Merge branch 'release/0.17.0'

* release/0.17.0: (29 commits)
  Update changelog
  Version 0.17.0
  apply clang-format
  Fix CGAL includes
  Compatibility with transi version 0.4.4
  Nabla holds reference counted FunctionSpace
  Access to vertical coordinates in Fortran
  Fix failing test atlas_fctest_trans
  Make OpenMP a private dependency, client software has to link with OpenMP directly
  Fix memory leak
  Make pkgconfig generation configurable
  Use target_link_libraries() with PUBLIC/PRIVATE keyword
  ECKIT-381 Remove eckit ScopedPtr includes
  ECKIT-381: fix compilation
  Revert ECKIT-382 [8554eb9] as atlas doesn't use eckit's Tokenizer any longer
  ATLAS-226 Install Fortran modules in <prefix>/module/atlas
  ATLAS-225 Spectral functionspace in a distributed environment
  Fix memory leaks with reusing StructuredColumns caches
  Fix valgrind warning in EqualRegionsPartitioner.cc
  Unit tests recognise ATLAS_LOG_FILE enironment variable
  ...

CHANGELOG.md

@@ -7,7 +7,23 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
-## [0.16.0] - 2018-02-14
+## [0.17.0] - 2019-04-02
+### Changed
+- OpenMP is now private dependency
+- Dependencies are now added in a modern CMake3 way
+- Fortran modules are installed in <install-prefix>/module/atlas
+
+### Added
+- Spectral functionspace better used in distributed context
+- Nabla now holds shared_ptr to Method
+- Fortran access to vertical coordinates from StructuredColumns
+
+### Fixed
+- Compilation with PGI/19.1 (regression)
+- Add missing halo_exchange for Fortran rank-4 arrays
+- Memory leaks with StructuredColumns
+
+## [0.16.0] - 2019-02-14
 ### Changed
 - Interpolation makes use of OpenMP
 - Cleanup of header includes
@@ -80,6 +96,7 @@ 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
+[0.17.0]: https://github.com/ecmwf/atlas/compare/0.16.0...0.17.0
 [0.16.0]: https://github.com/ecmwf/atlas/compare/0.15.2...0.16.0
 [0.15.2]: https://github.com/ecmwf/atlas/compare/0.15.1...0.15.2
 [0.15.1]: https://github.com/ecmwf/atlas/compare/0.15.0...0.15.1

CMakeLists.txt

@@ -44,13 +44,13 @@ ecbuild_find_python()
 
 ecbuild_add_option( FEATURE FORTRAN
                     DESCRIPTION "Provide Fortran bindings"
-                    REQUIRED_PACKAGES "PROJECT fckit VERSION 0.6" )
+                    REQUIRED_PACKAGES "PROJECT fckit VERSION 0.6.2" )
 
 if( ATLAS_HAVE_FORTRAN )
 
   if( FCKIT_HAVE_ECKIT )
 
-    ecbuild_enable_fortran( REQUIRED MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/module )
+    ecbuild_enable_fortran( REQUIRED MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/module )
     set( Fortran Fortran )
 
     if( ENABLE_TESTS )
@@ -86,17 +86,29 @@ if( NOT ECKIT_HAVE_MPI )
   ecbuild_warn("ecKit has been compiled without MPI. This causes Atlas to not be able to run parallel jobs.")
 endif()
 
-
 ### OMP ...
-
-ecbuild_add_option( FEATURE OMP
-                    DESCRIPTION "Support for OpenMP threaded parallelism"
-                    REQUIRED_PACKAGES "OMP COMPONENTS CXX ${Fortran}" )
-
-if( HAVE_OMP )
-  ecbuild_enable_omp()
+if( "${CMAKE_VERSION}" VERSION_LESS "3.11" )
+  if( ENABLE_OMP )
+    ecbuild_warn( "OpenMP only supported with CMake 3.11 onwards" )
+  endif()
 else()
-  ecbuild_enable_ompstubs()
+  find_package( OpenMP COMPONENTS CXX ${Fortran} )
+endif()
+ecbuild_add_option( FEATURE OMP
+                    DESCRIPTION "support for OpenMP shared memory parallelism"
+                    CONDITION OpenMP_Fortran_FOUND OR OpenMP_CXX_FOUND )
+ecbuild_add_option( FEATURE OMP_Fortran
+                    DESCRIPTION "support for Fortran OpenMP shared memory parallelism"
+                    CONDITION HAVE_OMP AND OpenMP_Fortran_FOUND )
+
+ecbuild_add_option( FEATURE OMP_CXX
+                    DESCRIPTION "support for CXX OpenMP shared memory parallelism"
+                    CONDITION HAVE_OMP AND OpenMP_CXX_FOUND )
+if( TARGET OpenMP::OpenMP_CXX )
+  set( OMP_CXX OpenMP::OpenMP_CXX )
+endif()
+if( TARGET OpenMP::OpenMP_Fortran )
+  set( OMP_Fortran OpenMP::OpenMP_Fortran )
 endif()
 
 ### FFTW ...
@@ -109,7 +121,7 @@ ecbuild_add_option( FEATURE FFTW
 
 ecbuild_add_option( FEATURE TRANS
                     DESCRIPTION "Support for spectral transforms"
-                    REQUIRED_PACKAGES "PROJECT transi VERSION 0.4.1 QUIET" )
+                    REQUIRED_PACKAGES "PROJECT transi VERSION 0.4.4 QUIET" )
 
 ### tesselation ...
 
@@ -226,59 +238,47 @@ ecbuild_add_option( FEATURE SANDBOX
                     DEFAULT OFF
                     DESCRIPTION "Build the sandbox stuff" )
 
-################################################################################
-# export package info
-
-set( ATLAS_INCLUDE_DIRS   ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src )
-
-list( APPEND ATLAS_LIBRARIES  atlas )
-
-if( ATLAS_HAVE_FORTRAN )
-  list( APPEND ATLAS_INCLUDE_DIRS ${CMAKE_Fortran_MODULE_DIRECTORY} )
-  set( ATLAS_LIBRARIES atlas_f ${ATLAS_LIBRARIES} )
-endif()
-
-get_directory_property( ATLAS_DEFINITIONS COMPILE_DEFINITIONS )
-
-foreach( _tpl ${ATLAS_TPLS} )
-  string( TOUPPER ${_tpl} TPL )
-  list( APPEND ATLAS_EXTRA_DEFINITIONS   ${${TPL}_DEFINITIONS}  ${${TPL}_TPL_DEFINITIONS}  )
-  list( APPEND ATLAS_EXTRA_INCLUDE_DIRS  ${${TPL}_INCLUDE_DIRS} ${${TPL}_TPL_INCLUDE_DIRS} )
-  list( APPEND ATLAS_EXTRA_LIBRARIES     ${${TPL}_LIBRARIES}    ${${TPL}_TPL_LIBRARIES}    )
-endforeach()
-
-ecbuild_debug_var( ATLAS_EXTRA_INCLUDE_DIRS )
-ecbuild_debug_var( ATLAS_EXTRA_LIBRARIES )
-
 
 ################################################################################
 # sources
 
-include_directories( ${ATLAS_INCLUDE_DIRS} ${ATLAS_EXTRA_INCLUDE_DIRS} )
+set( MIR_NEEDS_TRANSI TRUE CACHE BOOL "Deprecated" INTERNAL )
+
 include(CompileFlags)
 add_subdirectory( src )
 
+################################################################################
+# export package info
+
+if( TARGET atlas_f )
+  list( APPEND ATLAS_LIBRARIES atlas_f )
+endif()
+list( APPEND ATLAS_LIBRARIES  atlas )
+
 ################################################################################
 # pkg-config
 
+ecbuild_add_option( FEATURE PKGCONFIG DESCRIPTION "Atlas pkgconfig" )
 set( ATLAS_URL "https://software.ecmwf.int/wiki/display/ATLAS" )
 set( ATLAS_DESCRIPTION "Atlas framework for parallel mesh datastructures" )
 
-ecbuild_pkgconfig()
-
-ecbuild_pkgconfig(
- NAME             atlas-c++
- LANGUAGES        CXX
- LIBRARIES        atlas
-)
-
-if( ATLAS_HAVE_FORTRAN )
- ecbuild_pkgconfig(
-   NAME             atlas-fortran
-   LANGUAGES        Fortran
-   LIBRARIES        atlas_f
-   NO_PRIVATE_INCLUDE_DIRS
- )
+if( ATLAS_HAVE_PKGCONFIG )
+  ecbuild_pkgconfig()
+
+  ecbuild_pkgconfig(
+    NAME             atlas-c++
+    LANGUAGES        CXX
+    LIBRARIES        atlas
+  )
+
+  if( ATLAS_HAVE_FORTRAN )
+    ecbuild_pkgconfig(
+      NAME             atlas-fortran
+      LANGUAGES        Fortran
+      LIBRARIES        atlas_f
+      NO_PRIVATE_INCLUDE_DIRS
+    )
+  endif()
 endif()
 
 ################################################################################
@@ -304,7 +304,63 @@ ecbuild_add_resources(
 )
 
 if( ATLAS_HAVE_FORTRAN AND ECBUILD_INSTALL_FORTRAN_MODULES )
-    install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR} DESTINATION ${INSTALL_INCLUDE_DIR} )
+    install( DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}
+             DESTINATION module/atlas
+             COMPONENT modules )
+endif()
+
+macro( filter_tpl _tpl )
+  string( TOUPPER ${_tpl} _TPL )
+  unset( ${_tpl}_INCLUDE_DIRS )
+  unset( ${_TPL}_INCLUDE_DIRS )
+  unset( ${_tpl}_INCLUDE_DIR )
+  unset( ${_TPL}_INCLUDE_DIR )
+  unset( ${_tpl}_LIBRARIES )
+  unset( ${_TPL}_LIBRARIES )
+  unset( ${_tpl}_LIBRARY )
+  unset( ${_TPL}_LIBRARY )
+  if( ${_tpl}_INCLUDE_DIRS )
+    unset( ${_tpl}_INCLUDE_DIRS CACHE )
+  endif()
+  if( ${_TPL}_INCLUDE_DIRS )
+    unset( ${_TPL}_INCLUDE_DIRS CACHE )
+  endif()
+  if( ${_tpl}_INCLUDE_DIR )
+    unset( ${_tpl}_INCLUDE_DIR CACHE )
+  endif()
+  if( ${_TPL}_INCLUDE_DIR )
+    unset( ${_TPL}_INCLUDE_DIR CACHE )
+  endif()
+  if( ${_tpl}_LIBRARIES )
+    unset( ${_tpl}_LIBRARIES CACHE )
+  endif()
+  if( ${_TPL}_LIBRARIES )
+    unset( ${_TPL}_LIBRARIES CACHE )
+  endif()
+  if( ${_tpl}_LIBRARY )
+    unset( ${_tpl}_LIBRARY CACHE )
+  endif()
+  if( ${_TPL}_LIBRARY )
+    unset( ${_TPL}_LIBRARY CACHE )
+  endif()
+endmacro()
+filter_tpl( fckit )
+filter_tpl( CGAL )
+filter_tpl( FFTW )
+filter_tpl( Eigen3 )
+if( (NOT MIR_NEEDS_TRANSI) OR NOT( TRANSI_VERSION VERSION_LESS 0.6 ) )
+  filter_tpl( transi )
+endif()
+get_target_property( eckit_intf_incl_dirs eckit INTERFACE_INCLUDE_DIRECTORIES )
+set( eckit_can_be_filtered FALSE )
+foreach( eckit_intf_incl_dir ${eckit_intf_incl_dirs} )
+  string(FIND ${eckit_intf_incl_dir} "eckit" _found )
+  if( NOT( _found EQUAL "-1" ) )
+    set( eckit_can_be_filtered TRUE )
+  endif()
+endforeach()
+if( eckit_can_be_filtered )
+  filter_tpl(eckit)
 endif()
 
 ecbuild_install_project( NAME Atlas )

README.md

@@ -53,6 +53,8 @@ Optional dependencies:
 - gridtools-storage --- For GPU interoperability
 - transi --- For enabling IFS spherical harmonics transforms ( not open-source )
 - CGAL --- For enabling Delaunay triangulation of unstructured grids
+- Eigen3 -- For certain linear algebra operations
+- FFTW -- For enabling inverse spherical harmonics transforms (TransLocal)
 
 Installation
 ------------
@@ -83,6 +85,8 @@ TRANSI_PATH              # Path to transi prefix
 # For finding CGAL
 BOOST_ROOT               # Path to Boost prefix
 CGAL_DIR                 # Path to directory containing CGALConfig.cmake
+Eigen3_DIR               # Path to directory containing Eigen3Config.cmake
+FFTW_PATH                # Path to FFTW prefix
 ```
 
 Now proceed with installation as follows

VERSION.cmake

@@ -6,5 +6,5 @@
 # granted to it by virtue of its status as an intergovernmental organisation nor
 # does it submit to any jurisdiction.
 
-set  ( ${PROJECT_NAME}_VERSION_STR  "0.16.0" )
+set  ( ${PROJECT_NAME}_VERSION_STR  "0.17.0" )
 

bamboo/MACOSX-env.sh

@@ -0,0 +1,2 @@
+export PATH=$HOME/Applications/CMake.app/Contents/bin:$PATH
+

doc/user-guide/core-functionalities/fields/fields-on-grid.cc

@@ -1,6 +1,6 @@
 #include "atlas/array.h"
 #include "atlas/field/Field.h"
-#include "atlas/grid/Grid.h"
+#include "atlas/grid.h"
 #include "atlas/library/Library.h"
 #include "atlas/runtime/Log.h"
 
@@ -9,7 +9,7 @@ using atlas::Log;
 using atlas::array::make_datatype;
 using atlas::array::make_shape;
 using atlas::array::make_view;
-using atlas::grid::StructuredGrid;
+using atlas::StructuredGrid;
 
 int main( int argc, char* argv[] ) {
     atlas::Library::instance().initialise( argc, argv );

doc/user-guide/core-functionalities/functionspace/NodeColumns.cc

@@ -1,10 +1,9 @@
 #include "atlas/functionspace/NodeColumns.h"
 #include "atlas/array/ArrayView.h"
-#include "atlas/field/Field.h"
-#include "atlas/grid/Grid.h"
+#include "atlas/field.h"
+#include "atlas/grid.h"
 #include "atlas/library/Library.h"
-#include "atlas/mesh/Mesh.h"
-#include "atlas/mesh/Nodes.h"
+#include "atlas/mesh.h"
 #include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/runtime/Log.h"
@@ -15,7 +14,8 @@ using atlas::array::make_shape;
 using atlas::array::make_view;
 using atlas::functionspace::NodeColumns;
 using atlas::gidx_t;
-using atlas::grid::StructuredGrid;
+using atlas::idx_t;
+using atlas::StructuredGrid;
 using atlas::output::Gmsh;
 
 int main( int argc, char* argv[] ) {
@@ -109,7 +109,7 @@ int main( int argc, char* argv[] ) {
     /* .... */
 
     // Operations
-    size_t N;
+    idx_t N;
     gidx_t gidx_min, gidx_max;
     double min, max, sum, mean, stddev;
 

doc/user-guide/core-functionalities/global-grids/Structured/global-grids-Structured.cc

@@ -1,9 +1,9 @@
-#include "atlas/grid/Grid.h"
+#include "atlas/grid.h"
 #include "atlas/library/Library.h"
 #include "atlas/runtime/Log.h"
 
 using atlas::Log;
-using atlas::grid::StructuredGrid;
+using atlas::StructuredGrid;
 
 int main( int argc, char* argv[] ) {
     atlas::Library::instance().initialise( argc, argv );

doc/user-guide/core-functionalities/global-grids/Unstructured/global-grids-Unstructured.cc

@@ -1,12 +1,13 @@
 #include "atlas/grid.h"
+#include "atlas/mesh.h"
 #include "atlas/library/Library.h"
 #include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/runtime/Log.h"
 #include "atlas/util/Point.h"
 
 using namespace atlas;
-using atlas::grid::UnstructuredGrid;
+using atlas::UnstructuredGrid;
 using atlas::output::Gmsh;
 using atlas::util::Config;
 

src/CMakeLists.txt

@@ -6,16 +6,16 @@
 # granted to it by virtue of its status as an intergovernmental organisation nor
 # does it submit to any jurisdiction.
 
-if( CGAL_FOUND )
-  set( CGAL_FOUND 1 )
+if( ATLAS_HAVE_OMP_CXX )
+  set( ATLAS_HAVE_OMP_CXX 1 )
 else()
-  set( CGAL_FOUND 0 )
+  set( ATLAS_HAVE_OMP_CXX 0 )
 endif()
 
-if( ATLAS_HAVE_OMP )
-  set( ATLAS_HAVE_OMP 1 )
+if( ATLAS_HAVE_OMP_Fortran )
+  set( ATLAS_HAVE_OMP_Fortran 1 )
 else()
-  set( ATLAS_HAVE_OMP 0 )
+  set( ATLAS_HAVE_OMP_Fortran 0 )
 endif()
 
 if( ATLAS_HAVE_TESSELATION )