Merge branch 'release/0.34.0'

* release/0.34.0: (78 commits) Version 0.34.0 Fix global indexing for meshes from structured grids with pole patch Fix cells().global_index() metadata for RegularLonLat grids in StructuredMeshGenerator BuildHalo: mark interior added cells as ghost Add example-plugin in doc Introduce colon-separated environment variable ATLAS_PLUGIN_PATH to simplify plugin detection Interpolate from cubedsphere mesh to structured columns (#146) Fix FieldSet::field(std::string) when field has been renamed (fixes #147) Further separate compilation features Field with functionspace optional Introduce features to disable compilation of structural components Remove interdependencies between structural components CMake cleanup Move files to correct places Introduce atlas::mdspan, contributed from github.com/kokkos/mdspan Disable GHA "nvhpc-22.11" as there are random compilation errors, probably related to insufficient disk or memory space atlas_io: fix test command in standalone build Fix and test some use cases with / without calling atlas::initialise() Access to atlas::Library::dataPath without initialising Enable latitude normalisation in KDTree coordinate transform (#140) ...
ecmwf · Jul 10, 2023 · ea451cb · ea451cb
2 parents 3ba1bed + 35726ee
commit ea451cb
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diff --git a/.github/ci-config.yml b/.github/ci-config.yml
@@ -0,0 +1,5 @@
+dependencies: |
+  ecmwf/ecbuild
+  ecmwf/eckit
+dependency_branch: develop
+parallelism_factor: 8
diff --git a/.github/ci-hpc-config.yml b/.github/ci-hpc-config.yml
@@ -0,0 +1,27 @@
+matrix:
+  - mpi_on
+  - mpi_off
+
+mpi_on:
+  build:
+    modules:
+      - ninja
+    modules_package:
+      - 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
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -32,8 +32,10 @@ jobs:
         build_type: [Release,Debug]
         name:
           - linux gnu-10
+          - linux gnu-12
+          - linux gnu-7
           - linux clang-12
-          - linux nvhpc-21.9
+#          - linux nvhpc-22.11
           - linux intel
           - macos
 
@@ -46,6 +48,26 @@ jobs:
             compiler_cxx: g++-10
             compiler_fc: gfortran-10
             caching: true
+            coverage: true
+
+          - name: linux gnu-12
+            os: ubuntu-22.04
+            compiler: gnu-12
+            compiler_cc: gcc-12
+            compiler_cxx: g++-12
+            compiler_fc: gfortran-12
+            cmake_options: -DENABLE_OMP_CXX=OFF
+            caching: true
+            coverage: false
+
+          - name: linux gnu-7
+            os: ubuntu-20.04
+            compiler: gnu-7
+            compiler_cc: gcc-7
+            compiler_cxx: g++-7
+            compiler_fc: gfortran-7
+            caching: true
+            coverage: false
 
           - name: linux clang-12
             os: ubuntu-20.04
@@ -54,6 +76,7 @@ jobs:
             compiler_cxx: clang++-12
             compiler_fc: gfortran-10
             caching: true
+            coverage: false
 
           - name: linux clang-12
             build_type: Release
@@ -64,16 +87,18 @@ jobs:
             compiler_fc: gfortran-10
             ctest_options: "-LE mpi" # For now until Checkerboard fixed
             caching: true
-
-          - 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
@@ -82,6 +107,7 @@ jobs:
             compiler_cxx: icpc
             compiler_fc: ifort
             caching: true
+            coverage: false
 
           - name: macos
             # Xcode compiler requires empty environment variables, so we pass null (~) here
@@ -91,6 +117,7 @@ jobs:
             compiler_cxx: ~
             compiler_fc: gfortran-11
             caching: true
+            coverage: false
             cmake_options: -DMPI_SLOTS=4
 
     runs-on: ${{ matrix.os }}
@@ -120,6 +147,9 @@ jobs:
           brew install libomp
         else
           sudo apt-get update
+          if [[ "${{ matrix.compiler }}" =~ gnu-7 ]]; then
+            sudo apt-get install gcc-7 g++-7 gfortran-7
+          fi
           sudo apt-get install ninja-build
         fi
 
@@ -138,7 +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
@@ -189,7 +219,7 @@ jobs:
       id: build-test
       uses: ecmwf-actions/build-package@v2
       with:
-        self_coverage: true
+        self_coverage: ${{ matrix.coverage }}
         force_build: true
         cache_suffix: "${{ matrix.build_type }}-${{ env.CACHE_SUFFIX }}"
         recreate_cache: ${{ matrix.caching == false }}

diff --git a/.github/workflows/check-release-version.yml b/.github/workflows/check-release-version.yml
@@ -0,0 +1,11 @@
+name: Check VERSION file
+
+on:
+  push:
+    branches:
+      - "release/**"
+      - "hotfix/**"
+
+jobs:
+  check_version:
+    uses: ecmwf-actions/reusable-workflows/.github/workflows/check-release-version.yml@v2
diff --git a/.github/workflows/reusable-ci-hpc.yml b/.github/workflows/reusable-ci-hpc.yml
@@ -21,8 +21,7 @@ jobs:
           ecbuild
           ninja
         --modules-package: |
-          fftw
-          eigen
+          atlas:fftw,eigen
         --dependencies: |
           ${{ inputs.eckit || 'ecmwf/eckit@develop' }}
         --parallel: 64

diff --git a/AUTHORS b/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
diff --git a/CHANGELOG.md b/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

diff --git a/CMakeLists.txt b/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 )

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.33.0
+0.34.0
diff --git a/atlas_io/src/atlas_io/Data.h b/atlas_io/src/atlas_io/Data.h
@@ -10,6 +10,8 @@
 
 #pragma once
 
+#include <cstdint>
+
 #include "eckit/io/Buffer.h"
 
 namespace atlas {

diff --git a/atlas_io/src/atlas_io/Trace.h b/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;

diff --git a/atlas_io/tests/CMakeLists.txt b/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}
         )

diff --git a/cmake/atlas-import.cmake.in b/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@ )

diff --git a/cmake/atlas_compile_flags.cmake b/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()
diff --git a/cmake/features/ACC.cmake b/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()