Merge branch 'release/0.23.0'

* release/0.23.0: (44 commits) Update CHANGELOG.md Fixes for Cray 8.5 Version 0.23.0 clang-format ATLAS-301 [sandbox] atlas-parallel-interpolation: add 'fixup' option ATLAS-301 [sandbox] atlas-parallel-interpolation: Use default meshgenerator specified by grid ATLAS-301 atlas-meshgen: --fixup option e.g for ORCA grid custom fixes ATLAS-301 Gmsh output only non-missing values ATLAS-301 Do not add INVALID elements to kdtree ATLAS-301 Add INVALID topology flag ATLAS-301 Use new eckit Plugin system, requires eckit 1.15.0 ATLAS-315 Normalise target grid longitudes to source grid in StructuredInterpolation2D ATLAS-318 cleanup ATLAS-318 Example use of sparse_matrix_multiply in test_interpolation_finite_element_cached to do the interpolation manually ATLAS-318 atlas::linalg::sparse_matrix_multiply to abstract different implementations ATLAS-321 Implement eckit::KDTree::size() useful to compute KDTree memory footprint() ATLAS-321 Interpolation IndexKDTreeCache and use it within GridBoxAverage ATLAS-321 Interpolation MatrixCache and use it with FiniteElement Avoid costly polygon tests in case mpi::size() == 1 ATLAS_TRACE_MEMORY=1 to enable logging of some memory usage, also requires ATLAS_TRACE=1 ...
ecmwf · Jan 19, 2021 · 7e0a125 · 7e0a125
2 parents e55e9c7 + 31a3b26
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,17 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.23.0] - 2021-01-19
+### Fixed
+- Structured interpolation method interpolating to area straddling Greenwich.
+- Fixes when compiling with ATLAS_BITS_LOCAL=64
+
+### Changed
+- Possibility to link to alternative open-source version of IFS trans library.
+
+### Added
+- Caching mechanism for interpolation
+
 ## [0.22.1] - 2020-10-22
 ### Fixed
 - Installation of PGI compilers via tools/install-pgi.sh
@@ -250,6 +261,7 @@ 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
+[0.23.0]: https://github.com/ecmwf/atlas/compare/0.22.1...0.23.0
 [0.22.1]: https://github.com/ecmwf/atlas/compare/0.22.0...0.22.1
 [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

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -24,7 +24,7 @@ set( ATLAS_BITS_LOCAL  32 CACHE STRING "bits used to define a local index (atlas
 ################################################################################
 # Required packages
 
-ecbuild_find_package( NAME eckit VERSION 1.4.0 REQUIRED )
+ecbuild_find_package( NAME eckit VERSION 1.15.0 REQUIRED )
 ecbuild_debug( "   eckit_FEATURES : [${eckit_FEATURES}]" )
 
 ################################################################################

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.22.1
+0.23.0
diff --git a/cmake/atlas-import.cmake.in b/cmake/atlas-import.cmake.in
@@ -64,7 +64,12 @@ endif()
 
 ## transi
 if( atlas_HAVE_TRANS AND atlas_REQUIRES_PRIVATE_DEPENDENCIES )
-    find_dependency( transi HINTS ${CMAKE_CURRENT_LIST_DIR}/../transi @transi_DIR@ @transi_BINARY_DIR@ )
+    set( transi_DIR @transi_DIR@ )
+    if( transi_DIR )
+        find_dependency( transi HINTS ${CMAKE_CURRENT_LIST_DIR}/../transi @transi_DIR@ )
+    else()
+        find_dependency( trans COMPONENTS transi double HINTS ${CMAKE_CURRENT_LIST_DIR}/../trans @trans_DIR@ )
+    endif()
 endif()
 
 ## CGAL
@@ -86,11 +91,11 @@ 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 )
+  set( single_value_args VERSION LIBRARY URL NAMESPACE)
+  set( multi_value_args )
   cmake_parse_arguments( _PAR "${options}" "${single_value_args}" "${multi_value_args}"  ${_FIRST_ARG} ${ARGN} )
 
-  set( _plugin_file share/atlas/plugins/${name}.yml )
+  set( _plugin_file share/plugins/${name}.yml )
 
   if( NOT DEFINED _PAR_VERSION )
     set( _version ${${PROJECT_NAME}_VERSION} )
@@ -102,10 +107,23 @@ function( atlas_create_plugin 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 )
+  if( NOT DEFINED _PAR_URL )
+      set( _url "http://www.ecmwf.int" )
+  else()
+      set( _url ${_PAR_URL} )
+  endif()
+  if( NOT DEFINED _PAR_NAMESPACE )
+      set( _namespace "int.ecmwf" )
+  else()
+      set( _namespace ${_PAR_NAMESPACE} )
+  endif()
 
-endfunction()
+  file( WRITE  ${CMAKE_BINARY_DIR}/${_plugin_file} "plugin:\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "  name:      ${name}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "  namespace: ${_namespace}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "  url:       ${_url}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "  version:   ${_version}\n" )
+  file( APPEND ${CMAKE_BINARY_DIR}/${_plugin_file} "  library:   ${_library}\n" )
 
+  install( FILES ${CMAKE_BINARY_DIR}/${_plugin_file} DESTINATION share/plugins )
+endfunction()
diff --git a/cmake/features/OMP.cmake b/cmake/features/OMP.cmake
@@ -1,11 +1,5 @@
 ### OMP ...
-if( "${CMAKE_VERSION}" VERSION_LESS "3.11" )
-  if( ENABLE_OMP )
-    ecbuild_warn( "OpenMP only supported with CMake 3.11 onwards" )
-  endif()
-else()
-  find_package( OpenMP COMPONENTS CXX ${Fortran} )
-endif()
+find_package( OpenMP COMPONENTS CXX ${Fortran} )
 ecbuild_add_option( FEATURE OMP
                     DESCRIPTION "support for OpenMP shared memory parallelism"
                     CONDITION OpenMP_Fortran_FOUND OR OpenMP_CXX_FOUND )
@@ -56,4 +50,4 @@ if( HAVE_OMP_CXX )
     endif()
   endif()
 
-endif()
+endif()
diff --git a/cmake/features/TRANS.cmake b/cmake/features/TRANS.cmake
@@ -1,6 +1,21 @@
 ### trans ...
 
-ecbuild_find_package( NAME transi VERSION 0.4.4 QUIET )
+if( ENABLE_TRANS OR NOT DEFINED ENABLE_TRANS )
+    find_package( trans 47.2 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()
+    else()
+        find_package( transi 0.8 QUIET )
+    endif()
+endif()
+
 ecbuild_add_option( FEATURE TRANS
-                    DESCRIPTION "Support for spectral transforms"
+                    DESCRIPTION "Support for IFS spectral transforms"
                     CONDITION transi_FOUND )
diff --git a/doc/example-projects/README b/doc/example-projects/README
@@ -1,5 +1,5 @@
 
 Usage:
 
-    atlas_DIR=<path-to-install-or-build-tree> ./build_hello_world.sh
+    atlas_ROOT=<path-to-install-or-build-tree> ./build_hello_world.sh
 
diff --git a/doc/example-projects/project_hello_world/CMakeLists.txt b/doc/example-projects/project_hello_world/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.6 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 project( hello_world VERSION 0.0.0 LANGUAGES CXX )
 

diff --git a/doc/example-projects/project_hello_world_fortran/CMakeLists.txt b/doc/example-projects/project_hello_world_fortran/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.6 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.12 FATAL_ERROR)
 
 project( hello_world VERSION 0.0.0 LANGUAGES Fortran )
 

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -69,6 +69,9 @@ if( CMAKE_BUILD_TYPE MATCHES "Debug" )
   set( atlas_BUILD_TYPE_DEBUG 1 )
 endif()
 
+ecbuild_parse_version( ${eckit_VERSION} PREFIX ATLAS_ECKIT )
+math( EXPR ATLAS_ECKIT_VERSION_INT "( 10000 * ${ATLAS_ECKIT_VERSION_MAJOR} ) + ( 100 * ${ATLAS_ECKIT_VERSION_MINOR} ) + ${ATLAS_ECKIT_VERSION_PATCH}" )
+
 add_subdirectory( atlas_acc_support )
 
 add_subdirectory( atlas )

diff --git a/src/apps/atlas-meshgen.cc b/src/apps/atlas-meshgen.cc
@@ -66,7 +66,11 @@ MeshGenerator make_meshgenerator( const Grid& grid, const AtlasTool::Args& args
         config.set( "3d", false );
     }
 
-    config.set( "patch_pole", args.getBool( "patch_pole", false ) );
+    config.set( "include_pole", args.getBool( "include-pole", false ) );
+    config.set( "patch_pole", args.getBool( "patch-pole", false ) );
+    if ( args.has( "fixup" ) ) {
+        config.set( "fixup", args.getBool( "fixup" ) );
+    }
 
     return MeshGenerator{config};
 }
@@ -131,8 +135,8 @@ Meshgen2Gmsh::Meshgen2Gmsh( int argc, char** argv ) : AtlasTool( argc, argv ) {
         "partitioner", "Mesh partitioner [equal_regions,checkerboard,equal_bands,regular_bands" ) );
 
     add_option( new Separator( "Options for `--generator=structured`" ) );
-    add_option( new SimpleOption<bool>( "include_pole", "Include pole point" ) );
-    add_option( new SimpleOption<bool>( "patch_pole", "Patch poles with elements." ) );
+    add_option( new SimpleOption<bool>( "include-pole", "Include pole point" ) );
+    add_option( new SimpleOption<bool>( "patch-pole", "Patch poles with elements." ) );
     add_option( new SimpleOption<double>(
         "angle", "Maximum element-edge slant deviation from meridian in degrees. \n" + indent() +
                      "     Value range between 0 and 30\n" + indent() +
@@ -156,6 +160,7 @@ Meshgen2Gmsh::Meshgen2Gmsh( int argc, char** argv ) : AtlasTool( argc, argv ) {
         "water", "Output elements containing water points (not specifying --water or --land enables both)" ) );
     add_option( new SimpleOption<bool>(
         "land", "Output elements containing land points (not specifying --water or --land enables both)" ) );
+    add_option( new SimpleOption<bool>( "fixup", "Apply custom fixes to the mesh where it applies" ) );
 }
 
 //-----------------------------------------------------------------------------

diff --git a/src/atlas/CMakeLists.txt b/src/atlas/CMakeLists.txt
@@ -143,6 +143,8 @@ grid/detail/grid/LonLat.h
 grid/detail/grid/LonLat.cc
 grid/detail/grid/Regional.h
 grid/detail/grid/Regional.cc
+grid/detail/grid/Healpix.h
+grid/detail/grid/Healpix.cc
 
 grid/detail/distribution/DistributionImpl.h
 grid/detail/distribution/DistributionImpl.cc
@@ -350,6 +352,8 @@ meshgenerator/detail/MeshGeneratorImpl.cc
 meshgenerator/detail/MeshGeneratorImpl.h
 meshgenerator/detail/MeshGeneratorInterface.cc
 meshgenerator/detail/MeshGeneratorInterface.h
+meshgenerator/detail/HealpixMeshGenerator.h
+meshgenerator/detail/HealpixMeshGenerator.cc
 )
 
 list( APPEND atlas_output_srcs
@@ -477,6 +481,8 @@ endif()
 
 list( APPEND atlas_interpolation_srcs
 interpolation.h
+interpolation/Cache.cc
+interpolation/Cache.h
 interpolation/Interpolation.cc
 interpolation/Interpolation.h
 interpolation/NonLinear.cc
@@ -546,6 +552,18 @@ interpolation/nonlinear/Missing.cc
 interpolation/nonlinear/Missing.h
 interpolation/nonlinear/NonLinear.cc
 interpolation/nonlinear/NonLinear.h
+
+linalg/Indexing.h
+linalg/Introspection.h
+linalg/View.h
+linalg/sparse.h
+linalg/sparse/Backend.h
+linalg/sparse/Backend.cc
+linalg/sparse/SparseMatrixMultiply.h
+linalg/sparse/SparseMatrixMultiply_EckitLinalg.h
+linalg/sparse/SparseMatrixMultiply_EckitLinalg.cc
+linalg/sparse/SparseMatrixMultiply_OpenMP.h
+linalg/sparse/SparseMatrixMultiply_OpenMP.cc
 )
 
 

diff --git a/src/atlas/array/helpers/ArraySlicer.h b/src/atlas/array/helpers/ArraySlicer.h
@@ -149,37 +149,39 @@ class ArraySlicer {
     };
 
     template <typename Int>
-    static int offset_part( View& view, int& i_view, Int idx ) {
+    static idx_t offset_part( View& view, int& i_view, Int idx ) {
         return idx * view.stride( i_view++ );
     }
 
-    static int offset_part( View& view, int& i_view, Range range ) { return range.start() * view.stride( i_view++ ); }
+    static idx_t offset_part( View& view, int& i_view, Range range ) { return range.start() * view.stride( i_view++ ); }
 
-    static int offset_part( View& view, int& i_view, RangeAll range ) {
+    static idx_t offset_part( View& view, int& i_view, RangeAll range ) {
         return range.start() * view.stride( i_view++ );
     }
 
-    static int offset_part( View& view, int& i_view, RangeTo range ) { return range.start() * view.stride( i_view++ ); }
+    static idx_t offset_part( View& view, int& i_view, RangeTo range ) {
+        return range.start() * view.stride( i_view++ );
+    }
 
-    static int offset_part( View& view, int& i_view, RangeFrom range ) {
+    static idx_t offset_part( View& view, int& i_view, RangeFrom range ) {
         return range.start() * view.stride( i_view++ );
     }
 
-    static int offset_part( View&, int& /*i_view*/, RangeDummy ) { return 0; }
+    static idx_t offset_part( View&, int& /*i_view*/, RangeDummy ) { return 0; }
 
     template <int Dim, typename Int, typename... Ints>
-    static int offset_remaining( View& view, int& i_view, const Int idx, const Ints... next_idx ) {
-        const int p = offset_part( view, i_view, idx );
+    static idx_t offset_remaining( View& view, int& i_view, const Int idx, const Ints... next_idx ) {
+        const idx_t p = offset_part( view, i_view, idx );
         return p + offset_remaining<Dim + 1>( view, i_view, next_idx... );
     }
 
     template <int Dim, typename Int>
-    static int offset_remaining( View& view, int& i_view, const Int last_idx ) {
+    static idx_t offset_remaining( View& view, int& i_view, const Int last_idx ) {
         return offset_part( view, i_view, last_idx );
     }
 
     template <typename... Args>
-    static int offset( View& view, const Args... args ) {
+    static idx_t offset( View& view, const Args... args ) {
         int i_view( 0 );
         return offset_remaining<0>( view, i_view, args... );
     }

diff --git a/src/atlas/array/native/NativeDataStore.h b/src/atlas/array/native/NativeDataStore.h
@@ -17,6 +17,7 @@
 #include <sstream>
 
 #include "atlas/array/ArrayUtil.h"
+#include "atlas/library/Library.h"
 #include "atlas/library/config.h"
 #include "atlas/runtime/Exception.h"
 #include "atlas/runtime/Log.h"
@@ -39,14 +40,18 @@ struct MemoryHighWatermark {
     MemoryHighWatermark& operator+=( const size_t& bytes ) {
         bytes_ += bytes;
         update_maximum();
-        Log::trace() << "Memory: " << eckit::Bytes( double( bytes_ ) ) << "\t( +" << eckit::Bytes( double( bytes ) )
-                     << " \t| high watermark " << eckit::Bytes( double( high_ ) ) << "\t)" << std::endl;
+        if ( atlas::Library::instance().traceMemory() ) {
+            Log::trace() << "Memory: " << eckit::Bytes( double( bytes_ ) ) << "\t( +" << eckit::Bytes( double( bytes ) )
+                         << " \t| high watermark " << eckit::Bytes( double( high_ ) ) << "\t)" << std::endl;
+        }
         return *this;
     }
     MemoryHighWatermark& operator-=( const size_t& bytes ) {
         bytes_ -= bytes;
-        Log::trace() << "Memory: " << eckit::Bytes( double( bytes_ ) ) << "\t( -" << eckit::Bytes( double( bytes ) )
-                     << " \t| high watermark " << eckit::Bytes( double( high_ ) ) << "\t)" << std::endl;
+        if ( atlas::Library::instance().traceMemory() ) {
+            Log::trace() << "Memory: " << eckit::Bytes( double( bytes_ ) ) << "\t( -" << eckit::Bytes( double( bytes ) )
+                         << " \t| high watermark " << eckit::Bytes( double( high_ ) ) << "\t)" << std::endl;
+        }
         return *this;
     }
 
@@ -125,20 +130,27 @@ class DataStore : public ArrayDataStore {
     }
 
     void alloc_aligned( Value*& ptr, size_t n ) {
-        const size_t alignment = 64 * sizeof( Value );
-        size_t bytes           = sizeof( Value ) * n;
-        MemoryHighWatermark::instance() += bytes;
-
-        int err = posix_memalign( (void**)&ptr, alignment, bytes );
-        if ( err ) {
-            throw_AllocationFailed( bytes, Here() );
+        if ( n > 0 ) {
+            const size_t alignment = 64 * sizeof( Value );
+            size_t bytes           = sizeof( Value ) * n;
+            MemoryHighWatermark::instance() += bytes;
+
+            int err = posix_memalign( (void**)&ptr, alignment, bytes );
+            if ( err ) {
+                throw_AllocationFailed( bytes, Here() );
+            }
+        }
+        else {
+            ptr = nullptr;
         }
     }
 
     void free_aligned( Value*& ptr ) {
-        free( ptr );
-        ptr = nullptr;
-        MemoryHighWatermark::instance() -= footprint();
+        if ( size_ ) {
+            free( ptr );
+            ptr = nullptr;
+            MemoryHighWatermark::instance() -= footprint();
+        }
     }
 
     size_t footprint() const { return sizeof( Value ) * size_; }

diff --git a/src/atlas/functionspace/detail/StructuredColumns_setup.cc b/src/atlas/functionspace/detail/StructuredColumns_setup.cc
@@ -251,10 +251,12 @@ void StructuredColumns::setup( const grid::Distribution& distribution, const eck
     compute_j = [this, &compute_j, &periodic_y]( idx_t j ) -> idx_t {
         if ( periodic_y ) {
             const idx_t ny = grid_->ny();
-            while ( j < 0 )
+            while ( j < 0 ) {
                 j += ny;
-            while ( j >= ny )
+            }
+            while ( j >= ny ) {
                 j -= ny;
+            }
         }
         else {
             if ( j < 0 ) {
@@ -319,12 +321,13 @@ void StructuredColumns::setup( const grid::Distribution& distribution, const eck
         gidx_t g;
         jj = compute_j( j );
         ii = compute_i( i, jj );
-        if ( !periodic_y )
+        if ( !periodic_y ) {
             if ( jj != j ) {
                 ATLAS_ASSERT( grid_->nx( jj ) % 2 == 0 );  // assert even number of points
                 ii = ( ii < grid_->nx( jj ) / 2 ) ? ii + grid_->nx( jj ) / 2
                                                   : ( ii >= grid_->nx( jj ) / 2 ) ? ii - grid_->nx( jj ) / 2 : ii;
             }
+        }
         g = global_offsets[jj] + ii + 1;
         return g;
     };