Commit 3deda2d9 authored by Mulas, Giacomo's avatar Mulas, Giacomo
Browse files

Merge branch 'master' into containers-m10

parents 479992e8 3b4268e9

.gitlab-ci.yml

+5 −5
Original line number Diff line number Diff line
@@ -264,10 +264,10 @@ running_stage: 
      - mv c_TEDF c_TEDF_dev

      - mv c_TEDF.hd5 c_TEDF_dev.hd5

      - echo "Testing parallel execution of SPHERE"

      - ../../src/scripts/model_maker.py ../../test_data/sphere/config_181_xi.yml

      - ../../src/scripts/model_maker.py ../../test_data/sphere/config_two_layers.yml

      - echo "Running parallel np_sphere"

      - OMP_NUM_THREADS=2 ./np_sphere DEDFB_181_xi DSPH_181_xi .

      - mv c_OSPH c_OSPH_181_xi

      - OMP_NUM_THREADS=2 ./np_sphere DEDFB_two_layers DSPH_two_layers .

      - mv c_OSPH c_OSPH_two_layers

      - cd ../cluster

      - echo "Testing configurator for CLUSTER"

      - ../../src/scripts/model_maker.py ../../test_data/cluster/config_dev.yml
@@ -313,8 +313,8 @@ testing_stage: 
      - export FFILE=../../test_data/sphere/OSPH

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH_dev --html

      - echo "Comparing output of parallel SPHERE"

      - export FFILE=../../test_data/sphere/OSPH_181_xi

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH_181_xi --html

      - export FFILE=../../test_data/sphere/OSPH_two_layers

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH_two_layers --html

      - echo "Checking consistency among legacy and HDF5 configuration files"

      - ../testing/test_TEDF ../../test_data/sphere/DEDFB c_TEDF_dev c_TEDF_dev.hd5

      - cd ../inclusion

src/include/Configuration.h

+4 −0
Original line number Diff line number Diff line
@@ -312,6 +312,8 @@ protected: 
  double _wp;

  //! \brief Peak XI. QUESTION: correct?

  double _xip;

  //! \brief Maximum number of layers for the particle components.

  int _max_layers;

  //! \brief Flag to control whether to add an external layer.

  bool _use_external_sphere;
@@ -377,6 +379,8 @@ public: 
  const double& wp = _wp;

  //! \brief Read only view on peak XI.

  const double& xip = _xip;

  //! \brief Read only view on the maximum number of layers for the particle components.

  const int& max_layers = _max_layers;

  //! \brief Read only view on flag to control whether to add an external layer.

  const bool& use_external_sphere = _use_external_sphere;

src/libnptm/Configuration.cpp

+68 −57
Original line number Diff line number Diff line
@@ -356,10 +356,17 @@ ScattererConfiguration::ScattererConfiguration( 
  _iog_vec = iog_vector;

  _radii_of_spheres = ros_vector;

  _nshl_vec = nshl_vector;

  _use_external_sphere = is_external;

  _max_layers = 0;

  for (int li = 0; li < _configurations; li++) {

    if (_max_layers < _nshl_vec[li]) {

      _max_layers = _nshl_vec[li];

      if (li == 0 && _use_external_sphere) _max_layers += 1;

    }

  }

  _rcf = rcf_vector;

  _idfc = dielectric_func_type;

  _dc0_matrix = dc_matrix;

  _use_external_sphere = is_external;

  _exdc = ex;

  _wp = w;

  _xip = x;
@@ -391,12 +398,13 @@ ScattererConfiguration::ScattererConfiguration(const ScattererConfiguration& rhs 
  _exdc = rhs._exdc;

  _wp = rhs._wp;

  _xip = rhs._xip;

  _max_layers = rhs._max_layers;

  _iog_vec = new int[_number_of_spheres]();

  _radii_of_spheres = new double[_number_of_spheres]();

  _nshl_vec = new int[_configurations]();

  _rcf = new double*[_configurations];

  _scale_vec = new double[_number_of_scales]();

  _dc0_matrix = new dcomplex**[_configurations];

  _dc0_matrix = new dcomplex**[_max_layers];

  for (int si = 0; si < _number_of_scales; si++) _scale_vec[si] = rhs._scale_vec[si];

  for (int si = 0; si < _number_of_spheres; si++) {

    _iog_vec[si] = rhs._iog_vec[si];
@@ -406,11 +414,13 @@ ScattererConfiguration::ScattererConfiguration(const ScattererConfiguration& rhs 
    _radii_of_spheres[si] = rhs._radii_of_spheres[si];

    _nshl_vec[si] = rhs._nshl_vec[si];

    _rcf[si] = new double[_nshl_vec[si]]();

    _dc0_matrix[si] = new dcomplex*[_number_of_spheres];

    for (int sj = 0; sj < _nshl_vec[si]; sj++) _rcf[si][sj] = rhs._rcf[si][sj];

    for (int sj = 0; sj < _number_of_spheres; sj++) {

      _dc0_matrix[si][sj] = new dcomplex[dim3]();

      for (int sk = 0; sk < dim3; sk++) _dc0_matrix[si][sj][sk] = rhs._dc0_matrix[si][sj][sk];

  }

  for (int li = 0; li < _max_layers; li++) {

    _dc0_matrix[li] = new dcomplex*[_number_of_spheres];

    for (int lj = 0; lj < _number_of_spheres; lj++) {

      _dc0_matrix[li][lj] = new dcomplex[dim3]();

      for (int lk = 0; lk < dim3; lk++) _dc0_matrix[li][lj][lk] = rhs._dc0_matrix[li][lj][lk];

    }

  }

}
@@ -431,6 +441,7 @@ ScattererConfiguration::ScattererConfiguration(const mixMPI *mpidata) 
  itemp = sizeof(bool);

  char *ptemp = (char *) &_use_external_sphere;

  MPI_Bcast(ptemp, itemp, MPI_CHAR, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_max_layers, 1, MPI_INT, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_exdc, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_wp, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_xip, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
@@ -442,16 +453,18 @@ ScattererConfiguration::ScattererConfiguration(const mixMPI *mpidata) 
  MPI_Bcast(_nshl_vec, _configurations, MPI_INT, 0, MPI_COMM_WORLD);

  _rcf = new double*[_configurations];

  _scale_vec = new double[_number_of_scales]();

  _dc0_matrix = new dcomplex**[_configurations];

  _dc0_matrix = new dcomplex**[_max_layers];

  MPI_Bcast(_scale_vec, _number_of_scales, MPI_DOUBLE, 0, MPI_COMM_WORLD);

  int dim3 = (_idfc == 0) ? _number_of_scales : 1;

  for (int si = 0; si < _configurations; si++) {

    _rcf[si] = new double[_nshl_vec[si]]();

    MPI_Bcast(_rcf[si], _nshl_vec[si], MPI_DOUBLE, 0, MPI_COMM_WORLD);

    _dc0_matrix[si] = new dcomplex*[_number_of_spheres];

    for (int sj = 0; sj < _number_of_spheres; sj++) {

      _dc0_matrix[si][sj] = new dcomplex[dim3]();

      MPI_Bcast(_dc0_matrix[si][sj], dim3, MPI_C_DOUBLE_COMPLEX, 0, MPI_COMM_WORLD);

  }

  for (int li = 0; li < _max_layers; li++) {

    _dc0_matrix[li] = new dcomplex*[_number_of_spheres];

    for (int lj = 0; lj < _number_of_spheres; lj++) {

      _dc0_matrix[li][lj] = new dcomplex[dim3]();

      MPI_Bcast(_dc0_matrix[li][lj], dim3, MPI_C_DOUBLE_COMPLEX, 0, MPI_COMM_WORLD);

    }

  }

}
@@ -469,6 +482,7 @@ void ScattererConfiguration::mpibcast(const mixMPI *mpidata) { 
  itemp = sizeof(bool);

  char *ptemp = (char *) &_use_external_sphere;

  MPI_Bcast(ptemp, itemp, MPI_CHAR, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_max_layers, 1, MPI_INT, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_exdc, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_wp, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);

  MPI_Bcast(&_xip, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
@@ -479,15 +493,17 @@ void ScattererConfiguration::mpibcast(const mixMPI *mpidata) { 
  int dim3 = (_idfc == 0) ? _number_of_scales : 1;

  for (int si = 0; si < _configurations; si++) {

    MPI_Bcast(_rcf[si], _nshl_vec[si], MPI_DOUBLE, 0, MPI_COMM_WORLD);

    for (int sj = 0; sj < _number_of_spheres; sj++) {

      MPI_Bcast(_dc0_matrix[si][sj], dim3, MPI_C_DOUBLE_COMPLEX, 0, MPI_COMM_WORLD);

  }

  for (int li = 0; li < _max_layers; li++) {

    for (int lj = 0; lj < _number_of_spheres; lj++) {

      MPI_Bcast(_dc0_matrix[li][lj], dim3, MPI_C_DOUBLE_COMPLEX, 0, MPI_COMM_WORLD);

    }

  }

}

#endif



ScattererConfiguration::~ScattererConfiguration() {

  for (int i = 0; i < _configurations; i++) {

  for (int i = 0; i < _max_layers; i++) {

    for (int j = 0; j < _number_of_spheres; j++) {

      delete[] _dc0_matrix[i][j];

    }
@@ -697,6 +713,7 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(const std::string& de 
  double *ros_vector = new double[configurations]();

  int *nshl_vector = new int[configurations]();

  double **rcf_vector = new double*[configurations];

  int max_layers = 0;

  last_configuration = 0;

  for (int i113 = 1; i113 <= fnsph; i113++) {

    if (iog_vector[i113 - 1] < i113) continue;
@@ -705,6 +722,9 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(const std::string& de 
    re = regex("[0-9]+");

    regex_search(str_target, m, re);

    nshl_vector[last_configuration - 1] = stoi(m.str());

    if (max_layers < nshl_vector[last_configuration - 1])

      max_layers = nshl_vector[last_configuration - 1];

    if (last_configuration == 1 && fies == 1) max_layers += 1;

    str_target = m.suffix().str();

    re = regex("-?[0-9]+\\.[0-9]+([eEdD][-+]?[0-9]+)?");

    regex_search(str_target, m, re);
@@ -725,10 +745,10 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(const std::string& de 
    } // ns112 loop

  } // i113 loop



  dcomplex ***dc0m = new dcomplex**[configurations];

  dcomplex *dc0 = new dcomplex[configurations]();

  dcomplex ***dc0m = new dcomplex**[max_layers];

  dcomplex *dc0 = new dcomplex[max_layers]();

  int dim3 = (fidfc == 0) ? fnxi : 1;

  for (int di = 0; di < configurations; di++) {

  for (int di = 0; di < max_layers; di++) {

    dc0m[di] = new dcomplex*[fnsph];

    for (int dj = 0; dj < fnsph; dj++) dc0m[di][dj] = new dcomplex[dim3]();

  } // di loop
@@ -763,21 +783,9 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(const std::string& de 
  delete[] dc0;



  ScattererConfiguration *config = new ScattererConfiguration(

							      fnsph,

							      configurations,

							      variable_vector,

							      fnxi,

							      variable_name,

							      iog_vector,

							      ros_vector,

							      nshl_vector,

							      rcf_vector,

							      fidfc,

							      dc0m,

							      (fies > 0),

							      fexdc,

							      fwp,

							      fxip

    fnsph, configurations, variable_vector, fnxi, variable_name,

    iog_vector, ros_vector, nshl_vector, rcf_vector, fidfc,

    dc0m, (fies > 0), fexdc, fwp, fxip

  );

  delete[] file_lines;

  delete[] variable_vector;
@@ -820,12 +828,17 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(const std::string& fil 
    ros_vector = new double[configuration_count]();

    rcf_vector = new double*[configuration_count];

    last_configuration = 0;

    int max_layers = 0;

    for (int i115 = 1; i115 <= configuration_count; i115++) {

      if (iog[i115 - 1] < i115) continue;

      else last_configuration++;

      str_name = "NSHL_" + to_string(last_configuration);

      str_type = "INT32_(1)";

      status = hdf_file->read(str_name, str_type, (nshl_vector + last_configuration - 1));

      if (max_layers < nshl_vector[last_configuration - 1]) {

	max_layers = nshl_vector[last_configuration - 1];

	if (last_configuration == 1 && ies == 1) max_layers += 1;

      }

      str_name = "ROS_" + to_string(last_configuration);

      str_type = "FLOAT64_(1)";

      status = hdf_file->read(str_name, str_type, (ros_vector + last_configuration - 1));
@@ -841,14 +854,14 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(const std::string& fil 
    status = hdf_file->read(str_name, str_type, xi_vec);

      

    int dim3 = (_idfc == 0) ? nxi : 1;

    int element_size = 2 * dim3 * nsph * configuration_count;

    int element_size = 2 * dim3 * nsph * max_layers;

    double *elements = new double[element_size]();

    str_name = "DC0M";

    str_type = "FLOAT64_(" + to_string(element_size) + ")";

    status = hdf_file->read(str_name, str_type, elements);

    dc0m = new dcomplex**[configuration_count];

    dc0m = new dcomplex**[max_layers];

    int dc_index = 0;

    for (int di = 0; di < configuration_count; di++) {

    for (int di = 0; di < max_layers; di++) {

      dc0m[di] = new dcomplex*[nsph];

      for (int dj = 0; dj < nsph; dj++) {

	dc0m[di][dj] = new dcomplex[dim3]();
@@ -864,21 +877,9 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(const std::string& fil 
    status = hdf_file->close();

    delete hdf_file;

    conf = new ScattererConfiguration(

				      nsph,

				      configuration_count,

				      xi_vec,

				      nxi,

				      "XIV",

				      iog,

				      ros_vector,

				      nshl_vector,

				      rcf_vector,

				      _idfc,

				      dc0m,

				      (ies == 1),

				      _exdc,

				      _wp,

				      _xip

      nsph, configuration_count, xi_vec, nxi, "XIV",

      iog, ros_vector, nshl_vector, rcf_vector, _idfc,

      dc0m, (ies == 1), _exdc, _wp, _xip

    );

    delete[] xi_vec;

  }
@@ -932,9 +933,14 @@ ScattererConfiguration* ScattererConfiguration::from_legacy(const std::string& f 
    for (int nsi = 0; nsi < nsh; nsi++)

      input.read(reinterpret_cast<char *>(&(_rcf_vec[last_configuration - 1][nsi])), sizeof(double));

  }

  _dc0m = new dcomplex**[configurations];

  int max_layers = 0;

  for (int li = 0; li < configurations; li++) {

    if (max_layers < _nshl_vec[li]) max_layers = _nshl_vec[li];

    if (li == 0 && _ies == 1) max_layers += 1;

  }

  _dc0m = new dcomplex**[max_layers];

  int dim3 = (_idfc == 0) ? _nxi : 1;

  for (int di = 0; di < configurations; di++) {

  for (int di = 0; di < max_layers; di++) {

    _dc0m[di] = new dcomplex*[_nsph];

    for (int dj = 0; dj < _nsph; dj++) _dc0m[di][dj] = new dcomplex[dim3]();

  } // di loop
@@ -995,7 +1001,7 @@ void ScattererConfiguration::print() { 
  for (int i = 0; i < _number_of_scales; i++) printf("\t%lg", _scale_vec[i]);

  printf("\t]\n");

  printf("DC0M  = [\n");

  for (int i = 0; i < _configurations; i++) {

  for (int i = 0; i < _max_layers; i++) {

    printf("         [\n");

    for (int j = 0; j < _number_of_spheres; j++) {

      printf("          [");
@@ -1079,7 +1085,7 @@ void ScattererConfiguration::write_hdf5(const std::string& file_name) { 
  }



  int dim3 = (idfc == 0) ? _number_of_scales : 1;

  int dc0m_size = 2 * dim3 * _number_of_spheres * _configurations;

  int dc0m_size = 2 * dim3 * _number_of_spheres * _max_layers;

  double *dc0m = new double[dc0m_size]();

  int dc0_index = 0;

  for (int jxi468 = 1; jxi468 <= _number_of_scales; jxi468++) {
@@ -1376,6 +1382,9 @@ bool ScattererConfiguration::operator ==(const ScattererConfiguration &other) { 
  if (_idfc != other._idfc) {

    return false;

  }

  if (_max_layers != other._max_layers) {

    return false;

  }

  if (_exdc != other._exdc) {

    return false;

  }
@@ -1411,13 +1420,15 @@ bool ScattererConfiguration::operator ==(const ScattererConfiguration &other) { 
	return false;

      }

    } // rj loop

  } // ri loop

  for (int li = 0; li < _max_layers; li++) {

    for (int dj = 0; dj < _number_of_spheres; dj++) {

      for (int dk = 0; dk < dim3; dk++) {

	if (_dc0_matrix[ri][dj][dk] != other._dc0_matrix[ri][dj][dk]) {

	if (_dc0_matrix[li][dj][dk] != other._dc0_matrix[li][dj][dk]) {

	  return false;

	}

      } // dk loop

    } // dj loop

  } // ri loop

  }

  return true;

}

src/scripts/README.md

+1 −1
Original line number Diff line number Diff line
@@ -11,7 +11,7 @@ The code migration stage can be considered successfully fulfilled with the solut 
1. Follow the instructions to build and run the *FORTRAN* and *C++* versions of the code.

2. Run the `pycompare.py` script providing the following minimal arguments:



   > $PATH_TO_SCRIPT/pycompare.py --ffile=FORTRAN_OUTPUT --cfile=C++_OUTPUT

   > $PATH_TO_SCRIPT/pycompare.py --ffile FORTRAN_OUTPUT --cfile C++_OUTPUT



(The above assumes that `PATH_TO_SCRIPT` is a variable that expands to the path were the script is located). The required output files are called by default `OSPH` and `OCLU` by *FORTRAN* and `c_OSPH` and `c_OCLU` by *C++*, depending on whether the sphere or the cluster case was executed.