Merge branch 'release/0.35.0'

* release/0.35.0: (73 commits)
  Update Changelog
  Add single precision support to fvm::Nabla
  Version 0.35.0
  Add Mesh::nb_partitions with deprecation warning
  Implement PointCloud::gather/scatter
  Fix NodeColumns::gather/scatter with mpi_comm for broadcast of metadata
  Fixup 4f9b29c , fixing bug in PointCloud constructor regarding global index computation with nb_parts==1
  Add test for mpi_comm with functionspace::BlockStructuredColumns
  Add mpi_comm to HealpixMeshgenerator
  Add mpi_comm to RegularMeshgenerator
  Use mpi_comm in functionspace::PointCloud
  Add Configuration to PointCloud
  Use mpi_comm in DelaunayMeshGenerator
  Make Partitioner(std::string) explicit
  Use mpi_comm in Redistribute
  Use mpi_comm in CubedSphere(Dual)MeshGenerator
  Add test of mpi_comm with partitioners
  Use mpi_comm in EqualRegionsPartitioner
  Test mpi_comm with Mesh(grid,partitioner)
  Mesh(grid,partitioner) constructor inspects partitioner for mpi_comm
  ...

.github/ci-config.yml

@@ -1,5 +1,6 @@
 dependencies: |
   ecmwf/ecbuild
   ecmwf/eckit
+  ecmwf/fckit
 dependency_branch: develop
 parallelism_factor: 8

.github/ci-hpc-config.yml

@@ -12,6 +12,7 @@ mpi_on:
     dependencies:
       - ecmwf/ecbuild@develop
       - ecmwf/eckit@develop
+      - ecmwf/fckit@develop
     parallel: 64
     ntasks: 16
 
@@ -24,4 +25,5 @@ mpi_off:
     dependencies:
       - ecmwf/ecbuild@develop
       - ecmwf/eckit@develop
+      - ecmwf/fckit@develop
     parallel: 64

.github/workflows/build.yml

@@ -194,6 +194,12 @@ jobs:
         ${ATLAS_TOOLS}/install-fftw.sh --version 3.3.10 --prefix ${DEPS_DIR}/fftw
         echo "FFTW_ROOT=${DEPS_DIR}/fftw" >> $GITHUB_ENV
 
+    - name: Install Qhull
+      shell: bash -eux {0}
+      run: |
+        ${ATLAS_TOOLS}/install-qhull.sh --version 8.1-alpha3 --prefix ${DEPS_DIR}/qhull
+        echo "Qhull_ROOT=${DEPS_DIR}/qhull" >> $GITHUB_ENV
+
     - name: Install LZ4
       if: "!contains( matrix.compiler, 'nvhpc' )"
       run: |

.github/workflows/cd.yml

@@ -0,0 +1,11 @@
+name: cd
+
+on:
+  push:
+    tags:
+      - '**'
+
+jobs:
+  deploy:
+    uses: ecmwf-actions/reusable-workflows/.github/workflows/create-package.yml@v2
+    secrets: inherit

CHANGELOG.md

@@ -7,6 +7,25 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.35.0] - 2023-02-10
+### Added
+- Add accessors for the GridBox class (MIR-632)
+- Add FunctionSpace::partition() field
+- Add configurable MPI communicator to data structures (#131)
+- Add single precision support for fvm::Nabla
+- Implement PointCloud parallel construction with halo_radius
+
+### Fixed
+- Fix StructuredMeshGenerator for Gaussian grids that don't start at 0 degrees (ATLAS-375)
+- Remove functionspace::Spectral via Trans initialisation (fixes #153)
+- Enable MeshBuilder to set up the Grid (#152)
+- Fix use of cmake option ATLAS_ENABLE_TRANS as in a bundle
+
+### Changed
+- Cleanup long-standing temporary element types. API change but with deprecated old API
+- Deprecated rename Mesh::nb_partitions -> Mesh::nb_parts
+- Implement Delaunay triangulation using Qhull instead of CGAL but CGAL can still be enabled instead for now
+
 ## [0.34.0] - 2023-07-10
 ### Added
 - Fieldset::metadata (#126)
@@ -464,7 +483,8 @@ Fix StructuredInterpolation2D with retry for failed stencils
 ## 0.13.0 - 2018-02-16
 
 [Unreleased]: https://github.com/ecmwf/atlas/compare/master...develop
-[0.33.0]: https://github.com/ecmwf/atlas/compare/0.33.0...0.34.0
+[0.35.0]: https://github.com/ecmwf/atlas/compare/0.34.0...0.35.0
+[0.34.0]: https://github.com/ecmwf/atlas/compare/0.33.0...0.34.0
 [0.33.0]: https://github.com/ecmwf/atlas/compare/0.32.1...0.33.0
 [0.32.1]: https://github.com/ecmwf/atlas/compare/0.32.0...0.32.1
 [0.32.0]: https://github.com/ecmwf/atlas/compare/0.31.1...0.32.0

VERSION

@@ -1 +1 @@
-0.34.0
+0.35.0

cmake/features/ECTRANS.cmake

@@ -2,13 +2,16 @@ if( atlas_HAVE_ATLAS_TRANS )
 
 ### trans ...
 
+if( NOT DEFINED ATLAS_ENABLE_ECTRANS AND DEFINED ATLAS_ENABLE_TRANS )
+  ecbuild_warn("Atlas option ATLAS_ENABLE_TRANS is deprecated in favour of ATLAS_ENABLE_ECTRANS")
+  set( ATLAS_ENABLE_ECTRANS ${ATLAS_ENABLE_TRANS} )
+endif()
 if( NOT DEFINED ENABLE_ECTRANS AND DEFINED ENABLE_TRANS )
   ecbuild_warn("Atlas option ENABLE_TRANS is deprecated in favour of ENABLE_ECTRANS")
   set( ENABLE_ECTRANS ${ENABLE_TRANS} )
 endif()
-if( NOT DEFINED ATLAS_ENABLE_ECTRANS AND DEFINED ATLAS_ENABLE_TRANS )
-  ecbuild_warn("Atlas option ATLAS_ENABLE_TRANS is deprecated in favour of ATLAS_ENABLE_ECTRANS")
-  set( ATLAS_ENABLE_TRANS ${ENABLE_TRANS} )
+if( DEFINED ATLAS_ENABLE_ECTRANS )
+  set( ENABLE_ECTRANS ${ATLAS_ENABLE_ECTRANS} )
 endif()
 
 set( atlas_HAVE_PACKAGE_ECTRANS 0 )
@@ -32,4 +35,4 @@ ecbuild_add_option( FEATURE ECTRANS
                     DESCRIPTION "Support for IFS spectral transforms"
                     CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE AND transi_FOUND )
 
-endif()
+endif()

cmake/features/TESSELATION.cmake

@@ -1,16 +1,32 @@
 if( atlas_HAVE_ATLAS_FUNCTIONSPACE )
 ### tesselation ...
 
-set(Boost_USE_MULTITHREADED      ON )
-
 ecbuild_add_option( FEATURE TESSELATION
+                    DESCRIPTION "Support for unstructured mesh generation"
+                    CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE
+                    REQUIRED_PACKAGES "Qhull" )
+if(HAVE_TESSELATION)
+  set(QHULL_LIBRARIES Qhull::qhullcpp Qhull::qhull_r)
+  set(atlas_HAVE_QHULL 1)
+else()
+  set(atlas_HAVE_QHULL 0)
+endif()
+
+### NOTE
+#
+# CGAL is deprecated as TESSELATION backend. Qhull is to be used instead.
+# To use CGAL regardless, turn ON CGAL feature (-DENABLE_CGAL=ON)
+
+set(Boost_USE_MULTITHREADED ON )
+ecbuild_add_option( FEATURE CGAL
+                    DEFAULT OFF
                     DESCRIPTION "Support for unstructured mesh generation"
                     CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE
                     REQUIRED_PACKAGES
-                      "CGAL QUIET"
+                      "CGAL"
                       "Boost VERSION 1.45.0 QUIET" )
 
-if( HAVE_TESSELATION )
+if( HAVE_CGAL )
     list( APPEND CGAL_INCLUDE_DIRS ${Boost_INCLUDE_DIRS} )
     if ( TARGET CGAL::CGAL )
       list( APPEND CGAL_LIBRARIES CGAL::CGAL ${CGAL_3RD_PARTY_LIBRARIES} ${GMP_LIBRARIES} ${MPFR_LIBRARIES} ${Boost_THREAD_LIBRARY} ${Boost_SYSTEM_LIBRARY} )
@@ -27,8 +43,8 @@ if( HAVE_TESSELATION )
     endif()
 endif()
 
-if( NOT HAVE_TESSELATION )
+if( NOT HAVE_CGAL )
     unset( CGAL_LIBRARIES )
     unset( CGAL_INCLUDE_DIRS )
 endif()
-endif()
+endif()

src/CMakeLists.txt

@@ -24,6 +24,18 @@ else()
   set( atlas_HAVE_TESSELATION 0 )
 endif()
 
+if( atlas_HAVE_QHULL )
+  set( atlas_HAVE_QHULL 1 )
+else()
+  set( atlas_HAVE_QHULL 0 )
+endif()
+
+if( atlas_HAVE_CGAL )
+  set( atlas_HAVE_CGAL 1 )
+else()
+  set( atlas_HAVE_CGAL 0 )
+endif()
+
 if( atlas_HAVE_PROJ )
   set( atlas_HAVE_PROJ 1 )
 else()

src/atlas/CMakeLists.txt

@@ -341,6 +341,10 @@ mesh/Connectivity.cc
 mesh/Connectivity.h
 mesh/ElementType.cc
 mesh/ElementType.h
+mesh/elementtypes/Classification.h
+mesh/elementtypes/Triangle.h
+mesh/elementtypes/Quadrilateral.h
+mesh/elementtypes/Pentagon.h
 mesh/Elements.cc
 mesh/Elements.h
 mesh/Halo.cc
@@ -815,6 +819,10 @@ util/vector.h
 util/mdspan.h
 util/detail/mdspan/mdspan.hpp
 util/VectorOfAbstract.h
+util/QhullSphericalTriangulation.h
+util/QhullSphericalTriangulation.cc
+util/CGALSphericalTriangulation.h
+util/CGALSphericalTriangulation.cc
 util/detail/Cache.h
 util/detail/KDTree.h
 util/function/MDPI_functions.h
@@ -928,6 +936,7 @@ ecbuild_add_library( TARGET atlas
     ${CGAL_LIBRARIES}
     ${FFTW_LIBRARIES}
     ${PROJ_LIBRARIES}
+    ${QHULL_LIBRARIES}
 
   PUBLIC_LIBS
     eckit

src/atlas/functionspace/CellColumns.cc

@@ -95,7 +95,8 @@ class CellColumnsHaloExchangeCache : public util::Cache<std::string, parallel::H
 
     static value_type* create(const Mesh& mesh) {
         value_type* value = new value_type();
-        value->setup(array::make_view<int, 1>(mesh.cells().partition()).data(),
+        value->setup(mesh.mpi_comm(),
+                     array::make_view<int, 1>(mesh.cells().partition()).data(),
                      array::make_view<idx_t, 1>(mesh.cells().remote_index()).data(), REMOTE_IDX_BASE,
                      mesh.cells().size());
         return value;
@@ -129,7 +130,8 @@ class CellColumnsGatherScatterCache : public util::Cache<std::string, parallel::
 
     static value_type* create(const Mesh& mesh) {
         value_type* value = new value_type();
-        value->setup(array::make_view<int, 1>(mesh.cells().partition()).data(),
+        value->setup(mesh.mpi_comm(),
+                     array::make_view<int, 1>(mesh.cells().partition()).data(),
                      array::make_view<idx_t, 1>(mesh.cells().remote_index()).data(), REMOTE_IDX_BASE,
                      array::make_view<gidx_t, 1>(mesh.cells().global_index()).data(), mesh.cells().size());
         return value;
@@ -193,14 +195,14 @@ void CellColumns::set_field_metadata(const eckit::Configuration& config, Field&
 }
 
 idx_t CellColumns::config_size(const eckit::Configuration& config) const {
-    const idx_t rank = mpi::rank();
     idx_t size       = nb_cells();
     bool global(false);
     if (config.get("global", global)) {
         if (global) {
             idx_t owner(0);
             config.get("owner", owner);
             idx_t _nb_cells_global(nb_cells_global());
+            const idx_t rank = mpi::comm(mpi_comm()).rank();
             size = (rank == owner ? _nb_cells_global : 0);
         }
     }
@@ -269,7 +271,7 @@ CellColumns::CellColumns(const Mesh& mesh, const eckit::Configuration& config):
         return nb_cells;
     };
 
-    mesh::actions::build_nodes_parallel_fields(mesh_.nodes());
+    mesh::actions::build_nodes_parallel_fields(mesh_);
     mesh::actions::build_cells_parallel_fields(mesh_);
     mesh::actions::build_periodic_boundaries(mesh_);
 
@@ -587,6 +589,10 @@ Field CellColumns::ghost() const {
     return mesh_.cells().field("ghost");
 }
 
+Field CellColumns::partition() const {
+    return mesh_.cells().partition();
+}
+
 //------------------------------------------------------------------------------
 //------------------------------------------------------------------------------
 //------------------------------------------------------------------------------

src/atlas/functionspace/CellColumns.h

@@ -97,6 +97,10 @@ class CellColumns : public functionspace::FunctionSpaceImpl {
 
     Field ghost() const override;
 
+    Field partition() const override;
+
+    std::string mpi_comm() const override { return mesh_.mpi_comm(); }
+
 private:  // methods
     idx_t config_size(const eckit::Configuration& config) const;
     array::DataType config_datatype(const eckit::Configuration&) const;

src/atlas/functionspace/EdgeColumns.cc

@@ -96,7 +96,8 @@ class EdgeColumnsHaloExchangeCache : public util::Cache<std::string, parallel::H
 
     static value_type* create(const Mesh& mesh) {
         value_type* value = new value_type();
-        value->setup(array::make_view<int, 1>(mesh.edges().partition()).data(),
+        value->setup(mesh.mpi_comm(),
+                     array::make_view<int, 1>(mesh.edges().partition()).data(),
                      array::make_view<idx_t, 1>(mesh.edges().remote_index()).data(), REMOTE_IDX_BASE,
                      mesh.edges().size());
         return value;
@@ -130,7 +131,8 @@ class EdgeColumnsGatherScatterCache : public util::Cache<std::string, parallel::
 
     static value_type* create(const Mesh& mesh) {
         value_type* value = new value_type();
-        value->setup(array::make_view<int, 1>(mesh.edges().partition()).data(),
+        value->setup(mesh.mpi_comm(),
+                     array::make_view<int, 1>(mesh.edges().partition()).data(),
                      array::make_view<idx_t, 1>(mesh.edges().remote_index()).data(), REMOTE_IDX_BASE,
                      array::make_view<gidx_t, 1>(mesh.edges().global_index()).data(), mesh.edges().size());
         return value;
@@ -194,14 +196,14 @@ void EdgeColumns::set_field_metadata(const eckit::Configuration& config, Field&
 }
 
 idx_t EdgeColumns::config_size(const eckit::Configuration& config) const {
-    const idx_t rank = mpi::rank();
     idx_t size       = nb_edges();
     bool global(false);
     if (config.get("global", global)) {
         if (global) {
             idx_t owner(0);
             config.get("owner", owner);
             idx_t _nb_edges_global(nb_edges_global());
+            const idx_t rank = mpi::comm(mpi_comm()).rank();
             size = (rank == owner ? _nb_edges_global : 0);
         }
     }
@@ -266,7 +268,7 @@ EdgeColumns::EdgeColumns(const Mesh& mesh, const eckit::Configuration& config):
         return _nb_edges;
     };
 
-    mesh::actions::build_nodes_parallel_fields(mesh_.nodes());
+    mesh::actions::build_nodes_parallel_fields(mesh_);
     mesh::actions::build_periodic_boundaries(mesh_);
 
     if (halo_.size() > 0) {
@@ -570,6 +572,10 @@ Field EdgeColumns::remote_index() const {
     return edges().remote_index();
 };
 
+Field EdgeColumns::partition() const {
+    return edges().partition();
+}
+
 //------------------------------------------------------------------------------
 //------------------------------------------------------------------------------
 //------------------------------------------------------------------------------