ex.08.io-hdf5/main.cpp

Example demonstrating the use of dash::io::hdf5 to read and write HDF5 files.

#include <libdash.h>
#include <iostream>

#ifdef DASH_ENABLE_HDF5

// For more information on HDF5 files see
// https://www.hdfgroup.org/HDF5

#define FILENAME "example.hdf5"

using std::cout;
using std::cerr;
using std::endl;

using dash::io::hdf5::StoreHDF;
using dash::io::hdf5::hdf5_options;

typedef dash::Pattern<1, dash::ROW_MAJOR, long> pattern_t;
typedef dash::Array<int, long, pattern_t>       array_t;

void print_file(){
  // Print h5dump output
  int status;
  if(dash::myid() == 0){
    std::string syscall = "h5dump ";
    status = system((syscall + FILENAME).c_str());
  }
}

void print_separator(){
  if(dash::myid() == 0){
    cout << "=======================================================" << endl;
  }
}

int main(int argc, char * argv[])
{
  dash::init(&argc, &argv);

  long      extent = 100;
  int       myid   = dash::myid();

  pattern_t pattern_a(extent, dash::TILE(10));
  pattern_t pattern_b(extent, dash::TILE(7));
  array_t   array_a(pattern_a);
  array_t   array_b(pattern_b);

  // Fill Array
  dash::fill(array_a.begin(), array_a.end(), myid);
  dash::fill(array_b.begin(), array_a.end(), myid * 10);


  if(myid == 0){
    cout << "DASH HDF5 API example. After each change in the hdf5 file "
         << "the contents are printed using h5dump" << endl;
  }
  // Write Array to HDF5 file using defaults
  {
    if(myid == 0) {
      print_separator();
      cout << "Write Array A to " << FILENAME << " / group/data" << endl;
    }
    StoreHDF::write(array_a, FILENAME, "group/data");
    dash::barrier();
    print_file();
  }
  // Restore values from HDF5 dataset. Pattern gets reconstructed from
  // hdf5 metadata
  {
    if(myid == 0){
      print_separator();
      cout << "Read " << FILENAME << " / group/data into Array C, "
           << "reconstruct pattern" << endl;
    }
    // Use delayed allocation
    array_t array_c;
    StoreHDF::read(array_c, FILENAME, "group/data");
  }

  // OK, that was easy. Now let's have a slightly more complex setup
  // Convert between two patterns
  //
  {
    if(myid == 0){
      print_separator();
      cout << "Read " << FILENAME
           << " / group/data into already allocated Array C" << endl;
    }
    // pass allocated array to define custom pattern
    array_t array_c(pattern_b); // tilesize=7
    StoreHDF::read(array_c, FILENAME, "group/data");
    if(myid == 0){
      cout << "Array A Pattern: Tilesize: "
           << array_a.pattern().blocksize(0) << endl;
      cout << "Array C Pattern: Tilesize: "
           << array_c.pattern().blocksize(0) << endl;
    }
  }

  // Store multiple datasets in single file
  {
    // use options object to add a dataset instead
    // of overwriting the hdf5 file
    if(myid == 0){
      print_separator();
      cout << "Add dataset temperature to " << FILENAME << endl;
    }
    hdf5_options fopts;
    fopts.overwrite_file = false; // Do not overwrite existing file

    StoreHDF::write(array_b, FILENAME, "temperature", fopts);
    dash::barrier();
    print_file();
  }

  // Update dataset. IMPORTANT: the dataset extents must not change!
  {
    if(myid == 0){
      print_separator();
      cout << "Modify " << FILENAME << " / temperature dataset" << endl;
    }
    hdf5_options fopts;
    fopts.overwrite_file = false;
    fopts.modify_dataset = true;

    StoreHDF::write(array_a, FILENAME, "temperature", fopts);
    dash::barrier();
    print_file();
  }

  sleep(1);
  // Clean up
  if(myid == 0){
    remove(FILENAME);
  }

  dash::finalize();

  return EXIT_SUCCESS;
}

#else

int main(int argc, char * argv[])
{
  std::cout << "To run this example build DASH with HDF5 support" << std::endl;
  return EXIT_SUCCESS;
}

#endif // DASH_ENABLE_HDF5