Merge branch 'release/0.16.0'

* release/0.16.0: (202 commits)
  Update changelog
  Version 0.16.0
  Fix failing tests introduced since commit 6060345
  ATLAS-220 ATLAS_FINALISES_MPI environment variable
  ATLAS-219 Fix broken parallel interpolation from regular lonlat grids
  bug fix: number of levels needed min instead of max
  Fix compilation for travis clang build
  Fix compilation for travis clang build
  Fix compilation for travis clang build
  Provide Trans::listBackends( std::ostream& )
  Fix compilation with GPU
  Cleanup interpolation method factories
  Cleanup TransFactory
  Add missing license headers
  ATLAS-218 Remove atlas_mpi_module
  ATLAS-217 Remove error handling
  Fix compilation reported by Nils on Summit with gnu 8.1
  Be more explicit about which clang-format is used
  apply clang-format (5.0.1)
  Fix warnings
  ...

Author: wdeconinck

.gitignore

@@ -5,3 +5,6 @@ doc/html
 doc/latex
 *.sublime-workspace
 .nfs*
+build/*
+install/*
+env.sh

.travis.yml

@@ -67,7 +67,13 @@ matrix:
         - CXX_COMPILER='clang++' C_COMPILER='clang' Fortran_COMPILER='gfortran'
         - MPI=openmpi
         - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG"
-      osx_image: xcode9
+      osx_image: xcode10.1
+      addons:
+        homebrew:
+          packages:
+          - openmpi
+          - cgal
+          - fftw
 
     ##################################
     # KNOWN TO FAIL, so comment
@@ -92,16 +98,6 @@ matrix:
 
 before_install:
 
-  #################################################################
-  # Fixes to pre-installed packages
-  #################################################################
-  - |
-    ### Fix pre-installed packages
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      brew update
-      brew list oclint || brew cask uninstall oclint # Prevent conflict with gcc
-    fi
-
   #################################################################
   # Set compilers
   #################################################################
@@ -135,7 +131,9 @@ install:
   - |
     ### Install gcc (homebrew)
     if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      brew upgrade gcc || brew install gcc
+      export HOMEBREW_NO_AUTO_UPDATE=1
+      brew install gcc
+      brew link gcc
     fi
   - |
     ### Install PGI community edition
@@ -165,28 +163,26 @@ install:
         mkdir -p ${DEPS_DIR}/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C ${DEPS_DIR}/cmake
       fi
       export PATH=${DEPS_DIR}/cmake/bin:${PATH}
-    else
-      brew upgrade cmake || brew install cmake
     fi
     cmake --version
 
   #################################################################
   # Install FFTW
   #################################################################
-  - |
-    ### Install FFTW
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      brew upgrade fftw || brew install fftw
-    fi
+  # - |
+  #   ### Install FFTW
+  #   if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+  #     brew ls --versions fftw || brew install fftw
+  #   fi
 
   #################################################################
   # Install CGAL
   #################################################################
-  - |
-    ### Install CGAL
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      brew upgrade cgal || brew install cgal
-    fi
+  # - |
+  #   ### Install CGAL
+  #   if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+  #     brew ls --versions cgal || brew install cgal
+  #   fi
 
   #################################################################
   # Install ecbuild
@@ -240,7 +236,7 @@ script:
   #################################################################
   # Test Atlas
   #################################################################
-  - ctest -VV
+  - ctest
 
 after_success:
 

CHANGELOG.md

@@ -7,6 +7,28 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.16.0] - 2018-02-14
+### Changed
+- Interpolation makes use of OpenMP
+- Cleanup of header includes
+- fypp Fortran preprocessor is ported to fckit 0.6
+
+### Added
+- Parallel structured interpolation methods (2D,3D): linear, cubic, quasicubic
+- Interpolation for multi-level and multi-variable fields
+- atlas_Trace: Fortran API and use within OpenMP parallel regions
+- StructuredColumns halo-exchange for vector fields
+- Field::halo_exchange() function
+
+### Fixed
+- Fortran compilation with PGI 18.10
+- Access to Field view within OpenMP parallel region
+- FunctionSpaces use only required halo, even if larger halo is available in mesh
+- Fixed faulty name of a Field when created through Fortran API, wrapping existing memory
+- Fix NodeColumns functionspace when mesh is created from projected grid.
+- Parallel interpolation from regular lonlat grid.
+- Spectral spherical harmonics transforms for large cases
+
 ## [0.15.2] - 2018-08-31
 ### Changed
 - Initialisation of Fields to signalling NaN in debug builds, uninitialised in
@@ -58,6 +80,7 @@ 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
+[0.16.0]: 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
 [0.15.0]: https://github.com/ecmwf/atlas/compare/0.14.0...0.15.0

CMakeLists.txt

@@ -44,7 +44,7 @@ ecbuild_find_python()
 
 ecbuild_add_option( FEATURE FORTRAN
                     DESCRIPTION "Provide Fortran bindings"
-                    REQUIRED_PACKAGES "PROJECT fckit VERSION 0.5" )
+                    REQUIRED_PACKAGES "PROJECT fckit VERSION 0.6" )
 
 if( ATLAS_HAVE_FORTRAN )
 
@@ -123,6 +123,9 @@ if( ATLAS_HAVE_TESSELATION )
     list( APPEND CGAL_INCLUDE_DIRS ${Boost_INCLUDE_DIRS} )
     if ( TARGET CGAL::CGAL )
       list( APPEND CGAL_LIBRARIES CGAL::CGAL ${CGAL_3RD_PARTY_LIBRARIES} ${GMP_LIBRARIES} ${MPFR_LIBRARIES} ${Boost_THREAD_LIBRARY} ${Boost_SYSTEM_LIBRARY} )
+      # Reset INTERFACE_COMPILE_OPTIONS ( see ATLAS-193 )
+      get_target_property( CGAL_COMPILE_FLAGS CGAL::CGAL INTERFACE_COMPILE_OPTIONS )
+      set_target_properties( CGAL::CGAL PROPERTIES INTERFACE_COMPILE_OPTIONS "" )
     else()
       list( APPEND CGAL_LIBRARIES ${CGAL_LIBRARY} ${CGAL_3RD_PARTY_LIBRARIES} ${GMP_LIBRARIES} ${MPFR_LIBRARIES} ${Boost_THREAD_LIBRARY} ${Boost_SYSTEM_LIBRARY} )
     endif()
@@ -187,6 +190,7 @@ ecbuild_add_option( FEATURE EIGEN
 ### Type for Global indices and unique point id's
 
 set( ATLAS_BITS_GLOBAL 64 )
+set( ATLAS_BITS_LOCAL 32 )
 
 ### Bounds checking
 if( ${CMAKE_BUILD_TYPE} MATCHES "Debug" )

README.md

@@ -1,11 +1,12 @@
 Atlas
 =====
 
+[![atlas release version](https://img.shields.io/github/release/ecmwf/atlas.svg)](https://github.com/ecmwf/atlas/releases/latest)
 [![travis master](https://img.shields.io/travis/ecmwf/atlas/master.svg?label=master&logo=travis)](http://travis-ci.org/ecmwf/atlas "master")
 [![travis develop](https://img.shields.io/travis/ecmwf/atlas/develop.svg?label=develop&logo=travis)](http://travis-ci.org/ecmwf/atlas "develop")
 [![codecov](https://codecov.io/gh/ecmwf/atlas/branch/develop/graph/badge.svg)](https://codecov.io/gh/ecmwf/atlas)
 
-Project home: https://software.ecmwf.int/wiki/display/ATLAS  
+Project home: https://confluence.ecmwf.int/display/ATLAS  
 Contact: Willem Deconinck ([email protected])  
 Publication:
    >  [Deconinck et al, 2017](https://doi.org/10.1016/j.cpc.2017.07.006) --- 

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  "0.15.2" )
+set  ( ${PROJECT_NAME}_VERSION_STR  "0.16.0" )
 

bamboo/CLANG-env.sh

@@ -1,15 +1,24 @@
-# No module environment on the Mac
-[[ $(uname) == "Darwin" ]] && return
-# Initialise module environment if it is not
+#!/bin/bash
+
+if [[ $(uname) == "Darwin" ]]; then
+   # Up to date CMake version required
+   export PATH=${HOME}/Applications/CMake.app/Contents/bin:${PATH}
+   # No module environment on the Mac
+   return
+fi
+
+# initialise module environment if it is not
 if [[ ! $(command -v module > /dev/null 2>&1) ]]; then
   . /usr/local/apps/module/init/bash
 fi
 
+module unload grib_api
 module unload eccodes
 module unload emos
 module unload fftw
 module unload libemos
+module unload metview
 
-module switch gnu clang
-export FC=/usr/local/apps/gcc/6.3.0/bin/gfortran
+module load cmake/3.10.2
 
+module switch gnu clang

bamboo/CMakeLists.txt

@@ -0,0 +1,4 @@
+file( GLOB_RECURSE bamboo_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*" )
+
+ecbuild_add_resources(  TARGET ${PROJECT_NAME}_bamboo
+						SOURCES_DONT_PACK ${bamboo_files} )

bamboo/GCC-env.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+[[ $(uname) == "Darwin" ]] && return
+
+# initialise module environment if it is not
+if [[ ! $(command -v module > /dev/null 2>&1) ]]; then
+  . /usr/local/apps/module/init/bash
+fi
+
+module unload grib_api
+module unload eccodes
+module unload emos
+module unload fftw
+module unload libemos
+module unload metview
+
+module load cmake/3.10.2

bamboo/INTEL-env.sh

@@ -10,7 +10,8 @@ module unload eccodes
 module unload emos
 module unload fftw
 module unload libemos
+module unload metview
 
 module load cmake/3.10.2
 
-module switch gnu intel/16.0.3
+module switch gnu intel/17.0.3

bamboo/env.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+# export ctest_parallel="no"
+

cmake/CompileFlags.cmake

@@ -1,3 +1,11 @@
+# (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.
+
 if( CMAKE_CXX_COMPILER_ID MATCHES Cray )
 
   ecbuild_add_cxx_flags("-hnomessage=3140") # colon separated numbers

cmake/atlas_host_device.cmake

@@ -15,6 +15,8 @@ function( create_cuda_wrapper variable )
   get_filename_component(directory ${_PAR_SOURCE} DIRECTORY)
   get_filename_component(base      ${_PAR_SOURCE} NAME_WE)
   get_filename_component(name      ${_PAR_SOURCE} NAME)
+  get_filename_component(abspath   ${_PAR_SOURCE} ABSOLUTE)
+
   if( directory )
     set(cuda_wrapper ${CMAKE_CURRENT_BINARY_DIR}/${directory}/${base}.cu)
   else()
@@ -25,7 +27,9 @@ function( create_cuda_wrapper variable )
 "
 #include \"atlas/${directory}/${name}\"
 ")
-  file(WRITE ${cuda_wrapper} "${content}")
+  if( ${abspath} IS_NEWER_THAN ${cuda_wrapper} )
+    file(WRITE ${cuda_wrapper} "${content}")
+  endif()
 endfunction()
 
 

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

@@ -8,7 +8,6 @@
 using atlas::Field;
 using atlas::FieldSet;
 using atlas::Log;
-using atlas::array::ArrayView;
 using atlas::array::make_datatype;
 using atlas::array::make_shape;
 using atlas::array::make_view;

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

@@ -5,17 +5,17 @@
 #include "atlas/library/Library.h"
 #include "atlas/mesh/Mesh.h"
 #include "atlas/mesh/Nodes.h"
-#include "atlas/meshgenerator/StructuredMeshGenerator.h"
+#include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/runtime/Log.h"
 
 using namespace atlas;
+using atlas::StructuredMeshGenerator;
 using atlas::array::make_shape;
 using atlas::array::make_view;
 using atlas::functionspace::NodeColumns;
 using atlas::gidx_t;
 using atlas::grid::StructuredGrid;
-using atlas::meshgenerator::StructuredMeshGenerator;
 using atlas::output::Gmsh;
 
 int main( int argc, char* argv[] ) {

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

@@ -5,15 +5,14 @@
 #include "atlas/grid.h"
 #include "atlas/library/Library.h"
 #include "atlas/mesh.h"
-#include "atlas/meshgenerator/StructuredMeshGenerator.h"
+#include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/util/CoordinateEnums.h"
 
 using namespace atlas;
-using atlas::array::ArrayView;
+using atlas::StructuredMeshGenerator;
 using atlas::array::make_view;
 using atlas::functionspace::StructuredColumns;
-using atlas::meshgenerator::StructuredMeshGenerator;
 using atlas::output::Gmsh;
 
 int main( int argc, char* argv[] ) {

doc/user-guide/core-functionalities/meshes/meshes-Structured.cc

@@ -1,13 +1,13 @@
 #include "atlas/grid/Grid.h"
 #include "atlas/library/Library.h"
 #include "atlas/mesh/Mesh.h"
-#include "atlas/meshgenerator/StructuredMeshGenerator.h"
+#include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/util/Config.h"
 
 using atlas::Grid;
 using atlas::Mesh;
-using atlas::meshgenerator::StructuredMeshGenerator;
+using atlas::StructuredMeshGenerator;
 using atlas::output::Gmsh;
 using atlas::util::Config;