Merge branch 'release/0.26.0'

AUTHORS

@@ -13,19 +13,23 @@ Thanks for contributions from
 - Andreas Mueller
 - Baudouin Raoult
 - Florian Rathgeber
+- Marek Wlasak
+- Oliver Lomax
+- Daniel Holdaway
 - Daan Degrauwe
-- Gianmarco Mengaldo
 - Philippe Marguinaud
+- Gianmarco Mengaldo
 - James Hawkes
 - Mats Hamrud
-- Christian Kuehnlein
+- Benjamin Menetrier
 - Rahul Mahajan
 - Olivier Iffrig
+- Christian Kuehnlein
 - Iain Russell
-- Benjamin Menetrier
 - Domokos Sármány
-- Yannick Trémolet
+- Steven Vahl
 - Mark J. Olah
 - Michael Lange
-- Marek Wlasak
 - Peter Bispham
+- Slavko Brdar
+- Yannick Trémolet

CHANGELOG.md

@@ -7,6 +7,16 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.26.0] - 2021-08-23
+### Added
+- Support for Cubed sphere grids and preliminary support for cubes sphere mesh generation.
+
+### Fixed
+- Compilation with ALTAS_BITS_LOCAL=64
+- Too aggressive optimisation with GNU 11
+- Compatibility with CMake 3.20 and NVHPC compilers
+
+
 ## [0.25.0] - 2021-05-18
 ### Added
 - New concept Redistribution to redistribute field on same grid but with different partitioner
@@ -295,6 +305,7 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 ## 0.13.0 - 2018-02-16
 
 [Unreleased]: https://github.com/ecmwf/atlas/compare/master...develop
+[0.26.0]: https://github.com/ecmwf/atlas/compare/0.26.0...0.25.0
 [0.25.0]: https://github.com/ecmwf/atlas/compare/0.24.1...0.25.0
 [0.24.1]: https://github.com/ecmwf/atlas/compare/0.24.0...0.24.1
 [0.24.0]: https://github.com/ecmwf/atlas/compare/0.23.0...0.24.0

CMakeLists.txt

@@ -24,7 +24,12 @@ set( ATLAS_BITS_LOCAL  32 CACHE STRING "bits used to define a local index (atlas
 ################################################################################
 # Required packages
 
-ecbuild_find_package( NAME eckit VERSION 1.16 REQUIRED )
+if( ATLAS_BITS_LOCAL MATCHES 64 )
+  ecbuild_find_package( NAME eckit VERSION 1.17.1 REQUIRED )
+else()
+  ecbuild_find_package( NAME eckit VERSION 1.16 REQUIRED )
+endif()
+
 ecbuild_debug( "   eckit_FEATURES : [${eckit_FEATURES}]" )
 
 ################################################################################

VERSION

@@ -1 +1 @@
-0.25.0
+0.26.0

bamboo/CLANG-flags.cmake

@@ -1,3 +1,4 @@
 set( ENABLE_TRANS               ON  CACHE BOOL "Enable TRANS" )
 set( ENABLE_BOUNDSCHECKING      ON  CACHE BOOL "Enable bounds checking")
 set( ENABLE_TESSELATION         OFF CACHE BOOL "Disable CGAL" ) # cgal is old in leap42
+set( ENABLE_OMP_CXX             OFF CACHE BOOL "Disable OpenMP for C++" ) # because of problems with clang OpenMP

cmake/features/ACC.cmake

@@ -2,7 +2,7 @@
 
 set( ATLAS_ACC_CAPABLE FALSE )
 if( HAVE_CUDA )
-  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI" )
+  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI|NVHPC" )
     set( ATLAS_ACC_CAPABLE TRUE )
   endif()
 endif()
@@ -12,10 +12,10 @@ ecbuild_add_option( FEATURE ACC
                     CONDITION ATLAS_ACC_CAPABLE )
 
 if( atlas_HAVE_ACC )
-  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI" )
+  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI|NVHPC" )
     set( ACC_Fortran_FLAGS -acc -ta=tesla,nordc )
     set( ACC_C_FLAGS ${ACC_Fortran_FLAGS} )
-    find_program( ACC_C_COMPILER NAMES pgcc HINTS ${PGI_DIR} ENV PGI_DIR PATH_SUFFIXES bin )
+    find_program( ACC_C_COMPILER NAMES pgcc HINTS ${PGI_DIR} ${NVPHC_DIR} ENV PGI_DIR NVHPC_DIR PATH_SUFFIXES bin )
     if( NOT ACC_C_COMPILER )
       ecbuild_error( "Could not find OpenACC capable C compiler" )
     endif()

cmake/features/OMP/test_omp_untied.cc

@@ -16,12 +16,13 @@
 
 #include <algorithm>
 #include <vector>
+
 #include <omp.h>
 
 template <typename RandomAccessIterator>
 void merge_sort_recursive( const RandomAccessIterator& iterator, size_t begin, size_t end ) {
     auto size = end - begin;
-    if ( size >= 2 ) { // should be much larger in real case (e.g. 256)
+    if ( size >= 2 ) {  // should be much larger in real case (e.g. 256)
         auto mid = begin + size / 2;
         {
 #pragma omp task shared( iterator ) untied if ( size >= ( 1 << 15 ) )
@@ -41,11 +42,11 @@ template <typename RandomAccessIterator>
 void omp_sort( RandomAccessIterator first, RandomAccessIterator last ) {
 #pragma omp parallel
 #pragma omp single
-        merge_sort_recursive( first, 0, std::distance( first, last ) );
+    merge_sort_recursive( first, 0, std::distance( first, last ) );
 }
 
 int main() {
-    auto integers = std::vector<int>(8);
+    auto integers = std::vector<int>( 8 );
     omp_sort( integers.begin(), integers.end() );
     return 0;
 }

doc/example-grids/cubedsphere_equiangular.yml

@@ -0,0 +1,14 @@
+# Test for the cubed-sphere grid that uses the equiangular formulation and projection.
+# See following paper and references therein for a desciption of the grid.
+# Putman, W. M., and S.-J. Lin 2007 Finite-volume transport on various cubed-sphere grids.
+# J. Comput. Phys., 227, 55–78
+
+type   : "cubedsphere_equiangular"
+N : 12
+
+check :
+  size : 866
+  lonlat(first) : [315, -35.2644]
+  lonlat(last)  : [45.0000, -42.6612]
+  uid : 8aa0b472107ce06c53b5c760886b9fb1
+  bounding_box(n,w,s,e) : [90,0,-90,360]

doc/example-grids/cubedsphere_equidistant.yml

@@ -0,0 +1,16 @@
+# Test for  the Cubed-Sphere grid that uses the standard equiangular formulation and projection.
+# For decription and references see:
+# Lin, S.-J. 2004 A “vertically Lagrangian” finite-volume dynamical core for global models.
+# Mon. Wea. Rev., 132, 2293–2307.
+# Lin, S.-J., and R. B. Rood 1996 Multidimensional flux-form semi-Lagrangian transport schemes.
+# Mon. Wea. Rev., 124, 2046–2070.
+
+type   : "cubedsphere_equidistant"
+N : 12
+
+check :
+  size : 866
+  lonlat(first) : [315, -35.2644]
+  lonlat(last)  : [45.0000,-40.3155]
+  uid : 682db241b2f45498663d78d795ceb64d
+  bounding_box(n,w,s,e) : [90,0,-90,360]

src/apps/atlas-grids.cc

@@ -88,7 +88,7 @@ struct AtlasGrids : public atlas::AtlasTool {
                "       Browse catalogue of grids\n"
                "\n"
                "       GRID: unique identifier for grid \n"
-               "           Example values: N80, F40, O24, L32\n";
+               "           Example values: N80, F40, O24, L32, CS-ED-12\n";
     }
 
     AtlasGrids( int argc, char** argv ) : AtlasTool( argc, argv ) {
@@ -193,6 +193,10 @@ int AtlasGrids::execute( const Args& args ) {
             if ( auto gaussian = GaussianGrid( grid ) ) {
                 Log::info() << "   Gaussian N number:                  " << gaussian.N() << std::endl;
             }
+            if ( auto cubedsphere = CubedSphereGrid( grid ) ) {
+                Log::info() << "   Cubedsphere faces:                   " << cubedsphere.N() << "x" << cubedsphere.N()
+                            << "x6" << std::endl;
+            }
             Log::info() << "   number of points:                   " << grid.size() << std::endl;
 
             Log::info() << "   memory footprint of grid:           " << eckit::Bytes( grid.footprint() ) << std::endl;

src/apps/atlas-meshgen.cc

@@ -107,7 +107,7 @@ class Meshgen2Gmsh : public AtlasTool {
     std::string longDescription() override {
         return "    The 'GRID' argument can be either the name of a named grid, orthe path to a"
                " YAML configuration file that describes the grid.\n"
-               "Example values for grid names are: N80, F40, O24, L64x33. See the program "
+               "Example values for grid names are: N80, F40, O24, L64x33, CS-ED-12. See the program "
                "'atlas-grids' for a list of named grids.\n"
                "\n"
                "    The optional 'OUTPUT' argument contains the path to the output file. "
@@ -141,7 +141,7 @@ Meshgen2Gmsh::Meshgen2Gmsh( int argc, char** argv ) : AtlasTool( argc, argv ) {
                                         "case serial" ) );
     add_option( new SimpleOption<bool>( "ghost", "Output ghost elements" ) );
     add_option( new SimpleOption<std::string>(
-        "generator", "Mesh generator [structured,regular,delaunay] (default = structured)" ) );
+        "generator", "Mesh generator [structured,regular,delaunay,cubedsphere] (default = structured)" ) );
     add_option( new SimpleOption<std::string>(
         "partitioner", "Mesh partitioner [equal_regions,checkerboard,equal_bands,regular_bands" ) );
 

src/atlas/CMakeLists.txt

@@ -72,6 +72,12 @@ option/TransOptions.cc
 projection.h
 projection/Projection.cc
 projection/Projection.h
+projection/detail/CubedSphereEquiAnglProjection.cc
+projection/detail/CubedSphereEquiAnglProjection.h
+projection/detail/CubedSphereEquiDistProjection.cc
+projection/detail/CubedSphereEquiDistProjection.h
+projection/detail/CubedSphereProjectionBase.cc
+projection/detail/CubedSphereProjectionBase.h
 projection/detail/LambertAzimuthalEqualAreaProjection.cc
 projection/detail/LambertAzimuthalEqualAreaProjection.h
 projection/detail/LambertConformalConicProjection.cc
@@ -84,6 +90,7 @@ projection/detail/ProjectionFactory.cc
 projection/detail/ProjectionFactory.h
 projection/detail/ProjectionImpl.cc
 projection/detail/ProjectionImpl.h
+projection/detail/ProjectionUtilities.h
 projection/detail/SchmidtProjection.cc
 projection/detail/SchmidtProjection.h
 
@@ -104,6 +111,8 @@ domain/detail/DomainFactory.h
 domain/detail/DomainFactory.cc
 
 grid.h
+grid/CubedSphereGrid.cc
+grid/CubedSphereGrid.h
 grid/Grid.cc
 grid/Grid.h
 grid/SpecRegistry.cc
@@ -128,7 +137,11 @@ grid/StencilComputer.h
 grid/StencilComputer.cc
 grid/StructuredPartitionPolygon.h
 grid/StructuredPartitionPolygon.cc
+grid/Tiles.h
+grid/Tiles.cc
 
+grid/detail/grid/CubedSphere.cc
+grid/detail/grid/CubedSphere.h
 grid/detail/grid/GridBuilder.h
 grid/detail/grid/GridBuilder.cc
 grid/detail/grid/GridFactory.h
@@ -160,11 +173,18 @@ grid/detail/distribution/BandsDistribution.h
 grid/detail/distribution/SerialDistribution.cc
 grid/detail/distribution/SerialDistribution.h
 
+grid/detail/tiles/Tiles.cc
+grid/detail/tiles/Tiles.h
+grid/detail/tiles/TilesFactory.h
+grid/detail/tiles/TilesFactory.cc
+grid/detail/tiles/FV3Tiles.cc
+grid/detail/tiles/FV3Tiles.h
+grid/detail/tiles/LFRicTiles.cc
+grid/detail/tiles/LFRicTiles.h
 
 grid/detail/vertical/VerticalInterface.h
 grid/detail/vertical/VerticalInterface.cc
 
-
 grid/detail/partitioner/BandsPartitioner.cc
 grid/detail/partitioner/BandsPartitioner.h
 grid/detail/partitioner/CheckerboardPartitioner.cc
@@ -192,8 +212,6 @@ grid/detail/partitioner/RegularBandsPartitioner.h
 grid/detail/partitioner/SerialPartitioner.cc
 grid/detail/partitioner/SerialPartitioner.h
 
-
-
 grid/detail/spacing/Spacing.cc
 grid/detail/spacing/Spacing.h
 grid/detail/spacing/SpacingFactory.cc
@@ -343,6 +361,8 @@ mesh/actions/ReorderReverseCuthillMckee.cc
 meshgenerator.h
 meshgenerator/MeshGenerator.cc
 meshgenerator/MeshGenerator.h
+meshgenerator/detail/CubedSphereMeshGenerator.h
+meshgenerator/detail/CubedSphereMeshGenerator.cc
 meshgenerator/detail/DelaunayMeshGenerator.h
 meshgenerator/detail/DelaunayMeshGenerator.cc
 meshgenerator/detail/StructuredMeshGenerator.h

src/atlas/array/ArrayShape.h

@@ -42,6 +42,8 @@ class ArrayShape : public std::vector<idx_t> {
     ArrayShape( idx_t data[], size_t size ) : Base( data, data + size ) {}
     template <typename idx_t, std::size_t N>
     ArrayShape( const std::array<idx_t, N>& list ) : Base( list.begin(), list.end() ) {}
+    template <typename idx_t>
+    ArrayShape( const std::vector<idx_t>& list ) : Base( list.begin(), list.end() ) {}
 };
 
 namespace detail {

src/atlas/array/DataType.h

@@ -67,7 +67,7 @@ class DataType {
     template <typename DATATYPE>
     static std::string str( const DATATYPE );
 
-    static long str_to_kind( const std::string& );
+    static kind_t str_to_kind( const std::string& );
     static std::string kind_to_str( kind_t );
     static bool kind_valid( kind_t );