Merge branch 'release/0.15.0'

* release/0.15.0: (123 commits)
  Disable PGI build from travis ci
  Print more configuration information
  Reduce test times
  Remove warnings related to unreachable statements detected by PGI compiler
  Fix various warnings shown by pgi/18.4 -- still failing tests for pgi
  Version 0.15.0
  Fix a wrong template type
  Apply clang-format
  ATLAS-165 Fix intents in Fortran functions
  ATLAS-164 Array uses raw C pointer rather than std::vector and is initialised with signaling_NaN for debug builds
  ATLAS-163 Recompute weights on edges
  ATLAS-163 Introduce bit reproducibility for parallel interpolation for coinciding meshes
  ATLAS-163 Introduce bit reproducibility for parallel interpolation
  merging spectral U and V before the transform is now the default
  added option to merge U,V,scalars before transform with old vd2uv; this should be faster because the size of the dgemm calls is bigger
  work in progress: merging all spectral data into one array with vdoption
  Avoid inclusion of fftw3.h in TransLocal.h
  some clean-up. Unstructured grids are currently not working (ATLAS-162)
  fixed vd2uv for reduced grids and improved its performance by moving loop over wavenumbers inside vd2uv
  some cleanup
  ...

.travis.yml

@@ -46,29 +46,20 @@ matrix:
       addons:
         apt:
           sources:  ['ubuntu-toolchain-r-test']
-          packages: ['g++-5', 'gcc-5', 'gfortran-5']
+          packages: ['g++-5', 'gcc-5', 'gfortran-5', 'libfftw3-dev']
 
     - os: linux
       compiler: gcc
       env:
         - CACHE_NAME=linux-gcc7-mpich
         - CXX_COMPILER='g++-7' C_COMPILER='gcc-7' Fortran_COMPILER='gfortran-7'
         - MPI='mpich'
-        - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG"
+        - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG -DENABLE_GPROF=ON"
+        - COVERAGE=ON
       addons:
         apt:
           sources:  ['ubuntu-toolchain-r-test']
-          packages: ['g++-7', 'gcc-7', 'gfortran-7']
-
-    - os: linux
-      compiler: gcc
-      env:
-        - CACHE_NAME=linux-pgi-openmpi
-        - CXX_COMPILER='pgc++' C_COMPILER='pgcc' Fortran_COMPILER='pgfortran'
-        - MPI='openmpi'
-        - PGI_VERSION="CommunityEdition"
-        - ECKIT_CMAKE_OPTIONS="-DRT_LIB=/usr/lib/x86_64-linux-gnu/librt.so -DCURSES_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurses.so"
-        - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG -DENABLE_FORTRAN=OFF" # Fortran tests known to be broken with pgi/17.10
+          packages: ['g++-7', 'gcc-7', 'gfortran-7', 'libfftw3-dev', 'lcov']
 
     - os: osx
       env:
@@ -89,6 +80,16 @@ matrix:
     #     - MPI=mpich
     #   osx_image: xcode9
 
+    # - os: linux
+    #   compiler: gcc
+    #   env:
+    #     - CACHE_NAME=linux-pgi-openmpi
+    #     - CXX_COMPILER='pgc++' C_COMPILER='pgcc' Fortran_COMPILER='pgfortran'
+    #     - MPI='openmpi'
+    #     - PGI_VERSION="CommunityEdition"
+    #     - ECKIT_CMAKE_OPTIONS="-DRT_LIB=/usr/lib/x86_64-linux-gnu/librt.so -DCURSES_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurses.so"
+    #     - ATLAS_CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=DEBUG -DENABLE_FORTRAN=OFF" # Fortran tests known to be broken with pgi/17.10
+
 before_install:
 
   #################################################################
@@ -143,16 +144,6 @@ install:
       source ${DEPS_DIR}/pgi/env.sh
     fi
 
-
-  #################################################################
-  # Install CGAL
-  #################################################################
-  - |
-    ### Install CGAL
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      brew upgrade cgal || brew install cgal
-    fi
-
   #################################################################
   # Install MPI
   #################################################################
@@ -179,6 +170,24 @@ install:
     fi
     cmake --version
 
+  #################################################################
+  # Install FFTW
+  #################################################################
+  - |
+    ### Install FFTW
+    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+      brew upgrade fftw || brew install fftw
+    fi
+
+  #################################################################
+  # Install CGAL
+  #################################################################
+  - |
+    ### Install CGAL
+    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+      brew upgrade cgal || brew install cgal
+    fi
+
   #################################################################
   # Install ecbuild
   #################################################################
@@ -231,7 +240,20 @@ script:
   #################################################################
   # Test Atlas
   #################################################################
-  - ctest
+  - ctest -VV
+
+after_success:
+
+  - |
+    if [[ "${COVERAGE}" == "ON" ]]; then
+      # Creating report
+      cd ${ATLAS_BUILD_DIR}
+      lcov --directory . --capture --output-file coverage.info # capture coverage info
+      lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter out system
+      lcov --list coverage.info #debug info
+      # Uploading report to CodeCov
+      bash <(curl -s https://codecov.io/bash) -t 9c489980-d292-499c-8615-af02df3b20d1 || echo "Codecov did not collect coverage reports"
+    fi
 
 after_failure:
 

CHANGELOG.md

@@ -7,6 +7,15 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.15.0] - 2018-06-19
+### Changed
+- Native Array data storage uses now a raw C pointer instead of std::vector
+- Significant performance improvements to Spherical harmonics transforms
+
+### Fixed
+- Various bugs related to parallel halos
+- Bit reproducibility for parallel interpolation
+
 ## [0.14.0] - 2018-03-22
 ### Added
 - Spherical Harmonics transforms can receive a cache memory handle
@@ -30,6 +39,7 @@ 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
+[0.15.0]: https://github.com/ecmwf/atlas/compare/0.14.0...0.15.0
 [0.14.0]: https://github.com/ecmwf/atlas/compare/0.13.2...0.14.0
 [0.13.2]: https://github.com/ecmwf/atlas/compare/0.13.1...0.13.2
 [0.13.1]: https://github.com/ecmwf/atlas/compare/0.13.0...0.13.1

CMakeLists.txt

@@ -31,7 +31,7 @@ ecbuild_declare_project()
 
 ### eckit
 
-ecbuild_use_package( PROJECT eckit VERSION 0.20.0 REQUIRED )
+ecbuild_use_package( PROJECT eckit VERSION 0.21.0 REQUIRED )
 ecbuild_debug( "   ECKIT_FEATURES : [${ECKIT_FEATURES}]" )
 
 # options & dependencies
@@ -99,6 +99,12 @@ else()
   ecbuild_enable_ompstubs()
 endif()
 
+### FFTW ...
+
+ecbuild_add_option( FEATURE FFTW
+                    DESCRIPTION "Support for fftw"
+                    REQUIRED_PACKAGES "FFTW COMPONENTS double" )
+
 ### trans ...
 
 ecbuild_add_option( FEATURE TRANS
@@ -185,15 +191,29 @@ set( ATLAS_BITS_GLOBAL 64 )
 ### Bounds checking
 if( ${CMAKE_BUILD_TYPE} MATCHES "Debug" )
   set( DEFAULT_BOUNDSCHECKING ON )
+  set( DEFAULT_INIT_SNAN ON )
 else()
   set( DEFAULT_BOUNDSCHECKING OFF )
+  set( DEFAULT_INIT_SNAN OFF )
 endif()
+
 ecbuild_add_option( FEATURE BOUNDSCHECKING
                     DEFAULT ${DEFAULT_BOUNDSCHECKING}
                     DESCRIPTION "Bounds checking for atlas::ArrayView and atlas::IndexView" )
-if( ${CMAKE_BUILD_TYPE} MATCHES "Debug" AND NOT ATLAS_HAVE_BOUNDSCHECKING )
-  ecbuild_info( "Turning BOUNDSCHECKING ON for Debug build" )
-  set( ATLAS_HAVE_BOUNDSCHECKING 1 )
+
+ecbuild_add_option( FEATURE INIT_SNAN
+                    DEFAULT ${DEFAULT_INIT_SNAN}
+                    DESCRIPTION "Initialise atlas arrays with signaling_NaN (real types) or other invalid values (other types)" )
+
+if( ${CMAKE_BUILD_TYPE} MATCHES "Debug" )
+  if( NOT ATLAS_HAVE_INIT_SNAN )
+    ecbuild_info( "Turning INIT_SNAN ON for Debug build" )
+    set( ATLAS_HAVE_INIT_SNAN 1 )
+  endif()
+  if( NOT ATLAS_HAVE_BOUNDSCHECKING )
+    ecbuild_info( "Turning BOUNDSCHECKING ON for Debug build" )
+    set( ATLAS_HAVE_BOUNDSCHECKING 1 )
+  endif()
 endif()
 
 ### sandbox

README.md

@@ -3,6 +3,7 @@ Atlas
 
 [![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  
 Contact: Willem Deconinck ([email protected])  

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  "0.14.0" )
+set  ( ${PROJECT_NAME}_VERSION_STR  "0.15.0" )
 

bamboo/CLANG-env.sh

@@ -11,3 +11,5 @@ module unload fftw
 module unload libemos
 
 module switch gnu clang
+export FC=/usr/local/apps/gcc/6.3.0/bin/gfortran
+

bamboo/INTEL-env.sh

@@ -1,11 +1,16 @@
-# Initialise module environment if it is not
+#!/bin/bash
+
+# initialise module environment if it is not
 if [[ ! $(command -v module > /dev/null 2>&1) ]]; then
   . /usr/local/apps/module/init/bash
 fi
-# unload modules not available for intel
+
+module unload grib_api
 module unload eccodes
 module unload emos
 module unload fftw
 module unload libemos
 
-module switch gnu intel/16.0.3
+module load cmake/3.10.2
+
+module switch gnu intel/16.0.3

cmake/CompileFlags.cmake

@@ -8,3 +8,9 @@ if( CMAKE_CXX_COMPILER_ID MATCHES Cray )
 #          directives, ACC directives, or ASM intrinsics.
 
 endif()
+
+#ecbuild_add_cxx_flags("-Wl,-ydgemm_")
+#ecbuild_add_fortran_flags("-Wl,-ydgemm_")
+#ecbuild_add_cxx_flags("-fsanitize=address")
+#ecbuild_add_cxx_flags("-fsanitize=thread")
+#ecbuild_add_cxx_flags("-fsanitize=memory")

src/CMakeLists.txt

@@ -36,12 +36,24 @@ else()
   set( ATLAS_HAVE_TRANS 0 )
 endif()
 
+if( ATLAS_HAVE_FFTW )
+  set( ATLAS_HAVE_FFTW 1 )
+else()
+  set( ATLAS_HAVE_FFTW 0 )
+endif()
+
 if( ATLAS_HAVE_BOUNDSCHECKING )
   set( ATLAS_HAVE_BOUNDSCHECKING 1 )
 else()
   set( ATLAS_HAVE_BOUNDSCHECKING 0 )
 endif()
 
+if( ATLAS_HAVE_INIT_SNAN )
+  set( ATLAS_HAVE_INIT_SNAN 1 )
+else()
+  set( ATLAS_HAVE_INIT_SNAN 0 )
+endif()
+
 if( ATLAS_HAVE_GRIDTOOLS_STORAGE )
   set( ATLAS_HAVE_GRIDTOOLS_STORAGE 1 )
 else()

src/apps/atlas-benchmark.cc

@@ -89,13 +89,6 @@ using namespace atlas::functionspace;
 using namespace atlas::meshgenerator;
 using atlas::AtlasTool;
 
-namespace {
-void usage( const std::string& tool ) {
-    Log::info() << "Usage: " << tool << " [OPTIONS]..." << std::endl;
-}
-
-}  // namespace
-
 //----------------------------------------------------------------------------------------------------------------------
 
 struct TimerStats {

src/atlas/CMakeLists.txt

@@ -317,24 +317,28 @@ numerics/fvm/Method.cc
 numerics/fvm/Nabla.h
 numerics/fvm/Nabla.cc
 
+trans/Cache.h
+trans/Cache.cc
 trans/Trans.h
 trans/Trans.cc
 trans/VorDivToUV.h
 trans/VorDivToUV.cc
+trans/LegendreCacheCreator.h
+trans/LegendreCacheCreator.cc
 trans/local/TransLocal.h
 trans/local/TransLocal.cc
 trans/local/LegendrePolynomials.h
 trans/local/LegendrePolynomials.cc
-trans/local/LegendreTransforms.h
-trans/local/LegendreTransforms.cc
-trans/local/FourierTransforms.h
-trans/local/FourierTransforms.cc
 trans/local/VorDivToUVLocal.h
 trans/local/VorDivToUVLocal.cc
+trans/local/LegendreCacheCreatorLocal.h
+trans/local/LegendreCacheCreatorLocal.cc
 
 )
 if( ATLAS_HAVE_TRANS )
 list( APPEND atlas_numerics_srcs
+  trans/ifs/LegendreCacheCreatorIFS.h
+  trans/ifs/LegendreCacheCreatorIFS.cc
   trans/ifs/TransIFS.h
   trans/ifs/TransIFS.cc
   trans/ifs/TransIFSNodeColumns.h
@@ -555,7 +559,9 @@ ecbuild_add_library( TARGET atlas
   PRIVATE_INCLUDES
     "${CGAL_INCLUDE_DIRS}"
     "${TRANSI_INCLUDE_DIRS}"
-    "${MPI_CXX_INCLUDE_DIRS}"
+
+  PUBLIC_INCLUDES "${FFTW_INCLUDES}"
+
   LIBS
     eckit_geometry
     eckit_linalg
@@ -564,9 +570,10 @@ ecbuild_add_library( TARGET atlas
     "${CGAL_LIBRARIES}"
     "${TRANSI_LIBRARIES}"
     "${FCKIT_LIBRARIES}"
+    "${FFTW_LIBRARIES}"
   DEFINITIONS
     ${ATLAS_DEFINITIONS}
- )
+)
 
 if( ATLAS_HAVE_GRIDTOOLS_STORAGE )
   target_link_libraries( atlas gridtools::storage )

src/atlas/array/SVector.h

@@ -28,7 +28,6 @@ namespace array {
 template <typename T>
 class SVector {
 public:
-
     ATLAS_HOST_DEVICE
     SVector() : data_( nullptr ), size_( 0 ), externally_allocated_( false ) {}
 
@@ -41,13 +40,13 @@ class SVector {
     ATLAS_HOST_DEVICE
     SVector( T* data, size_t size ) : data_( data ), size_( size ) {}
 
-    SVector( size_t N ) : data_( nullptr), size_( N ), externally_allocated_( false ) {
-        if( N != 0 ) {
+    SVector( size_t N ) : data_( nullptr ), size_( N ), externally_allocated_( false ) {
+        if ( N != 0 ) {
 #if ATLAS_GRIDTOOLS_STORAGE_BACKEND_CUDA
-          cudaError_t err = cudaMallocManaged( &data_, N * sizeof( T ) );
-          if ( err != cudaSuccess ) throw eckit::AssertionFailed( "failed to allocate GPU memory" );
+            cudaError_t err = cudaMallocManaged( &data_, N * sizeof( T ) );
+            if ( err != cudaSuccess ) throw eckit::AssertionFailed( "failed to allocate GPU memory" );
 #else
-          data_ = (T*)malloc( N * sizeof( T ) );
+            data_ = (T*)malloc( N * sizeof( T ) );
 #endif
         }
     }

src/atlas/array/gridtools/GridToolsTraits.h

@@ -1,7 +1,7 @@
 #pragma once
 
-#include "gridtools/common/generic_metafunctions/is_all_integrals.hpp"
 #include "gridtools/common/generic_metafunctions/accumulate.hpp"
+#include "gridtools/common/generic_metafunctions/is_all_integrals.hpp"
 #include "gridtools/storage/storage-facility.hpp"
 
 #include "atlas/array/ArrayViewDefs.h"

src/atlas/array/helpers/ArraySlicer.h

@@ -162,15 +162,13 @@ class ArraySlicer {
         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 int 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 ) {
         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 int 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 ) {
         return range.start() * view.stride( i_view++ );