Merge branch 'release/0.21.0'

* release/0.21.0: (145 commits)
  Version 0.21.0
  ATLAS-300 Fix plugin install
  ATLAS-301 Support for ORCA grid patches at pole using quads
  ATLAS-300 Atlas plugin support
  Grid::footprint() API (unimplemented)
  Compatibility with eckit < 1.12
  Fix minor memory issue in test
  Increase timeout for atlas_test_fvm_nabla_validation
  travis: 300s timeout for tests
  Assertions
  Increase timeout for test
  Improve performance for debug builds with new ATLAS_ALWAYS_INLINE macro
  travis: Remove addons for osx
  travis: ATLAS_TRACE=1
  Fix clang-tidy warnings
  Use Serial partitioner in StructuredMeshGenerator if possible.
  travis: 60s timeout for tests
  Fix warnings
  Remove unused subroutine atlas_write_to_fortran_unit
  ATLAS-299 (Github #42) Factor 2 speedup in BandsDistribution by using int32_t for its arithmetics if we are sure no overflow will occur. This helps L40000x20000 with 'regular_bands' partitioner
  ...

.gitignore

@@ -4,7 +4,9 @@ CMakeLists.txt.user*
 doc/html
 doc/latex
 *.sublime-workspace
+*.swp
 .nfs*
 build/*
 install/*
 env.sh
+*.DS_Store

.travis.yml

@@ -67,13 +67,8 @@ matrix:
         - CXX_COMPILER='clang++' C_COMPILER='clang' Fortran_COMPILER='gfortran'
         - MPI=openmpi
         - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG"
+        - ATLAS_CTEST_OPTIONS="-E atlas_test_stencil_parallel_mpi16"
       osx_image: xcode10.1
-      addons:
-        homebrew:
-          packages:
-          - openmpi
-          - cgal
-          - fftw
 
     - os: osx
       env:
@@ -232,7 +227,7 @@ script:
   #################################################################
   # Test Atlas
   #################################################################
-  - ctest
+  - ATLAS_TRACE=1 ATLAS_DEBUG=1 ctest --output-on-failure --timeout 300 ${ATLAS_CTEST_OPTIONS}
 
 after_success:
 
@@ -250,5 +245,5 @@ after_success:
 after_failure:
 
   - cd ${ATLAS_BUILD_DIR}
-  - ctest -VV --rerun-failed
+  - ATLAS_TRACE=1 ctest -VV --rerun-failed --timeout 60 ${ATLAS_CTEST_OPTIONS}
   - cat ecbuild.log

CHANGELOG.md

@@ -7,11 +7,45 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
-## [0.20.2] - 2019-04-27
+## [0.21.0] - 2020-06-23
+### Fixed
+- Fixed Rotation order of applying the rotation angle
+- Fix nabla computation of surface vector fields
+- Fix registration and destruction issues of halo-exchange caches
+- Workaround Clang compiler problem with OpenMP tasking, using introspection
+- Fix bug in conversion of negative degrees to microdegrees
+- Fix problem in distribution of work amongst OpenMP threads in StructuredColumns::setup
+- Fix problem with StructuredColumns creation for grids defined with domains with negative West
+- Fix computation of Grid::lonlatBoundingBox for arbitrary projections crossing the dateline.
+
+### Changed
+- Snap LinearSpacing values to start and endpoint to allow exact comparisons
+- Improved performance and memory requirement of cropping of large StructuredGrids
+- Regional grids by default now have a positive y-numbering (previously negative).
+
+### Added
+- PolygonLocator based on functionspace partition polygons.
+- KDTree class which abstracts eckit concrete implementations, including Fortran interface
+- Geometry class with factory mechanism to configure which spheroid to use, including Fortran interface
+- StrcutredGrid function for i,j to index and inverse
+- Fortran interface to create StructuredColumns with custom distribution
+- Fortran interface to grid spec
+- Fortran interface to Projection
+- Adjoint of HaloExchange
+- Plugin mechanism to load plugins at runtime.
+- Fortran constructors for atlas_RegionalGrid
+- Fortran constructors for projected reduced Gaussian grids
+- Add copy constructor and assignment operator for atlas::vector
+- Mercator projection support for scaling, and operation on ellipsoid.
+- Grid Distribution can now also be created as a function, e.g. for Serial or Bands
+
+
+
+## [0.20.2] - 2020-04-27
 ### Fixed
 - Avoid 100ds of compilation warnings introduced in version 0.20.0
 
-## [0.20.1] - 2019-04-08
+## [0.20.1] - 2020-04-08
 ### Fixed
 - Make feature BOUNDSCHECKING work again. It was not turned on for DEBUG builds
 - Workaround clang OpenMP bug
@@ -20,7 +54,7 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 ### Added
 - atlas-grids tool can now be used to compute approximate North-South grid resolution
 
-## [0.20.0] - 2019-03-06
+## [0.20.0] - 2020-03-06
 ### Fixed
 - Pole edges hould not be created for global regular grids with points at poles
 - Update compatibility with more recent GridTools 
@@ -189,6 +223,7 @@ 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
+[0.21.0]: 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
 [0.20.0]: https://github.com/ecmwf/atlas/compare/0.20.0...0.19.2

VERSION

@@ -1 +1 @@
-0.20.2
+0.21.0

atlas-import.cmake.in

@@ -80,3 +80,31 @@ elseif( atlas_FIND_REQUIRED_FORTRAN )
 endif()
 
 set( @PROJECT_NAME@_DIR ${CMAKE_CURRENT_LIST_DIR} CACHE STRING "" )
+
+
+function( atlas_create_plugin name )
+
+  set( options )
+  set( single_value_args VERSION )
+  set( multi_value_args LIBRARY )
+  cmake_parse_arguments( _PAR "${options}" "${single_value_args}" "${multi_value_args}"  ${_FIRST_ARG} ${ARGN} )
+
+  set( _plugin_file share/atlas/plugins/${name}.yml )
+
+  if( NOT DEFINED _PAR_VERSION )
+    set( _version ${${PROJECT_NAME}_VERSION} )
+  else()
+    set( _version ${_PAR_VERSION} )
+  endif()
+  if( NOT DEFINED _PAR_LIBRARY )
+    set( _library "${name}" )
+  else()
+    set( _library "${_PAR_LIBRARY}" )
+  endif()
+  file( WRITE  ${CMAKE_BINARY_DIR}/${_plugin_file} "name: ${name}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "version: ${_version}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "library: ${_library}" )
+  install( FILES ${CMAKE_BINARY_DIR}/${_plugin_file} DESTINATION share/atlas/plugins )
+
+endfunction()
+

cmake/features/DOCS.cmake

@@ -1,9 +1,9 @@
 ################################################################################
 # documentation
-if( ENABLE_DOCS ) 
-  find_package(Latex)
+if( ENABLE_DOCS )
+  find_package(LATEX COMPONENTS PDFLATEX BIBTEX OPTIONAL_COMPONENTS MAKEINDEX HTLATEX)
 endif()
 ecbuild_add_option( FEATURE DOCS
                     DESCRIPTION "Atlas documentation"
                     DEFAULT OFF
-                    CONDITION Latex_FOUND )
+                    CONDITION LATEX_FOUND )

cmake/features/OMP.cmake

@@ -22,3 +22,38 @@ endif()
 if( TARGET OpenMP::OpenMP_Fortran )
   set( OMP_Fortran OpenMP::OpenMP_Fortran )
 endif()
+
+if( HAVE_OMP_CXX )
+
+  if( NOT CMAKE_CXX_COMPILER_ID MATCHES Clang )
+    set( ATLAS_OMP_TASK_UNTIED_SUPPORTED 1 )
+  endif()
+
+  if( NOT DEFINED ATLAS_OMP_TASK_UNTIED_SUPPORTED )
+    try_run( execute_result compile_result 
+                     ${CMAKE_CURRENT_BINARY_DIR}
+                     ${PROJECT_SOURCE_DIR}/cmake/features/OMP/test_omp_untied.cc
+                     LINK_LIBRARIES ${OMP_CXX}
+                     COMPILE_OUTPUT_VARIABLE compile_output
+                     RUN_OUTPUT_VARIABLE execute_output )
+
+    ecbuild_debug("Compiling and running ${PROJECT_SOURCE_DIR}/cmake/features/OMP/test_omp_untied.cc")
+    ecbuild_debug_var( compile_result )
+    ecbuild_debug_var( compile_output )
+    ecbuild_debug_var( execute_result )
+    ecbuild_debug_var( execute_output )
+
+    if( compile_result )
+      if( execute_result MATCHES 0 )
+        set( ATLAS_OMP_TASK_UNTIED_SUPPORTED 1 )
+      else()
+        ecbuild_info("    Compiler failed to run program with omp pragma with 'untied if' construct."
+                     "Workaround will be enabled.")
+        set( ATLAS_OMP_TASK_UNTIED_SUPPORTED 0 )
+      endif()
+    else() 
+      set( ATLAS_OMP_TASK_UNTIED_SUPPORTED 0 )
+    endif()
+  endif()
+
+endif()

cmake/features/OMP/test_omp_untied.cc

@@ -0,0 +1,51 @@
+/*
+ * (C) Copyright 2013 ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+// This test mirrors functionality from src/atlas/parallel/omp/sort.h
+// It appears that on some installations / compilers the "untied if" in the
+// openmp pragma compiles but leads to runtime errors. This executable is
+// added to allow compiler introspection for this feature.
+
+#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)
+        auto mid = begin + size / 2;
+        {
+#pragma omp task shared( iterator ) untied if ( size >= ( 1 << 15 ) )
+            merge_sort_recursive( iterator, begin, mid );
+#pragma omp task shared( iterator ) untied if ( size >= ( 1 << 15 ) )
+            merge_sort_recursive( iterator, mid, end );
+#pragma omp taskwait
+        }
+        std::inplace_merge( iterator + begin, iterator + mid, iterator + end );
+    }
+    else {
+        std::sort( iterator + begin, iterator + end );
+    }
+}
+
+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 ) );
+}
+
+int main() {
+    auto integers = std::vector<int>(8);
+    omp_sort( integers.begin(), integers.end() );
+    return 0;
+}

doc/CMakeLists.txt

@@ -39,9 +39,11 @@ add_custom_target(atlas_doc_pdf)
 add_dependencies (atlas_doc_pdf
                   atlas-user-guide-pdf )
 
-add_custom_target(atlas_doc_html)
-add_dependencies (atlas_doc_html
-                  atlas-user-guide-html )
+if( LATEX_HTLATEX_FOUND )
+  add_custom_target(atlas_doc_html)
+  add_dependencies (atlas_doc_html
+                    atlas-user-guide-html )
+endif()
 
 add_custom_target(atlas_doc)
 add_dependencies (atlas_doc
@@ -63,27 +65,27 @@ if( NOT DEFINED ATLAS_DOC_VERSION )
 endif()
 
 if( NOT DEFINED ATLAS_DOXYGEN_GENERATOR )
-  set( ATLAS_DOXYGEN_GENERATOR "m.css")
+  set( ATLAS_DOXYGEN_GENERATOR "stock")
 endif()
 
 if( ATLAS_DOXYGEN_GENERATOR STREQUAL "m.css" )
-  if( NOT DEFINED ATLAS_DOXYGEN_EXECUTABLE )
-    set( ATLAS_DOXYGEN_EXECUTABLE doxygen.py )
-  endif()
   set( ATLAS_DOXYFILE Doxyfile-mcss )
+  set( ATLAS_DOXYGEN_EXECUTABLE doxygen.py )
 else()
-  if( NOT DEFINED ATLAS_DOXYGEN_EXECUTABLE )
-    if( DOXYGEN_EXECUTABLE )
-      set( ATLAS_DOXYGEN_EXECUTABLE ${DOXYGEN_EXECUTABLE} )
-    else()
-      set( ATLAS_DOXYGEN_EXECUTABLE doxygen )
-    endif()    
-  endif()
   set( ATLAS_DOXYFILE Doxyfile-stock )
 endif()
 
+if( NOT DEFINED ATLAS_DOXYGEN_EXECUTABLE )
+  find_package(Doxygen COMPONENTS dot)
+  if( DOXYGEN_FOUND )
+    set( ATLAS_DOXYGEN_EXECUTABLE ${DOXYGEN_EXECUTABLE} )
+  else()
+    set( ATLAS_DOXYGEN_EXECUTABLE doxygen )
+  endif()
+endif()
+
 foreach( doxyfile Doxyfile-default Doxyfile-custom Doxyfile-mcss Doxyfile-stock )
-  execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink 
+  execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink
       ${CMAKE_CURRENT_SOURCE_DIR}/${doxyfile}
       ${CMAKE_CURRENT_BINARY_DIR}/${doxyfile} )
 endforeach()

doc/example-grids/regional_lambert_azimuthal_equal_area_1.yml

@@ -15,5 +15,9 @@ check :
   size : 2000
   lonlat(first) : [-10.4643,40.1877]
   lonlat(last)  : [24.6228,57.1968]
-  uid : 16663e1f4f3deb724712dd2698008915
-  bounding_box(n,w,s,e) : [58.7776,-16.6238,40.1867,24.6238]
+  uid : 0ee521e7f37c21d50b2f66655f178b65
+  bounding_box(n,w,s,e) : [58.7766,-16.6228,40.1877,24.6228]
+  xmin : -1225000.00
+  ymin : -975000.00
+  proj : "+proj=laea +lat_0=50 +lon_0=4 +R=6371229.0"
+

doc/example-grids/regional_lambert_azimuthal_equal_area_2.yml

@@ -22,7 +22,9 @@ check :
   size : 950000
   lonlat(first) : [-35.034,66.9821]
   lonlat(last)  : [41.2436,23.8962]
-  bounding_box(n,w,s,e) : [72.647, -35.035, 23.895, 74.144]
-  uid : 2ef4f1bb005cf8e24ecc9464f8b7e089
+  bounding_box(n,w,s,e) : [72.6459, -35.034, 23.8962, 74.1431]
+  uid : 92fd7b766b66cce3829ce1b0af3bac15
   xmin : 2510375.79
   ymin : 748404.45
+  proj : "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +R=6371229.0"
+

doc/example-grids/regional_lambert_azimuthal_equal_area_3.yml

@@ -20,7 +20,7 @@ check :
   size : 950000
   lonlat(first) : [-35.034,66.9821]
   lonlat(last)  : [41.2436,23.8962]
-  bounding_box(n,w,s,e) : [72.647, -35.035, 23.895, 74.144]
-  uid : cc74ce2b099e3ae15f2f9f9caf52ddda
+  bounding_box(n,w,s,e) : [72.6459, -35.034, 23.8962, 74.1431]
+  uid : 7e489e060265f549856481f44d001c69
   xmin : 2510375.79
   ymin : 748404.45

doc/example-grids/regional_lambert_azimuthal_equal_area_4.yml

@@ -20,7 +20,7 @@ check :
   size : 950000
   lonlat(first) : [-35.034,66.9821]
   lonlat(last)  : [41.1397,23.9423]
-  bounding_box(n,w,s,e) : [72.6426, -35.035, 23.9413, 73.9386]
-  uid : bd42a9d7bbf089251667a4cc553a664c
+  bounding_box(n,w,s,e) : [72.6416, -35.034, 23.9423, 73.9376]
+  uid : dba9a7e48d9a5274ece3aea98335b6f0
   xmin : 2502497.60
   ymin : 752495.56

doc/example-grids/regional_lambert_conformal_conic_1.yml

@@ -8,15 +8,15 @@ lonlat(centre) : [4,50]
 projection :
     type : "lambert_conformal_conic"
     longitude0 : 4
-    latitude1  : 50
+    latitude0  : 50
 
 y_numbering : +1
 
 check : 
   size : 2000
   lonlat(first) : [-10.3173,40.22]
   lonlat(last)  : [24.4368,57.2335]
-  uid : 2e01d66aa6df870b0ad346da4e80c4ff
-  bounding_box(n,w,s,e) : [58.7333,-16.4378,40.219,24.4378]
+  uid : 0914f1a75b5c5226e2b09ceed834a822
+  bounding_box(n,w,s,e) : [58.7320,-16.4368,40.2200,24.4368]
   xmin : -1225000.00
   ymin : -975000.00