Merge branch 'develop' into feature/interpolation_comparisons

.github/ci-hpc-config.yml

@@ -1,22 +1,27 @@
-build:
-  modules:
-    - ecbuild
-    - ninja
-  modules_package:
-    - atlas:fftw,eigen
-  dependencies:
-    - ecmwf/eckit@develop
-  parallel: 64
+matrix:
+  - mpi_on
+  - mpi_off
 
-nvidia-22.11:
+mpi_on:
   build:
     modules:
-      - ecbuild
       - ninja
     modules_package:
-      - atlas:fftw,eigen/3.4.0
+      - atlas:fftw,eigen,openmpi
+      - eckit:openmpi
     dependencies:
+      - ecmwf/ecbuild@develop
+      - ecmwf/eckit@develop
+    parallel: 64
+    ntasks: 16
+
+mpi_off:
+  build:
+    modules:
+      - ninja
+    modules_package:
+      - atlas:fftw,eigen
+    dependencies:
+      - ecmwf/ecbuild@develop
       - ecmwf/eckit@develop
     parallel: 64
-    env:
-      - ATLAS_FPE=0

.github/workflows/build.yml

@@ -35,7 +35,7 @@ jobs:
           - linux gnu-12
           - linux gnu-7
           - linux clang-12
-          - linux nvhpc-21.9
+#          - linux nvhpc-22.11
           - linux intel
           - macos
 
@@ -89,16 +89,16 @@ jobs:
             caching: true
             coverage: false
 
-          - name: linux nvhpc-21.9
-            os: ubuntu-20.04
-            compiler: nvhpc-21.9
-            compiler_cc: nvc
-            compiler_cxx: nvc++
-            compiler_fc: nvfortran
-            cmake_options: -DCMAKE_CXX_FLAGS=--diag_suppress177
-            ctest_options: "-LE mpi" # For now until Checkerboard fixed
-            caching: false
-            coverage: false
+#          - name: linux nvhpc-22.11
+#            os: ubuntu-20.04
+#            compiler: nvhpc-22.11
+#            compiler_cc: nvc
+#            compiler_cxx: nvc++
+#            compiler_fc: nvfortran
+#            cmake_options: -DCMAKE_CXX_FLAGS=--diag_suppress177
+#            ctest_options: "-LE mpi" # For now until Checkerboard fixed
+#            caching: false
+#            coverage: false
 
           - name : linux intel
             os: ubuntu-20.04
@@ -168,7 +168,7 @@ jobs:
       if: contains( matrix.compiler, 'nvhpc' )
       shell: bash -eux {0}
       run: |
-        ${ATLAS_TOOLS}/install-nvhpc.sh --prefix ${DEPS_DIR}/nvhpc
+        ${ATLAS_TOOLS}/install-nvhpc.sh --prefix ${DEPS_DIR}/nvhpc --version 22.11
         source ${DEPS_DIR}/nvhpc/env.sh
         echo "${NVHPC_DIR}/compilers/bin"                   >> $GITHUB_PATH
         [ -z ${MPI_HOME+x} ] || echo "MPI_HOME=${MPI_HOME}" >> $GITHUB_ENV

.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

AUTHORS

@@ -13,23 +13,31 @@ Thanks for contributions from
 - Andreas Mueller
 - Baudouin Raoult
 - Florian Rathgeber
-- Marek Wlasak
 - Oliver Lomax
+- Marek Wlasak
 - Daniel Holdaway
 - Daan Degrauwe
 - Philippe Marguinaud
+- Slavko Brdar
 - Gianmarco Mengaldo
+- Dušan Figala
+- Benjamin Menetrier
 - James Hawkes
 - Mats Hamrud
-- Benjamin Menetrier
 - Rahul Mahajan
+- Toby Searle
 - Olivier Iffrig
 - Christian Kuehnlein
 - Iain Russell
+- Marco Milan
+- Daniel Tipping
 - Domokos Sármány
-- Steven Vahl
+- Lorenzo Milazzo
+- Francois Hebert
+- Yannick Trémolet
 - Mark J. Olah
-- Michael Lange
+- Sam Hatfield
 - Peter Bispham
-- Slavko Brdar
-- Yannick Trémolet
+- Paul Cresswell
+- Steven Vahl
+- Michael Lange

CHANGELOG.md

@@ -7,6 +7,27 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.34.0] - 2023-07-10
+### Added
+- Fieldset::metadata (#126)
+- Fieldset::adjointHaloExchange
+- Field/Fieldset::clone method
+- Functions to enable/disable FPE
+- Add function to build mesh from imported connectivity data (#135)
+- Implement field::for_each capabilities (#139)
+- Introduce colon-separated environment variable ATLAS_PLUGIN_PATH to simplify plugin detection
+- Introduce atlas::mdspan, contributed from github.com/kokkos/mdspan
+- Add function Field::horizontal_dimension() -> std::vector<idx_t>
+- Setup horizontal_dimensions() for BlockStructuredColumns fields
+- Upgrade the halo exchange procedure for the function space 'PointCloud' (#120)
+
+### Fixed
+- Enable latitude normalisation in KDTree coordinate transform (#140)
+- Fix LocalView indexing bug for non-contiguous slices
+- C++17 flag public propagation to downstream C++ CMake packages
+- Fix cells().global_index() metadata for RegularLonLat grids in StructuredMeshGenerator
+- BuildHalo: mark interior added cells as ghost
+
 ## [0.33.0] - 2023-04-03
 ### Added
 - Add support for StructuredPartitionPolygon with halo > 0
@@ -443,6 +464,7 @@ 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
 [0.33.0]: 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

CMakeLists.txt

@@ -38,12 +38,39 @@ find_package(atlas_io)
 ################################################################################
 # Features that can be enabled / disabled with -DENABLE_<FEATURE>
 
+ecbuild_add_option( FEATURE ATLAS_GRID
+                    DESCRIPTION "Build grid related features" )
+
+ecbuild_add_option( FEATURE ATLAS_FIELD
+                    DESCRIPTION "Build field and memory management related features" )
+
+ecbuild_add_option( FEATURE ATLAS_FUNCTIONSPACE
+                    DESCRIPTION "Build functionspace related features (mesh, functionspace, parallel)"
+                    CONDITION atlas_HAVE_ATLAS_GRID AND atlas_HAVE_ATLAS_FIELD )
+
+ecbuild_add_option( FEATURE ATLAS_INTERPOLATION
+                    DESCRIPTION "Build interpolation related features"
+                    CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE )
+
+ecbuild_add_option( FEATURE ATLAS_TRANS
+                    DESCRIPTION "Build transform related features"
+                    CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE )
+
+ecbuild_add_option( FEATURE ATLAS_NUMERICS
+                    DESCRIPTION "Build numerics related features"
+                    CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE )
+
+ecbuild_add_option( FEATURE ECKIT_DEVELOP
+                    DESCRIPTION "Used to enable new features or API depending on eckit develop branch, not yet in a tagged release"
+                    DEFAULT OFF )
+
+
 include( features/BOUNDSCHECKING )
 include( features/FORTRAN )
 include( features/MPI )
 include( features/OMP )
 include( features/FFTW )
-include( features/TRANS )
+include( features/ECTRANS )
 include( features/TESSELATION )
 include( features/GRIDTOOLS_STORAGE )
 include( features/ACC )

VERSION

@@ -1 +1 @@
-0.33.0
+0.34.0

atlas_io/src/atlas_io/Trace.h

@@ -15,6 +15,7 @@
 #include <memory>
 #include <string>
 #include <vector>
+#include <limits>
 
 namespace eckit {
 class CodeLocation;
@@ -51,6 +52,7 @@ struct TraceHookRegistry {
     static bool enabled(size_t id) { return instance().enabled_[id]; }
     static size_t size() { return instance().hooks.size(); }
     static TraceHookBuilder& hook(size_t id) { return instance().hooks[id]; }
+    static size_t invalidId() { return std::numeric_limits<size_t>::max(); }
 
 private:
     TraceHookRegistry() = default;

atlas_io/tests/CMakeLists.txt

@@ -28,7 +28,7 @@ foreach( algorithm none bzip2 aec lz4 snappy )
     string( TOUPPER ${algorithm} feature )
     if( eckit_HAVE_${feature} OR algorithm MATCHES "none" )
         ecbuild_add_test( TARGET atlas_io_test_record_COMPRESSION_${algorithm}
-            COMMAND atlas_test_io_record
+            COMMAND atlas_io_test_record
             ARGS --suffix ".${algorithm}"
             ENVIRONMENT ${ATLAS_TEST_ENVIRONMENT} ATLAS_IO_COMPRESSION=${algorithm}
         )

cmake/atlas-import.cmake.in

@@ -5,7 +5,7 @@ set( atlas_HAVE_MPI                          @atlas_HAVE_MPI@ )
 set( atlas_HAVE_OMP                          @atlas_HAVE_OMP@ )
 set( atlas_HAVE_OMP_CXX                      @atlas_HAVE_OMP_CXX@ )
 set( atlas_HAVE_OMP_Fortran                  @atlas_HAVE_OMP_Fortran@ )
-set( atlas_HAVE_TRANS                        @atlas_HAVE_TRANS@ )
+set( atlas_HAVE_ECTRANS                      @atlas_HAVE_ECTRANS@ )
 set( atlas_HAVE_FORTRAN                      @atlas_HAVE_FORTRAN@ )
 set( atlas_HAVE_EIGEN                        @atlas_HAVE_EIGEN@ )
 set( atlas_HAVE_GRIDTOOLS_STORAGE            @atlas_HAVE_GRIDTOOLS_STORAGE@ )
@@ -65,7 +65,7 @@ if( atlas_OMP_COMPONENTS )
 endif()
 
 ## transi
-if( atlas_HAVE_TRANS AND atlas_REQUIRES_PRIVATE_DEPENDENCIES )
+if( atlas_HAVE_ECTRANS AND atlas_REQUIRES_PRIVATE_DEPENDENCIES )
     set( transi_DIR @transi_DIR@ )
     if( transi_DIR )
         find_dependency( transi HINTS ${CMAKE_CURRENT_LIST_DIR}/../transi @transi_DIR@ )

cmake/atlas_compile_flags.cmake

@@ -20,3 +20,8 @@ if( CMAKE_CXX_COMPILER_ID MATCHES Cray )
 #          directives, ACC directives, or ASM intrinsics.
 
 endif()
+
+if( CMAKE_CXX_COMPILER_ID MATCHES NVHPC )
+  ecbuild_add_cxx_flags("--diag_suppress declared_but_not_referenced --display_error_number" NAME atlas_cxx_disable_warnings )
+  # For all the variables with side effects (constructor/dectructor functionality)
+endif()

cmake/features/ACC.cmake

@@ -1,5 +1,7 @@
 ### OpenACC
 
+if( atlas_HAVE_ATLAS_FIELD )
+
 set( ATLAS_ACC_CAPABLE FALSE )
 if( HAVE_CUDA )
   if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI|NVHPC" )
@@ -21,3 +23,8 @@ if( atlas_HAVE_ACC )
     endif()
   endif()
 endif()
+
+else()
+  set( HAVE_ACC 0 )
+  set( atlas_HAVE_ACC 0 )
+endif()

cmake/features/ECTRANS.cmake

@@ -0,0 +1,35 @@
+if( atlas_HAVE_ATLAS_TRANS )
+
+### trans ...
+
+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} )
+endif()
+
+set( atlas_HAVE_PACKAGE_ECTRANS 0 )
+if( atlas_HAVE_ATLAS_FUNCTIONSPACE AND (ENABLE_ECTRANS OR NOT DEFINED ENABLE_ECTRANS) )
+    find_package( ectrans 1.1 COMPONENTS transi double QUIET )
+    if( TARGET transi_dp )
+        set( transi_FOUND TRUE )
+        if( NOT TARGET transi )
+            get_target_property( transi_dp_IMPORTED transi_dp IMPORTED )
+            if( transi_dp_IMPORTED )
+                set_target_properties( transi_dp PROPERTIES IMPORTED_GLOBAL TRUE) # required for aliasing imports
+            endif()
+            add_library( transi ALIAS transi_dp )
+        endif()
+        set( atlas_HAVE_PACKAGE_ECTRANS 1 )
+    else()
+        find_package( transi 0.8 QUIET )
+    endif()
+endif()
+ecbuild_add_option( FEATURE ECTRANS
+                    DESCRIPTION "Support for IFS spectral transforms"
+                    CONDITION atlas_HAVE_ATLAS_FUNCTIONSPACE AND transi_FOUND )
+
+endif()