Merge branch 'release/0.19.0'

* release/0.19.0: (40 commits) Version 0.19.0 Fix compilation of test_mesh_reorder.cc for Cray/8.5 MIR-77, MIR-385, MIR-386 Replace native Lambert projection with LambertConformalConic projection MIR-77, MIR-385, MIR-386: preliminary support for interpolation from Lambert Conformal projected grids MIR-77, MIR-385, MIR-386: preliminary support for interpolation from Lambert Conformal projected grids Test Proj projections using yml Add false_easting and false_northing to LambertAzimuthalEqualAreaProjection Fix testing of grids ATLAS-245 Test reordering for unstructured meshes Stay backwards compatibile with eckit 1.0.2 for now Update to eckit 1.4 Fix gridtools_storage backend Compatibility with eckit master branch [1.3.2] (was working already as of eckit 0a9743cb) ATLAS-246: Proj-based projections unit test (from Proj examples) ATLAS-247 Comment regarding status ATLAS-247 cleanup ATLAS-247 Preliminary support for CellColumns functionspace and Gmsh output mesh::Elements::indexview() function added Fix EdgeColumns::haloExchange for fields with rank!=2 LocalView::shape() function added ...
ecmwf · Oct 1, 2019 · e058524 · e058524
2 parents 0ef1dad + e68f021
commit e058524
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,12 +7,26 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+
+## [0.19.0] - 2019-10-01
+### Fixed
+- Lambert ( conformal conic ) projection xy coordinates are now corrected
+
+### Changed
+- LambertProjection renamed to LambertConformalConic
+
+### Added
+- Reordering of nodes strategies (Hilbert curve, ReverseCuthillMckee)
+- Preliminary CellColumns functionspace with Gmsh IO; halos are not yet fully supported
+
+
 ## [0.18.1] - 2019-08-10
 ### Fixed
 - Match vertical structured interpolation to IFS
 - Fix in creating vertical dimension in StructuredColumns using interval
 - Fix in caching StructuredColumnsHaloExchange
 
+
 ## [0.18.0] - 2019-07-15
 ### Changed
 - Make grid hashes crossplatform
@@ -28,6 +42,7 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 - StructuredColumns bug with iSend
 - Memory corruption in Spectral functionspace with GT CUDA backend
 
+
 ## [0.17.2] - 2019-06-04
 ### Fixed
 - Compilation with PGI 19.4
@@ -134,6 +149,7 @@ 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
+[0.19.0]: https://github.com/ecmwf/atlas/compare/0.18.1...0.19.0
 [0.18.1]: https://github.com/ecmwf/atlas/compare/0.18.0...0.18.1
 [0.18.0]: https://github.com/ecmwf/atlas/compare/0.17.2...0.18.0
 [0.17.2]: https://github.com/ecmwf/atlas/compare/0.17.1...0.17.2

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -31,7 +31,7 @@ ecbuild_declare_project()
 
 ### eckit
 
-ecbuild_use_package( PROJECT eckit VERSION 0.21.0 REQUIRED )
+ecbuild_use_package( PROJECT eckit VERSION 1.0.2 REQUIRED )
 ecbuild_debug( "   ECKIT_FEATURES : [${ECKIT_FEATURES}]" )
 
 # options & dependencies
@@ -200,6 +200,13 @@ ecbuild_add_option( FEATURE EIGEN
                     DESCRIPTION "Use Eigen linear algebra library"
                     REQUIRED_PACKAGES Eigen3 )
 
+### Proj
+
+ecbuild_add_option( FEATURE PROJ
+                    DESCRIPTION "PROJ-based projections"
+                    DEFAULT OFF
+                    REQUIRED_PACKAGES PROJ4 )
+
 ### Type for Global indices and unique point ids
 
 set( ATLAS_BITS_GLOBAL 64 )

diff --git a/VERSION.cmake b/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  "0.18.1" )
+set  ( ${PROJECT_NAME}_VERSION_STR  "0.19.0" )
 
diff --git a/cmake/FeatureClangTidy.cmake b/cmake/FeatureClangTidy.cmake
@@ -21,6 +21,22 @@ ecbuild_add_option( FEATURE CLANG_TIDY
                     CONDITION CLANG_TIDY_EXE )
 
 if (HAVE_CLANG_TIDY)
-  set(CLANG_TIDY_CHECKS "-*,readability-braces-around-statements,redundant-string-init")
-  set(CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_EXE};-checks=${CLANG_TIDY_CHECKS};-header-filter='${CMAKE_SOURCE_DIR}/*'")
+
+  # Uncomment to apply fixes. Make sure to use a clean build, and apply clang-format afterwards!
+  # set( CLANG_TIDY_FIXIT ";-fix" )
+
+  set( CLANG_TIDY_CHECKS "-*" )
+  foreach( _clang_tidy_check
+    readability-braces-around-statements
+    redundant-string-init
+    modernize-use-nullptr
+    modernize-use-using
+    modernize-use-override
+    modernize-use-emplace
+    modernize-use-equals-default
+    modernize-use-equals-delete
+    )
+    set( CLANG_TIDY_CHECKS "${CLANG_TIDY_CHECKS},${_clang_tidy_check}" )
+  endforeach()
+  set( CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_EXE};-checks=${CLANG_TIDY_CHECKS};-header-filter='${CMAKE_SOURCE_DIR}/*'${CLANG_TIDY_FIXIT}" )
 endif()
diff --git a/doc/example-grids/cropped_shifted_lonlat_1.yml b/doc/example-grids/cropped_shifted_lonlat_1.yml
@@ -11,5 +11,5 @@ check :
   size : 4140
   lonlat(first) : [1,89]
   lonlat(last)  : [359,45]
-  uid : a1426cb32c8694d07d997cd224805947
+  uid : 18b1a156853d2cca30b7d13ef8400510
   bounding_box(n,w,s,e) : [90,0,45,360]
diff --git a/doc/example-grids/regional_lambert_azimuthal_equal_area_2.yml b/doc/example-grids/regional_lambert_azimuthal_equal_area_2.yml
@@ -1,4 +1,7 @@
-# EFAS grid
+# Close resemblance to EFAS grid
+# Here the sphere is used instead of "GRS80" ellipsoid
+# Actual EFAS grid uses "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs"
+# For real EFAS grid, check "regional_lambert_azimuthal_equal_area_4.yml"
 
 type : "regional"
 nx : 1000
@@ -10,6 +13,8 @@ projection :
     type : "lambert_azimuthal_equal_area"
     standard_parallel : 52
     central_longitude : 10
+    false_easting : 4321000
+    false_northing : 3210000
 y_numbering : -1
 
 
@@ -18,4 +23,6 @@ check :
   lonlat(first) : [-35.034,66.9821]
   lonlat(last)  : [41.2436,23.8962]
   bounding_box(n,w,s,e) : [72.647, -35.035, 23.895, 74.144]
-  uid : a87b2f233e26156d01c05a9ef2466721
+  uid : 2ef4f1bb005cf8e24ecc9464f8b7e089
+  xmin : 2510375.79
+  ymin : 748404.45
diff --git a/doc/example-grids/regional_lambert_azimuthal_equal_area_3.yml b/doc/example-grids/regional_lambert_azimuthal_equal_area_3.yml
@@ -0,0 +1,26 @@
+# !!! Requires proj external package (aka proj4) --> ENABLE_PROJ=ON
+
+# Close resemblance to EFAS grid ( equivalent to regional_lambert_azimuthal_equal_area_2.yml )
+# Here the sphere is used instead of ellipsoid
+# Actual EFAS grid uses "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs"
+
+type : "regional"
+nx : 1000
+ny : 950
+dx : 5000
+dy : 5000
+lonlat(xmin,ymax) : [-35.034,66.9821]
+projection :
+    type : "proj"
+    proj : "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +R=6371229.0"
+y_numbering : -1
+
+
+check : 
+  size : 950000
+  lonlat(first) : [-35.034,66.9821]
+  lonlat(last)  : [41.2436,23.8962]
+  bounding_box(n,w,s,e) : [72.647, -35.035, 23.895, 74.144]
+  uid : da2de78744323533eff5069272924741
+  xmin : 2510375.79
+  ymin : 748404.45
diff --git a/doc/example-grids/regional_lambert_azimuthal_equal_area_4.yml b/doc/example-grids/regional_lambert_azimuthal_equal_area_4.yml
@@ -0,0 +1,26 @@
+# !!! Requires proj external package (aka proj4) --> ENABLE_PROJ=ON
+
+# EFAS grid
+
+type : "regional"
+nx : 1000
+ny : 950
+dx : 5000
+dy : 5000
+lonlat(xmin,ymax) : [-35.034,66.9821]
+projection :
+    type : "proj"
+    proj : "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs"
+# Equivalent proj string, but leads to different uid (a71208b89dc4bc8d20494514e562c6b7)
+#    proj : "EPSG:3035"
+y_numbering : -1
+
+
+check : 
+  size : 950000
+  lonlat(first) : [-35.034,66.9821]
+  lonlat(last)  : [41.1397,23.9423]
+  bounding_box(n,w,s,e) : [72.6426, -35.035, 23.9413, 73.9386]
+  uid : fe4ea53ff38ccefeae02e53ee307ab42
+  xmin : 2502497.60
+  ymin : 752495.56
diff --git a/doc/example-grids/regional_lambert_1.yml → ...ds/regional_lambert_conformal_conic_1.yml b/doc/example-grids/regional_lambert_1.yml → ...ds/regional_lambert_conformal_conic_1.yml
@@ -4,16 +4,19 @@ ny : 40
 dx : 50000
 dy : 50000
 lonlat(centre) : [4,50]
+
 projection :
-    type : "lambert"
-    latitude1  : 50
+    type : "lambert_conformal_conic"
     longitude0 : 4
-y_numbering : +1
+    latitude1  : 50
 
+y_numbering : +1
 
 check : 
   size : 2000
   lonlat(first) : [-10.3173,40.22]
   lonlat(last)  : [24.4368,57.2335]
-  uid : 1cb0b7c8f91617c3b6065d72b85c65c4
+  uid : 2e01d66aa6df870b0ad346da4e80c4ff
   bounding_box(n,w,s,e) : [58.7333,-16.4378,40.219,24.4378]
+  xmin : -1225000.00
+  ymin : -975000.00
diff --git a/doc/example-grids/regional_lambert_2.yml → ...ds/regional_lambert_conformal_conic_2.yml b/doc/example-grids/regional_lambert_2.yml → ...ds/regional_lambert_conformal_conic_2.yml
@@ -5,7 +5,7 @@ dx : 13545.0
 dy : 13545.0
 lonlat(xmin,ymin): [-126.138,16.281]
 projection :  
-    type : "lambert"
+    type : "lambert_conformal_conic"
     latitude1  : 25.0
     longitude0 : -95.0
 y_numbering : +1
@@ -15,5 +15,7 @@ check :
   size : 151987
   lonlat(first) : [-126.138,16.281]
   lonlat(last)  : [-57.3811,55.4813]
-  uid : ec98b263e57286710aeb4131a614b5f9
+  uid : 5c9a0f242e68ff6dd7711ba3ab6f5c7b
   bounding_box(n,w,s,e) : [58.3664,-139.857,16.28,-57.3801]
+  xmin : -3332155.29
+  ymin : -588892.76
diff --git a/doc/example-grids/regular_lonlat_2.yml b/doc/example-grids/regular_lonlat_2.yml
@@ -18,4 +18,5 @@ check:
   bounding_box(n,w,s,e) : [60.001, -164.730, 39.999, -151.270]
   lonlat(first) : [-158., 40.]
   lonlat(last) : [-164.729, 59.547]
+  uid : 5ba0c02a9508d662d751ba34fdb4279e
 
diff --git a/doc/example-grids/regular_lonlat_3.yml b/doc/example-grids/regular_lonlat_3.yml
@@ -18,4 +18,5 @@ check:
   bounding_box(n,w,s,e) : [-19.999, 18.370, -40.001, 25.630]
   lonlat(first) : [18.371, -20.243]
   lonlat(last) : [22., -40.]
+  uid : 8c3901b64831fa8418485aba519874df
 
diff --git a/doc/example-grids/update_uid.py b/doc/example-grids/update_uid.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 #
 # This script checks all example-grids and updates the uid to a newly calculated uid
@@ -25,29 +25,33 @@ def run_program_get_error(file):
 
 def process_file( file, newfile ):
 
-  import string
-  print( "File: " , file )
+    import string
+    print( "File: " , file )
 
-  f = open(file,"r+")
-  text = f.read()
-  f.close()
+    f = open(file,"r+")
+    text = f.read()
+    f.close()
 
-  line = run_program_get_error( file )
-  if line:
-      print( line )
-      import re
-      replace = re.match( r"Check failed: grid uid (.*) expected to be (.*)$", line ).group(1)
-      uid = re.findall( r"^  uid : (.*)$", text, re.MULTILINE)[0]
-      print("Search/Replace ",uid, " to ", replace )
-      newtext = text.replace( uid, replace )
-  else:
-      print( "Nothing to replace, copy-only" )
-      newtext = text
+    newtext = text
 
-  print( "New file: ", newfile)
-  f = open(newfile,"w")
-  f.write(newtext)
-  f.close()
+    lines = run_program_get_error( file )
+    if lines:
+        for line in lines.splitlines():
+            import re
+            matched = re.match( r"Check failed: grid uid (.*) expected to be (.*)$", line )
+            if matched :
+                print( line )
+                replace = matched.group(1)
+                uid = re.findall( r"^  uid : (.*)$", text, re.MULTILINE)[0]
+                print("Search/Replace ",uid, " to ", replace )
+                newtext = text.replace( uid, replace )
+    else:
+        print( "Nothing to replace, copy-only" )
+
+    print( "New file: ", newfile)
+    f = open(newfile,"w")
+    f.write(newtext)
+    f.close()
 
 
 import sys

diff --git a/src/apps/atlas-benchmark.cc b/src/apps/atlas-benchmark.cc
@@ -47,6 +47,7 @@
 #include "atlas/mesh/actions/BuildHalo.h"
 #include "atlas/mesh/actions/BuildParallelFields.h"
 #include "atlas/mesh/actions/BuildPeriodicBoundaries.h"
+#include "atlas/mesh/actions/Reorder.h"
 #include "atlas/meshgenerator.h"
 #include "atlas/output/Gmsh.h"
 #include "atlas/parallel/Checksum.h"
@@ -126,7 +127,7 @@ struct TimerStats {
 //----------------------------------------------------------------------------------------------------------------------
 
 class AtlasBenchmark : public AtlasTool {
-    virtual int execute( const Args& args );
+    int execute( const Args& args ) override;
 
 public:
     AtlasBenchmark( int argc, char** argv ) : AtlasTool( argc, argv ) {
@@ -138,6 +139,8 @@ class AtlasBenchmark : public AtlasTool {
         add_option( new SimpleOption<bool>( "output", "Write output in gmsh format" ) );
         add_option( new SimpleOption<long>( "exclude", "Exclude number of iterations in statistics (default=1)" ) );
         add_option( new SimpleOption<bool>( "details", "Show detailed timers (default=false)" ) );
+        add_option( new SimpleOption<std::string>( "reorder", "Reorder mesh (default=none)" ) );
+        add_option( new SimpleOption<bool>( "sort_edges", "Sort edges by lowest node local index" ) );
     }
 
     void setup();
@@ -169,6 +172,8 @@ class AtlasBenchmark : public AtlasTool {
     long omp_threads;
     double dz;
     std::string gridname;
+    std::string reorder{"none"};
+    bool sort_edges{false};
 
     TimerStats iteration_timer;
     TimerStats haloexchange_timer;
@@ -196,6 +201,8 @@ int AtlasBenchmark::execute( const Args& args ) {
     args.get( "exclude", exclude );
     output = false;
     args.get( "output", output );
+    args.get( "reorder", reorder );
+    args.get( "sort_edges", sort_edges );
     bool help( false );
     args.get( "help", help );
 
@@ -308,9 +315,12 @@ void AtlasBenchmark::setup() {
     ATLAS_TRACE_SCOPE( "Create mesh" ) {
         mesh = MeshGenerator( "structured", util::Config( "partitioner", "equal_regions" ) ).generate( grid );
     }
+    mesh::actions::Reorder{option::type( reorder )}( mesh );
 
     ATLAS_TRACE_SCOPE( "Create node_fs" ) { nodes_fs = functionspace::NodeColumns( mesh, option::halo( halo ) ); }
-    ATLAS_TRACE_SCOPE( "Create edges_fs" ) { edges_fs = functionspace::EdgeColumns( mesh, option::halo( halo ) ); }
+    ATLAS_TRACE_SCOPE( "Create edges_fs" ) {
+        edges_fs = functionspace::EdgeColumns( mesh, option::halo( halo ) | util::Config( "sort_edges", sort_edges ) );
+    }
 
     // mesh.polygon(0).outputPythonScript("plot_polygon.py");
     //  atlas::output::Output gmsh = atlas::output::Gmsh( "edges.msh",

diff --git a/src/apps/atlas-gaussian-latitudes.cc b/src/apps/atlas-gaussian-latitudes.cc
@@ -35,7 +35,7 @@ using atlas::grid::spacing::GaussianSpacing;
 //------------------------------------------------------------------------------------------------------
 
 class AtlasGaussianLatitudes : public eckit::Tool {
-    virtual void run();
+    void run() override;
 
 public:
     AtlasGaussianLatitudes( int argc, char** argv ) : eckit::Tool( argc, argv ) {

diff --git a/src/apps/atlas-gmsh-extract.cc b/src/apps/atlas-gmsh-extract.cc
@@ -33,7 +33,7 @@ using namespace atlas;
 //------------------------------------------------------------------------------------------------------
 
 class gmsh_extract : public eckit::Tool {
-    virtual void run();
+    void run() override;
 
 public:
     gmsh_extract( int argc, char** argv ) : eckit::Tool( argc, argv ) {