp → examples/heatTransfer/write/IO_adios1.x.cpp

@@ -27,7 +27,8 @@ static int rank_saved;
 IO::IO(const Settings &s, MPI_Comm comm)
 {
     rank_saved = s.rank;
-    m_outputfilename = s.outputfile + ".bp";
+    m_outputfilename = MakeFilename(s.outputfile, ".bp");
+
     adios_init_noxml(comm);
     adios_declare_group(&group, "heat", "", adios_stat_default);
     adios_select_method(group, "POSIX", "", "");

examples/heatTransfer/write/IO_adios2.cpp

@@ -21,25 +21,18 @@ adios2::Variable<unsigned int> *varGndx = nullptr;
 
 IO::IO(const Settings &s, MPI_Comm comm)
 {
-    m_outputfilename = s.outputfile + ".bp";
-    ad = new adios2::ADIOS(s.configfile, comm, adios2::DebugON);
+    m_outputfilename = MakeFilename(s.outputfile, ".bp");
 
-    // Define method for engine creation
+    ad = new adios2::ADIOS(s.configfile, comm, adios2::DebugON);
 
     adios2::IO &bpio = ad->DeclareIO("writer");
     if (!bpio.InConfigFile())
     {
         // if not defined by user, we can change the default settings
         // BPFileWriter is the default engine
-
-        // Allow an extra thread for data processing
         // ISO-POSIX file is the default transport
-        // Passing parameters to the transport
     }
 
-    varGndx = &bpio.DefineVariable<unsigned int>("gndx");
-    bpio.DefineVariable<unsigned int>("gndy");
-
     // define T as 2D global array
     varT = &bpio.DefineVariable<double>(
         "T",
@@ -50,11 +43,6 @@ IO::IO(const Settings &s, MPI_Comm comm)
         // local size, could be defined later using SetSelection()
         {s.ndx, s.ndy});
 
-    // add transform to variable
-    // adios2::Transform tr = adios2::transform::BZIP2( );
-    // varT.AddTransform( tr, "" );
-    // varT.AddTransform( tr,"accuracy=0.001" );  // for ZFP
-
     bpWriter = &bpio.Open(m_outputfilename, adios2::Mode::Write, comm);
 }
 
@@ -68,26 +56,11 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
                MPI_Comm comm)
 {
     bpWriter->BeginStep();
-    /* 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()
-    varT->SetSelection(
-        adios2::Box<adios2::Dims>({s.offsx, s.offsy}, {s.ndx, s.ndy}));
-
-    if (!step)
-    {
-        int rank;
-        MPI_Comm_rank(comm, &rank);
-        if (!rank)
-        {
-            bpWriter->PutSync<unsigned int>(*varGndx, s.gndx);
-            bpWriter->PutSync<unsigned int>("gndy", s.gndy);
-        }
-    }
-    bpWriter->PutSync<double>(*varT, ht.data_noghost().data());
-    // bpWriter->PerformPuts();
+    // using PutDeferred() you promise the pointer to the data will be intact
+    // until the end of the output step.
+    // We need to have the vector object here not to destruct here until the end
+    // of function.
+    std::vector<double> v = ht.data_noghost();
+    bpWriter->PutDeferred<double>(*varT, v.data());
     bpWriter->EndStep();
 }

examples/heatTransfer/write/IO_ascii.cpp

@@ -27,10 +27,8 @@ IO::IO(const Settings &s, MPI_Comm comm)
     }
     else
     {
-        int rank;
-        MPI_Comm_rank(comm, &rank);
-        std::string rs = std::to_string(rank);
-        of.open(m_outputfilename + rs + ".txt");
+        m_outputfilename = MakeFilename(s.outputfile, ".txt", s.rank);
+        of.open(m_outputfilename);
         buf = of.rdbuf();
     }
 }
@@ -67,12 +65,13 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
         out << std::endl;
     }
 
+    out << std::fixed;
     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(9) << ht.T(i, j);
+            out << std::setw(9) << std::setprecision(5) << ht.T(i, j);
         }
         out << std::endl;
     }

examples/heatTransfer/write/IO_h5mixer.cpp

@@ -33,15 +33,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
 {
     rank_saved = s.rank;
 
-    m_outputfilename = s.outputfile;
-    std::string suffix = ".h5";
-
-    int ss = s.outputfile.size();
-    if ((ss > suffix.size()) && s.outputfile.find(suffix) != ss - suffix.size())
-    {
-        // Your code here
-        m_outputfilename += suffix;
-    }
+    m_outputfilename = MakeFilename(s.outputfile, ".h5");
 
     /*ad = new adios2::ADIOS(std::string(DEFAULT_CONFIG_STR), comm,
                            adios2::DebugON);

examples/heatTransfer/write/IO_hdf5_a.cpp

@@ -27,9 +27,7 @@ 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";
+    m_outputfilename = MakeFilename(s.outputfile, ".h5", s.rank, step);
 
     // for time measurements, let's synchronize the processes
     MPI_Barrier(comm);
@@ -39,8 +37,8 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
                        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 file = H5Fcreate(m_outputfilename.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);
 

examples/heatTransfer/write/IO_ph5.cpp

@@ -276,18 +276,7 @@ std::shared_ptr<HDF5NativeWriter> h5writer;
 
 IO::IO(const Settings &s, MPI_Comm comm)
 {
-    std::string suffix = ".h5";
-    m_outputfilename = s.outputfile + suffix;
-
-    int ss = s.outputfile.size();
-    int pos = s.outputfile.find(suffix);
-    if ((ss > suffix.size()) && (pos == ss - suffix.size()))
-    {
-        // Your code here
-        m_outputfilename = s.outputfile;
-    }
-
-    //    m_outputfilename = s.outputfile + ".h5";
+    m_outputfilename = MakeFilename(s.outputfile, ".h5");
 
     if (s.outputfile[0] == '0')
     {

examples/heatTransfer/write/IO_ph5_adios2.cpp

@@ -21,16 +21,7 @@ adios2::Variable<unsigned int> *varGndx = nullptr;
 
 IO::IO(const Settings &s, MPI_Comm comm)
 {
-    std::string suffix = ".h5";
-    m_outputfilename = s.outputfile + suffix;
-
-    int ss = s.outputfile.size();
-    int pos = s.outputfile.find(suffix);
-    if ((ss > suffix.size()) && (pos == ss - suffix.size()))
-    {
-        // Your code here
-        m_outputfilename = s.outputfile;
-    }
+    m_outputfilename = MakeFilename(s.outputfile, ".h5");
 
     ad = new adios2::ADIOS(comm, adios2::DebugOFF);