Merge branch 'release/0.22.0'

* release/0.22.0: (161 commits)
  Update Changelog
  Version 0.22.0
  Add a jacobian method to atlas::Projection object
  travis: Use nproc for faster compilation
  travis: Update CMake to 3.18.4
  travis: Update OSX version
  Fix tools/install-pgi.sh download link
  Grid convenience constructors taking Projection
  Formatting
  Simplify version C++ file
  Gmsh control output of LAND/WATER elements
  Move Topology to util namespace, created BitflagsView
  atlas-grids outputs footprint of grid
  Gmsh output of idx_t coordinate fields
  Support mesh::PartitionPolygon::outputPythonScript to output polygon in "xy" or "lonlat" coordinates (default="xy")
  Tool atlas-meshgen now uses by default the Grid's recommended MeshGenerator and Partitioner
  Added constructor `Mesh::Mesh( const Grid& )`
  Added new function `MeshGenerator::generate(Mesh,Partitioner)`
  Added function `string MeshGenerator::type()`
  Polygon can return lonlat points in addition to xy points
  ...

.travis.yml

@@ -1,13 +1,6 @@
-sudo: false
 
 language: cpp
 
-
-# Workaround for https://github.com/travis-ci/travis-ci/issues/4681
-matrix:
-  - TRAVIS_EMPTY_JOB_WORKAROUND=true
-
-
 cache:
   directories:
     - ${HOME}/deps/cmake
@@ -17,11 +10,7 @@ cache:
     - ${HOME}/deps/fckit
 
 
-matrix:
-  exclude:
-
-    - env: TRAVIS_EMPTY_JOB_WORKAROUND
-
+jobs:
   include:
 
     - os: linux
@@ -68,14 +57,14 @@ matrix:
         - MPI=openmpi
         - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG"
         - ATLAS_CTEST_OPTIONS="-E atlas_test_stencil_parallel_mpi16"
-      osx_image: xcode10.1
+      osx_image: xcode12
 
     - os: osx
       env:
         - CACHE_NAME=osx-clang-mpich
         - CXX_COMPILER='clang++' C_COMPILER='clang' Fortran_COMPILER='gfortran'
         - MPI=mpich
-      osx_image: xcode9
+      osx_image: xcode12
 
     - os: linux
       compiler: gcc
@@ -84,8 +73,8 @@ matrix:
         - CXX_COMPILER='pgc++' C_COMPILER='pgcc' Fortran_COMPILER='pgfortran'
         - MPI='openmpi'
         - PGI_VERSION="CommunityEdition"
-        - ECKIT_CMAKE_OPTIONS="-DENABLE_ECKIT-395=OFF -DRT_LIB=/usr/lib/x86_64-linux-gnu/librt.so -DCURSES_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurses.so"
-        - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG"
+        - ECKIT_CMAKE_OPTIONS="-DENABLE_ECKIT-395=OFF -DRT_LIB=/usr/lib/x86_64-linux-gnu/librt.so -DCURSES_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurses.so -DMPI_ARGS=--oversubscribe"
+        - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG -DMPI_ARGS=--oversubscribe"
 
 before_install:
 
@@ -129,7 +118,7 @@ install:
   - |
     ### Install PGI community edition
     if [[ "${PGI_VERSION:-notset}" == "CommunityEdition" ]]; then
-      install-pgi.sh --mpi --prefix ${DEPS_DIR}/pgi
+      install-pgi.sh --prefix ${DEPS_DIR}/pgi
       source ${DEPS_DIR}/pgi/env.sh
     fi
 
@@ -149,11 +138,30 @@ install:
   - |
     ### Install CMake
     if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
+      CMAKE_VERSION=3.18.4
       if [[ -z "$(ls -A ${DEPS_DIR}/cmake)" ]]; then
-        CMAKE_URL="https://cmake.org/files/v3.15.2/cmake-3.15.2-Linux-x86_64.tar.gz"
-        mkdir -p ${DEPS_DIR}/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C ${DEPS_DIR}/cmake
+        if [[ "${TRAVIS_ARCH}" == "amd64" ]]; then
+          CMAKE_URL="https://cmake.org/files/v${CMAKE_VERSION%.*}/cmake-${CMAKE_VERSION}-Linux-x86_64.tar.gz"
+          mkdir -p ${DEPS_DIR}/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C ${DEPS_DIR}/cmake
+        fi
+        if [[ "${TRAVIS_ARCH}" = "ppc64le" ]]; then
+          # Build from source
+          CMAKE_URL="https://cmake.org/files/v${CMAKE_VERSION%.*}/cmake-${CMAKE_VERSION}.tar.gz"
+          mkdir -p ${DEPS_DIR}/cmake-source && travis_retry wget --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C ${DEPS_DIR}/cmake-source
+          (
+            cd ${DEPS_DIR}/cmake-source
+            mkdir -p build && cd build
+            ../bootstrap --prefix=${DEPS_DIR}/cmake && make -j4 install
+          )
+        fi
+      else
+        echo "CMake already found in cache"
       fi
       export PATH=${DEPS_DIR}/cmake/bin:${PATH}
+    else
+      brew upgrade cmake || brew install cmake
+      brew install openssl
+      export OPENSSL_ROOT_DIR=/usr/local/opt/openssl
     fi
     cmake --version
 
@@ -221,7 +229,7 @@ script:
   #################################################################
   - mkdir -p ${ATLAS_BUILD_DIR} && cd ${ATLAS_BUILD_DIR}
   - cmake -DCMAKE_MODULE_PATH=${ECBUILD_MODULE_PATH} ${ATLAS_CMAKE_OPTIONS} ${ATLAS_SOURCE_DIR}
-  - make -j4
+  - make -j$(nproc)
   - bin/atlas --info
 
   #################################################################

AUTHORS

@@ -0,0 +1,31 @@
+Authors
+=======
+
+- Willem Deconinck
+- Pedro Maciel
+- Tiago Quintino
+
+Thanks for contributions from
+=============================
+
+- Carlos Osuna
+- Avi Bahra
+- Andreas Mueller
+- Baudouin Raoult
+- Florian Rathgeber
+- Daan Degrauwe
+- Gianmarco Mengaldo
+- Philippe Marguinaud
+- James Hawkes
+- Mats Hamrud
+- Christian Kuehnlein
+- Rahul Mahajan
+- Olivier Iffrig
+- Iain Russell
+- Benjamin Menetrier
+- Domokos Sármány
+- Yannick Trémolet
+- Mark J. Olah
+- Michael Lange
+- Marek Wlasak
+- Peter Bispham

CHANGELOG.md

@@ -7,6 +7,28 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.22.0] - 2020-10-14
+### Fixed
+- Feature INIT_SNAN was not working
+- Support KNearestNeighbour interpolation for functionspace with
+  smaller halo than the mesh contains
+- Support array size up to size_t limit
+
+### Changed
+- Migration to use ecbuild 3.4
+- ATLAS_BITS_LOCAL can be configured to 32 or 64
+
+### Added
+- Fields can be created with given alignment, which adds padding in innermost dimension
+- Added conservative interpolation with "grid-box average" and "grid-box maximum"
+- Missing value definition for fields
+- Add support for missing values in matrix-based interpolation methods
+- Floating point trapping and signal handling mechanism
+- Fortran: GridDistribution constructors
+- Fortran: Domain access
+- Fortran: Get lonlat_bounding_box via domain
+- Possibility to access Jacobian of projections (with only some projections implemented)
+
 ## [0.21.0] - 2020-06-23
 ### Fixed
 - Fixed Rotation order of applying the rotation angle
@@ -223,6 +245,7 @@ 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
+[0.22.0]: https://github.com/ecmwf/atlas/compare/0.21.0...0.22.0
 [0.21.0]: https://github.com/ecmwf/atlas/compare/0.20.2...0.21.0
 [0.20.2]: https://github.com/ecmwf/atlas/compare/0.20.1...0.20.2
 [0.20.1]: https://github.com/ecmwf/atlas/compare/0.20.0...0.20.1

CMakeLists.txt

@@ -9,23 +9,17 @@
 ############################################################################################
 # Atlas
 
-cmake_minimum_required( VERSION 3.6 FATAL_ERROR )
-if( POLICY CMP0074 )
-  cmake_policy( SET CMP0074 NEW )
-  # This policy allows to search for packages with <package>_ROOT variables
-  #                        (only supported with CMake 3.12 and above)
-  # This policy can be removed once cmake_minimum_required( VERSION 3.12 ) is used
-endif()
+cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
 
-find_package( ecbuild 3.1.0 REQUIRED )
+find_package( ecbuild 3.4 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild )
 
 ################################################################################
 # Initialise project Atlas
 
 project( atlas LANGUAGES CXX )
 
-set( ATLAS_BITS_GLOBAL 64 ) # bits used to define a global index (atlas::gidx_t)
-set( ATLAS_BITS_LOCAL 32 )  # bits used to define a local index  (atlas::idx_t)
+set( ATLAS_BITS_GLOBAL 64 CACHE STRING "bits used to define a global index (atlas::gidx_t)" )
+set( ATLAS_BITS_LOCAL  32 CACHE STRING "bits used to define a local index (atlas::idx_t)" )
 
 ################################################################################
 # Required packages
@@ -50,7 +44,9 @@ include( features/PROJ )
 include( features/SANDBOX )
 include( features/CLANG_TIDY )
 include( features/INCLUDE_WHAT_YOU_USE )
+include( features/INIT_SNAN )
 include( features/DOCS )
+include( features/ATLAS_RUN )
 
 ################################################################################
 # sources

VERSION

@@ -1 +1 @@
-0.21.0
+0.22.0

bamboo/CLANG-env.sh

@@ -20,6 +20,6 @@ module unload libemos
 module unload metview
 module unload netcdf4
 
-module load cmake/3.10.2
+module load cmake/3.16.5
 
 module switch gnu clang

bamboo/GCC-env.sh

@@ -15,5 +15,5 @@ module unload libemos
 module unload metview
 module unload netcdf4
 
-module load cmake/3.10.2
+module load cmake/3.16.5
 module load proj/6.1.1

bamboo/INTEL-env.sh

@@ -15,6 +15,6 @@ module unload libemos
 module unload metview
 module unload netcdf4
 
-module load cmake/3.10.2
+module load cmake/3.16.5
 
 module switch gnu intel/17.0.3

cmake/features/ACC.cmake

@@ -1,7 +1,7 @@
 ### OpenACC
 
 set( ATLAS_ACC_CAPABLE FALSE )
-if( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA )
+if( HAVE_CUDA )
   if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI" )
     set( ATLAS_ACC_CAPABLE TRUE )
   endif()

cmake/features/EIGEN.cmake

@@ -1,5 +1,6 @@
 ### Eigen
 
+set( Eigen3_NO_MODULE ON )
 ecbuild_find_package( NAME Eigen3 VERSION 3.3 QUIET )
 ecbuild_add_option( FEATURE EIGEN
                     DESCRIPTION "Use Eigen linear algebra library"

cmake/features/GRIDTOOLS_STORAGE.cmake

@@ -20,12 +20,16 @@ ecbuild_add_option(
   DESCRIPTION "Arrays internally use GridTools storage layer"
   CONDITION GridTools_FOUND )
 
-if( atlas_HAVE_GRIDTOOLS_STORAGE )
+ecbuild_add_option( FEATURE CUDA
+                    DESCRIPTION "Enable CUDA support via GridTools CUDA backend"
+                    CONDITION GRIDTOOLS_HAS_BACKEND_CUDA )
+
+set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_HOST 0 )
+set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA 0 )
 
-  set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_HOST 1 )
-  set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA 0 )
+if( atlas_HAVE_GRIDTOOLS_STORAGE )
 
-  if( GRIDTOOLS_HAS_BACKEND_CUDA )
+  if( atlas_HAVE_CUDA )
 
     ecbuild_info( "GridTools found with CUDA support" )
 
@@ -48,14 +52,12 @@ if( atlas_HAVE_GRIDTOOLS_STORAGE )
       find_package( CUDA )
     endif()
 
-    set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_HOST 0 )
     set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA 1 )
-  endif()
 
-else()
+  else()
 
-  set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_HOST 0 )
-  set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA 0 )
+    set( ATLAS_GRIDTOOLS_STORAGE_BACKEND_HOST 1 )
 
-endif()
+  endif()
 
+endif()

cmake/features/INIT_SNAN.cmake

@@ -17,3 +17,23 @@ if( ${CMAKE_BUILD_TYPE} MATCHES "Debug" )
   endif()
 endif()
 
+
+cmake_push_check_state(RESET)
+include(CheckSymbolExists)
+  set(CMAKE_REQUIRED_DEFINITIONS -D_GNU_SOURCE)
+  if(UNIX)
+    set(CMAKE_REQUIRED_LIBRARIES m)
+  endif()
+  check_symbol_exists(feenableexcept "fenv.h" atlas_HAVE_FEENABLEEXCEPT)
+  check_symbol_exists(fedisableexcept "fenv.h" atlas_HAVE_FEDISABLEEXCEPT)
+  if( atlas_HAVE_FEENABLEEXCEPT )
+      set( atlas_HAVE_FEENABLEEXCEPT 1 )
+  else()
+      set( atlas_HAVE_FEENABLEEXCEPT 0 )
+  endif()
+  if( atlas_HAVE_FEDISABLEEXCEPT )
+      set( atlas_HAVE_FEDISABLEEXCEPT 1 )
+  else()
+      set( atlas_HAVE_FEDISABLEEXCEPT 0 )
+  endif()
+cmake_pop_check_state()