Merge pull request #26 from nextsimhub/transpose-mask

Transpose input to match changing on indices in nextsimdg

.github/workflows/actions.yml

@@ -25,8 +25,8 @@ jobs:
           -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
           -DTrilinos_ENABLE_Zoltan:BOOL=ON \
           -DTrilinos_ENABLE_Fortran:BOOL=OFF \
-          -DZoltan_ENABLE_EXAMPLES:BOOL=ON \
-          -DZoltan_ENABLE_TESTS:BOOL=ON \
+          -DZoltan_ENABLE_EXAMPLES:BOOL=OFF \
+          -DZoltan_ENABLE_TESTS:BOOL=OFF \
           -DBUILD_SHARED_LIBS=ON \
           -Bbuild -S.
           sudo cmake --build build --config Release --target install
@@ -35,7 +35,7 @@ jobs:
           cd PnetCDF
           autoreconf -i
           CXX=mpicxx CC=mpicc ./configure --disable-fortran --enable-shared
-          make -j2
+          make
           sudo make install
           cd ..
           git clone -b v4.8.1 https://github.com/Unidata/netcdf-c.git
@@ -45,6 +45,8 @@ jobs:
           -DCMAKE_C_COMPILER=mpicc \
           -DCMAKE_CXX_COMPILER=mpicxx \
           -DCMAKE_BUILD_TYPE=Release \
+          -DENABLE_TESTS=OFF \
+          -DENABLE_PARALLEL_TESTS=OFF \
           -Bbuild -S.
           sudo cmake --build build --config Release --target install
           cd ..
@@ -69,7 +71,7 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake
-          brew extract --version=2.13.9 catch2 homebrew/cask
+          brew extract --version=2.13.9 catch2 homebrew/cask-versions
           brew install catch2@2.13.9
           brew install boost
           brew install hdf5-mpi
@@ -81,8 +83,8 @@ jobs:
           -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
           -DTrilinos_ENABLE_Zoltan:BOOL=ON \
           -DTrilinos_ENABLE_Fortran:BOOL=OFF \
-          -DZoltan_ENABLE_EXAMPLES:BOOL=ON \
-          -DZoltan_ENABLE_TESTS:BOOL=ON \
+          -DZoltan_ENABLE_EXAMPLES:BOOL=OFF \
+          -DZoltan_ENABLE_TESTS:BOOL=OFF \
           -DBUILD_SHARED_LIBS=ON \
           -Bbuild -S.
           sudo cmake --build build --config Release --target install
@@ -94,6 +96,8 @@ jobs:
           -DCMAKE_C_COMPILER=mpicc \
           -DCMAKE_CXX_COMPILER=mpicxx \
           -DCMAKE_BUILD_TYPE=Release \
+          -DENABLE_TESTS=OFF \
+          -DENABLE_PARALLEL_TESTS=OFF \
           -Bbuild -S.
           sudo cmake --build build --config Release --target install
           cd ..

Grid.cpp

@@ -71,17 +71,21 @@ Grid::Grid(MPI_Comm comm, const std::string& filename,
   if (ret != NC_NOERR)
     data_nc_id = nc_id;
   int dim0_nc_id, dim1_nc_id;
-  NC_CHECK(nc_inq_dimid(data_nc_id, dim0_name.c_str(), &dim0_nc_id));
-  NC_CHECK(nc_inq_dimid(data_nc_id, dim1_name.c_str(), &dim1_nc_id));
+  // I have switched the order of the dimensions here to reflect the change of
+  // indices in nextsim-dg
+  NC_CHECK(nc_inq_dimid(data_nc_id, dim1_name.c_str(), &dim0_nc_id));
+  NC_CHECK(nc_inq_dimid(data_nc_id, dim0_name.c_str(), &dim1_nc_id));
 
   CHECK_MPI(MPI_Comm_rank(comm, &_rank));
 
   // Retrieve the extent of each dimension of interest. The dimensions of
   // interest are the spatial dimensions of the grid. These are named "x" and
   // "y" by default.
+  // I have switched the order of the dimensions here to reflect the change of
+  // indices in nextsim-dg
   size_t tmp_0, tmp_1;
-  NC_CHECK(nc_inq_dimlen(data_nc_id, dim0_nc_id, &tmp_0));
-  NC_CHECK(nc_inq_dimlen(data_nc_id, dim1_nc_id, &tmp_1));
+  NC_CHECK(nc_inq_dimlen(data_nc_id, dim1_nc_id, &tmp_0));
+  NC_CHECK(nc_inq_dimlen(data_nc_id, dim0_nc_id, &tmp_1));
   _global_ext_0 = static_cast<int>(tmp_0);
   _global_ext_1 = static_cast<int>(tmp_1);
   _global_ext_blk_0 = ceil(static_cast<float>(_global_ext_0) / _blk_factor_0);
@@ -138,24 +142,40 @@ Grid::Grid(MPI_Comm comm, const std::string& filename,
     int dim_id[NDIMS];
     char dim_name[NDIMS][128];
     NC_CHECK(nc_inq_vardimid(data_nc_id, mask_nc_id, &dim_id[0]));
-    NC_CHECK(nc_inq_dimname(data_nc_id, dim_id[0], &dim_name[0][0]));
-    NC_CHECK(nc_inq_dimname(data_nc_id, dim_id[1], &dim_name[1][0]));
+    // I have switched the order of the dimensions here to reflect the change of
+    // indices in nextsim-dg
+    NC_CHECK(nc_inq_dimname(data_nc_id, dim_id[1], &dim_name[0][0]));
+    NC_CHECK(nc_inq_dimname(data_nc_id, dim_id[0], &dim_name[1][0]));
     if (dim_name[0] != dim0_name || dim_name[1] != dim1_name) {
       throw std::runtime_error("Dimension ordering provided does not match "
                                "ordering in netCDF grid file");
     }
 
     _land_mask.resize(_num_objects);
     size_t start[NDIMS], count[NDIMS];
+    // I have switched the order of the dimensions here to reflect the change of
+    // indices in nextsim-dg
     // Coordinate of first element
-    start[0] = _global_0;
-    start[1] = _global_1;
+    start[1] = _global_0;
+    start[0] = _global_1;
     // Number of elements in every extension
-    count[0] = _local_ext_0;
-    count[1] = _local_ext_1;
+    count[1] = _local_ext_0;
+    count[0] = _local_ext_1;
     NC_CHECK(nc_get_vara_int(data_nc_id, mask_nc_id, start, count,
                              _land_mask.data()));
 
+    // create copy of land mask ready to transpose
+    std::vector<int> _land_mask_copy(_land_mask);
+
+    // transpose _land_mask to reflect the change of indices in nextsim-dg
+    int index = 0;
+    for (size_t j = 0; j < count[1]; j++) {
+      for (size_t i = 0; i < count[0]; i++) {
+        _land_mask[index] = _land_mask_copy[i*count[1]+j];
+        index++;
+      }
+    }
+
     // Apply land mask
     if (_blk_factor_0 == 1 && _blk_factor_1 == 1) {
       for (int i = 0; i < _num_objects; i++) {

Grid.hpp

@@ -52,14 +52,20 @@ class LIB_EXPORT Grid
    * dim1) dimensions of the Grid class, where dim1 is defined as the fastest
    * increasing dimension. For example, if the dimensions of interest in the
    * netCDF file are named x and y and the variables are dimensioned as (y, x),
-   * then the y dimension will be mapped to dim0 and x to dim1 of the Grid
+   * then the y dimension will be mapped to dim1 and x to dim0 of the Grid
    * class, since the netCDF C/C++ convention is that the last dimension in the
    * CDL notation is the fastest increasing dimension. The default dimension
    * names for the netCDF file are "x" for dim0 and "y" for dim1, and the
    * default name for the land mask variable is "mask". the We assume that all
    * variables defined in the netCDF file follow the same convention in terms of
    * dimension ordering.
    *
+   * The code was originally written with the assumption that nextsim-dg would
+   * store arrays in (x,y) order. However, the indices have since been swapped
+   * and now nextsim-dg uses (y,x) order. To account for the switch of indices
+   * the grid input netcdf file is now transposed when it is read-in and the x
+   * and y dims are swapped in Grid.cpp.
+   *
    * @param comm MPI communicator.
    * @param filename Grid file in netCDF format.
    * @param dim0_name Name of 1st grid dimension in netCDF file (optional)