Merge remote-tracking branch 'ecmwf/develop' into bugfix/qhull

.github/workflows/build.yml

@@ -121,11 +121,11 @@ jobs:
 
           - name: macos
             # Xcode compiler requires empty environment variables, so we pass null (~) here
-            os: macos-12
-            compiler: clang-14
+            os: macos-14
+            compiler: clang-15
             compiler_cc: ~
             compiler_cxx: ~
-            compiler_fc: gfortran-11
+            compiler_fc: gfortran-13
             caching: true
             coverage: false
             cmake_options: -DMPI_SLOTS=4

.github/workflows/ci.yml

@@ -73,3 +73,20 @@ jobs:
           repository: private-downstream-ci
           event_type: downstream-ci-hpc
           payload: '{"atlas": "ecmwf/atlas@${{ github.event.pull_request.head.sha || github.sha }}"}'
+
+
+  notify:
+    runs-on: ubuntu-latest
+    needs:
+      - downstream-ci
+      - private-downstream-ci
+      - downstream-ci-hpc
+      - private-downstream-ci-hpc
+    if: ${{ always() && !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
+    steps:
+      - name: Trigger Teams notification
+        uses: ecmwf-actions/notify-teams@v1
+        with:
+          incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}
+          needs_context: ${{ toJSON(needs) }}
+

.github/workflows/notify-new-issue.yml

@@ -0,0 +1,15 @@
+name: Notify new issue
+
+on:
+  issues:
+    types:
+      - "opened"
+
+jobs:
+  notify:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Notify new issue
+        uses: ecmwf-actions/notify-teams-issue@v1
+        with:
+          incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}

.github/workflows/notify-new-pr.yml

@@ -0,0 +1,16 @@
+name: Notify new PR
+
+# Needs the worklow to be located in the branche the PR is merged to
+on:
+  pull_request_target:
+    types:
+      - "opened"
+
+jobs:
+  notify:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Notify new PR
+        uses: ecmwf-actions/notify-teams-pr@v1
+        with:
+          incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}

CHANGELOG.md

@@ -7,6 +7,43 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.39.0] - 2024-09-18
+
+### Added
+- Add HIC abstraction layer for HIP and CUDA by @wdeconinck in https://github.com/ecmwf/atlas/pull/219
+- Support for HIP via HIC
+- Add regional interpolation by @benjaminmenetrier in https://github.com/ecmwf/atlas/pull/215
+- Pack vector components into higher-rank vector fields. by @odlomax in https://github.com/ecmwf/atlas/pull/218
+
+### Fixed
+- Fix missing header in FieldImpl.h by @tehrengruber in https://github.com/ecmwf/atlas/pull/214
+- Bug fixes to vector interpolation with StructuredColumns and spherical vector interpolation by @MarekWlasak in https://github.com/ecmwf/atlas/pull/222
+
+
+## [0.38.1] - 2024-07-15
+
+### Fixed
+- Compilation and running with NAG compiler
+- Wrap out-of-bounds source cells into the domain (#211)
+
+## [0.38.0] - 2024-06-20
+
+### Added
+- Make non_linear interpolation independent of a chosen value type by @wdeconinck in https://github.com/ecmwf/atlas/pull/176
+- Procedure to carry out a regridding from high to low resolution (binning) by @mo-lormi in https://github.com/ecmwf/atlas/pull/191
+- Add Fortran interface for node-to-edge connectivity building by @benjaminmenetrier in https://github.com/ecmwf/atlas/pull/209
+- CUDA/OpenACC capable fields with Native storage backend  @sbrdar and @wdeconinck in https://github.com/ecmwf/atlas/pull/182
+
+### Changed
+- Make non_linear interpolation independent of a chosen value type by @wdeconinck in https://github.com/ecmwf/atlas/pull/176
+
+### Fixed
+- Remove float in Triag2D intersection algorithm by @fmahebert in https://github.com/ecmwf/atlas/pull/203
+- Allow zero-sized interpolation target functionspace by @odlomax in https://github.com/ecmwf/atlas/pull/206
+- Made sure cubed-sphere interpolation method always sets metadata. by @odlomax in https://github.com/ecmwf/atlas/pull/208
+- Avoid silent errors accessing Fieldset fields by ambiguous names by @wdeconinck in https://github.com/ecmwf/atlas/pull/210
+- Fixes opposite pole coordinates by @benjaminmenetrier in https://github.com/ecmwf/atlas/pull/202
+
 ## [0.37.0] - 2024-04-09
 ### Added
 - Add SphericalVector interpolation method using parallel transport (#163)
@@ -527,6 +564,9 @@ Fix StructuredInterpolation2D with retry for failed stencils
 ## 0.13.0 - 2018-02-16
 
 [Unreleased]: https://github.com/ecmwf/atlas/compare/master...develop
+[0.39.0]: https://github.com/ecmwf/atlas/compare/0.38.1...0.39.0
+[0.38.1]: https://github.com/ecmwf/atlas/compare/0.38.0...0.38.1
+[0.38.0]: https://github.com/ecmwf/atlas/compare/0.37.0...0.38.0
 [0.37.0]: https://github.com/ecmwf/atlas/compare/0.36.0...0.37.0
 [0.36.0]: https://github.com/ecmwf/atlas/compare/0.35.1...0.36.0
 [0.35.1]: https://github.com/ecmwf/atlas/compare/0.35.0...0.35.1

CMakeLists.txt

@@ -64,6 +64,16 @@ 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 )
 
+if (DEFINED ATLAS_ENABLE_CUDA AND NOT DEFINED HIC_ENABLE_CUDA )
+  set( HIC_ENABLE_CUDA ${ATLAS_ENABLE_CUDA} )
+endif()
+if (DEFINED ATLAS_ENABLE_HIP AND NOT DEFINED HIC_ENABLE_HIP )
+  set( HIC_ENABLE_HIP ${ATLAS_ENABLE_HIP} )
+endif()
+
+add_subdirectory( hic )
+find_package(hic)
+
 
 include( features/BOUNDSCHECKING )
 include( features/FORTRAN )

VERSION

@@ -1 +1 @@
-0.37.0
+0.39.0

cmake/atlas-import.cmake.in

@@ -23,6 +23,7 @@ if( atlas_HAVE_FORTRAN )
 endif()
 
 find_dependency( atlas_io HINTS ${CMAKE_CURRENT_LIST_DIR}/../atlas_io @atlas_io_DIR@ @atlas_io_BINARY_DIR@ )
+find_dependency( hic HINTS ${CMAKE_CURRENT_LIST_DIR}/../hic @hic_DIR@ @hic_BINARY_DIR@ )
 
 ## Eigen3
 set( Eigen3_HINT @Eigen3_DIR@ )

cmake/atlas_compile_flags.cmake

@@ -11,8 +11,9 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 if( CMAKE_CXX_COMPILER_ID MATCHES Cray )
 
-
-  ecbuild_add_cxx_flags("-hnomessage=3140" NAME atlas_cxx_disable_warnings ) # colon separated numbers
+  if( NOT CMAKE_CXX_COMPILER_ID MATCHES CrayClang )
+    ecbuild_add_cxx_flags("-hnomessage=3140" NAME atlas_cxx_disable_warnings ) # colon separated numbers
+  endif()
   ecbuild_add_fortran_flags("-hnomessage=3140" NAME atlas_fortran_disable_warnings ) # colon separated numbers
 
 # CC-3140 crayc++: WARNING File = atlas/functionspace/NodeColumns.cc, Line = 1, Column = 1

cmake/atlas_host_device.cmake

@@ -6,7 +6,7 @@
 # granted to it by virtue of its status as an intergovernmental organisation nor
 # does it submit to any jurisdiction.
 
-function( create_cuda_wrapper variable )
+function( create_hic_wrapper variable )
   set( options "" )
   set( single_value_args SOURCE )
   set( multi_value_args "" )
@@ -17,18 +17,24 @@ function( create_cuda_wrapper variable )
   get_filename_component(name      ${_PAR_SOURCE} NAME)
   get_filename_component(abspath   ${_PAR_SOURCE} ABSOLUTE)
 
+  if( HAVE_CUDA )
+    set( extension "cu" )
+  elseif( HAVE_HIP )
+    set( extension "hip" )
+  endif()
+
   if( directory )
-    set(cuda_wrapper ${CMAKE_CURRENT_BINARY_DIR}/${directory}/${base}.cu)
+    set(hic_wrapper ${CMAKE_CURRENT_BINARY_DIR}/${directory}/${base}.${extension})
   else()
-    set(cuda_wrapper ${CMAKE_CURRENT_BINARY_DIR}/${base}.cu)
+    set(hic_wrapper ${CMAKE_CURRENT_BINARY_DIR}/${base}.${extension})
   endif()
-  set(${variable} ${cuda_wrapper} PARENT_SCOPE)
+  set(${variable} ${hic_wrapper} PARENT_SCOPE)
   set(content
 "
 #include \"atlas/${directory}/${name}\"
 ")
-  if( ${abspath} IS_NEWER_THAN ${cuda_wrapper} )
-    file(WRITE ${cuda_wrapper} "${content}")
+  if( ${abspath} IS_NEWER_THAN ${hic_wrapper} )
+    file(WRITE ${hic_wrapper} "${content}")
   endif()
 endfunction()
 
@@ -40,12 +46,12 @@ function( atlas_host_device srclist )
   set( multi_value_args SOURCES )
   cmake_parse_arguments( _PAR "${options}" "${single_value_args}" "${multi_value_args}" ${ARGN} )
 
-  if( ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA )
-    set( use_cuda_srclist ${_PAR_SOURCES} )
+  if( HAVE_GPU )
+    set( use_hic_srclist ${_PAR_SOURCES} )
 
-    foreach( src ${use_cuda_srclist} )
-      create_cuda_wrapper( cuda_wrapper SOURCE ${src} )
-      list( APPEND ${srclist} ${cuda_wrapper} )
+    foreach( src ${use_hic_srclist} )
+      create_hic_wrapper( hic_wrapper SOURCE ${src} )
+      list( APPEND ${srclist} ${hic_wrapper} )
       ecbuild_list_exclude_pattern( LIST ${srclist} REGEX ${src} )
     endforeach()
 

cmake/features/ACC.cmake

@@ -1,32 +1,27 @@
 ### OpenACC
 
-if( atlas_HAVE_ATLAS_FIELD )
+if( atlas_HAVE_ATLAS_FIELD AND HAVE_GPU )
 
-set( ATLAS_ACC_CAPABLE FALSE )
-if( HAVE_CUDA )
-  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI|NVHPC" )
-    set( ATLAS_ACC_CAPABLE TRUE )
+  if( DEFINED ATLAS_ENABLE_ACC )
+    set( ENABLE_ACC ${ATLAS_ENABLE_ACC} )
   endif()
-endif()
-
-ecbuild_add_option( FEATURE ACC
-                    DESCRIPTION  "OpenACC capable data structures"
-                    CONDITION ATLAS_ACC_CAPABLE )
-
-if( atlas_HAVE_ACC )
-  if( CMAKE_Fortran_COMPILER_ID MATCHES "PGI|NVHPC" )
-      #set( ACC_Fortran_FLAGS -acc -ta=tesla,nordc )
-    set( ACC_Fortran_FLAGS "-acc=gpu;-gpu=gvmode,lineinfo,fastmath,rdc" )
-    set( ACC_C_FLAGS ${ACC_Fortran_FLAGS} )
-    find_program( ACC_C_COMPILER NAMES pgcc HINTS ${PGI_DIR} ${NVPHC_DIR} ENV PGI_DIR NVHPC_DIR PATH_SUFFIXES bin )
-    if( NOT ACC_C_COMPILER )
-      ecbuild_error( "Could not find OpenACC capable C compiler" )
+  if( ENABLE_ACC )
+    if( NOT HAVE_FORTRAN )
+      enable_language(Fortran)
     endif()
+    find_package( OpenACC COMPONENTS Fortran CXX )
+  endif()
+
+  ecbuild_add_option( FEATURE ACC
+                      DESCRIPTION  "OpenACC capable data structures"
+                      CONDITION OpenACC_Fortran_FOUND )
+  if( HAVE_ACC )
+    set( ACC_LINK_OPTIONS ${OpenACC_Fortran_FLAGS} )
   endif()
-endif()
 
 else()
+
   set( HAVE_ACC 0 )
   set( atlas_HAVE_ACC 0 )
-endif()
 
+endif()

cmake/features/CUDA.cmake

@@ -1,15 +1,37 @@
 
-ecbuild_add_option( FEATURE CUDA
-                    DESCRIPTION "Enable CUDA support"
-                    DEFAULT OFF
-                  )
+# ecbuild_add_option( FEATURE CUDA
+#                     DESCRIPTION "Enable CUDA support"
+#                     DEFAULT OFF
+#                   )
+# ecbuild_add_option( FEATURE HIP
+#                     DESCRIPTION "Enable CUDA support"
+#                     DEFAULT OFF
+#                   )
 
-if( HAVE_CUDA )
-
-    enable_language( CUDA )
-    ecbuild_info( "CUDA language enabled" )
-
-    find_package( CUDAToolkit REQUIRED )
+set( atlas_HAVE_CUDA 0 )
+set( atlas_HAVE_HIP  0 )
+set( atlas_HAVE_GPU  0 )
 
+if( hic_HAVE_CUDA )
+  enable_language( CUDA )
+  ecbuild_info( "CUDA language enabled" )
+  find_package(CUDAToolkit REQUIRED)
+  set( atlas_HAVE_CUDA 1 )
+  set( atlas_HAVE_GPU  1 )
+elseif( hic_HAVE_HIP )
+  enable_language( HIP )
+  ecbuild_info( "HIP language enabled" )
+  find_package(hip CONFIG REQUIRED)
+  set( atlas_HAVE_HIP 1 )
+  set( atlas_HAVE_GPU 1 )
 endif()
 
+set( HAVE_CUDA ${atlas_HAVE_CUDA} )
+set( HAVE_HIP  ${atlas_HAVE_HIP} )
+set( HAVE_GPU  ${atlas_HAVE_GPU} )
+
+if( HAVE_GPU )
+  ecbuild_info("GPU support enabled")
+else()
+  ecbuild_info("GPU support not enabled")
+endif()

cmake/features/ECTRANS.cmake

@@ -20,9 +20,13 @@ if( atlas_HAVE_ATLAS_FUNCTIONSPACE AND (ENABLE_ECTRANS OR NOT DEFINED ENABLE_ECT
     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
+            if( CMAKE_VERSION VERSION_LESS 3.18 )
+                # Before CMake 3.18 it is not possible to alias a non-global imported target
+                # Make the import global. Warning, this may break further find_package
+                get_target_property( transi_dp_IMPORTED transi_dp IMPORTED )
+                if( transi_dp_IMPORTED )
+                    set_target_properties( transi_dp PROPERTIES IMPORTED_GLOBAL TRUE)
+                endif()
             endif()
             add_library( transi ALIAS transi_dp )
         endif()

cmake/project_summary.cmake

@@ -42,9 +42,7 @@ endif()
 if( atlas_HAVE_ACC )
 
     ecbuild_info( "ACC" )
-    ecbuild_info( "    ACC_C_COMPILER     : [${ACC_C_COMPILER}]" )
-    ecbuild_info( "    ACC_C_FLAGS        : [${ACC_C_FLAGS}]" )
-    ecbuild_info( "    ACC_Fortran_FLAGS  : [${ACC_Fortran_FLAGS}]" )
+    ecbuild_info( "    OpenACC_Fortran_FLAGS  : [${OpenACC_Fortran_FLAGS}]" )
 
 endif()
 
@@ -60,10 +58,10 @@ if( atlas_HAVE_GRIDTOOLS_STORAGE )
 
 else()
 
-    if( NOT atlas_HAVE_CUDA )
+    if( NOT atlas_HAVE_GPU )
         ecbuild_info( "Array storage backend: Native [HOST]" )
     else()
-        ecbuild_info( "Array storage backend: Native [CUDA]" )
+        ecbuild_info( "Array storage backend: Native [GPU]" )
     endif()
 
 endif()

doc/CMakeLists.txt

@@ -6,6 +6,10 @@
 # granted to it by virtue of its status as an intergovernmental organisation nor
 # does it submit to any jurisdiction.
 
+if(atlas_HAVE_FORTRAN)
+  add_subdirectory(example-fortran)
+endif()
+
 if(atlas_HAVE_DOCS)
 
 add_subdirectory(user-guide)

doc/example-fortran/CMakeLists.txt

@@ -0,0 +1,10 @@
+# (C) Copyright 2024- 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.
+
+add_subdirectory(structured-grid-stencils)
+

doc/example-fortran/structured-grid-stencils/CMakeLists.txt

@@ -0,0 +1,12 @@
+# (C) Copyright 2024- 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.
+
+ecbuild_add_executable( TARGET example-fortran-structured-grid-stencils
+                        OUTPUT_NAME program NOINSTALL
+                        SOURCES program.F90
+                        LIBS atlas_f )