Feature/update atlas 0.38.1 (#107)

* test changes for atlas 0.38.1 * specify minimum atlas version
MetOffice · Aug 29, 2024 · 02e0994 · 02e0994
1 parent 0f16f83
commit 02e0994
Show file tree

Hide file tree

Showing 14 changed files with 37 additions and 38 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,7 +7,7 @@ on:
     branches: [develop]
 env:
     REGISTRY: ghcr.io
-    IMAGE_NAME: twsearle/orca-jedi/ci-almalinux9:v1.2.0
+    IMAGE_NAME: twsearle/orca-jedi/ci-almalinux9:v1.3.0
 jobs:
   build:
     runs-on: ubuntu-latest

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -27,7 +27,7 @@ ecbuild_debug( "   NetCDF_FEATURES: [${NetCDF_FEATURES}]" )
 find_package( eckit 1.18 COMPONENTS LZ4 REQUIRED )
 ecbuild_debug( "   eckit_FEATURES : [${eckit_FEATURES}]" )
 
-find_package( atlas 0.29 REQUIRED )
+find_package( atlas 0.38.1 REQUIRED )
 ecbuild_debug( "   atlas_FEATURES: [${atlas_FEATURES}]" )
 
 find_package( atlas-orca REQUIRED )

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.2.0
+1.3.0
diff --git a/ci/build-and-test.sh b/ci/build-and-test.sh
@@ -58,7 +58,7 @@ ecbuild -S "${HERE}"
 make -j "${NPROC}"
 
 env OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
-    ATLAS_TRACE=1 ATLAS_DEBUG=1 \
+    OOPS_TRACE=1 OOPS_DEBUG=1 \
     LD_LIBRARY_PATH="${HERE}/lib:${LD_LIBRARY_PATH}" \
     ATLAS_DATA_PATH="${HERE}/atlas-data" \
     ctest -j "${NPROC}" -V --output-on-failure --test-dir "./orca-jedi"

diff --git a/src/orca-jedi/geometry/Geometry.cc b/src/orca-jedi/geometry/Geometry.cc
@@ -87,10 +87,12 @@ Geometry::Geometry(const eckit::Configuration & config,
     grid_ = construct_grid_from_name(params_.gridName.value());
 
     int64_t halo = params_.sourceMeshHalo.value();
-    if ( ( (params_.partitioner.value() == "serial") || (comm.size() == 1) )
+    std::string partitioner_name = params_.partitioner.value();
+    if ( ( (partitioner_name == "serial") || (comm.size() == 1) )
          && (halo > 0) ) {
       halo = 0;
-      oops::Log::info() << "Warning: forcing halo = 0"
+      partitioner_name = "serial";
+      oops::Log::info() << "Warning: forcing halo = 0 and serial partitioner"
                         << " as settings imply all processors have all data" << std::endl;
     }
     auto meshgen_config = grid_.meshgenerator()
@@ -99,8 +101,7 @@ Geometry::Geometry(const eckit::Configuration & config,
     atlas::MeshGenerator meshgen(meshgen_config);
     log_status();
     auto partitioner_config = grid_.partitioner();
-    partitioner_config.set("type",
-        params_.partitioner.value());
+    partitioner_config.set("type", partitioner_name);
     partitioner_ = atlas::grid::Partitioner(partitioner_config);
     log_status();
     mesh_ = meshgen.generate(grid_, partitioner_);

diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
@@ -34,7 +34,7 @@ ecbuild_add_test( TARGET test_orcamodel_hofx_ssh_parallel_checkerboard
                   ARGS testinput/hofx_nc_ssh_checkerboard.yaml
                   COMMAND orcamodel_hofx.x )
 
-# Disabled until halos are available from atlas-orca
+# Requires atlas-orca halos > 0 change (https://github.com/ecmwf/atlas-orca/pull/20)
 #ecbuild_add_test( TARGET test_orcamodel_hofx_ssh_parallel_eorca025
 #                  OMP 1
 #                  MPI 2

diff --git a/src/tests/orca-jedi/CMakeLists.txt b/src/tests/orca-jedi/CMakeLists.txt
@@ -1,7 +1,5 @@
 include_directories( ${PROJECT_SOURCE_DIR}/src )
 
-#target_link_libraries( meara_test_nemo_feedback NetCDF::NetCDF_CXX )
-
 ecbuild_add_test( TARGET  test_orcajedi_nemo_io_field_reader.x
                   SOURCES test_nemo_io_field_reader.cc
                   LIBS    orcamodel )

diff --git a/src/tests/orca-jedi/test_interpolator.cc b/src/tests/orca-jedi/test_interpolator.cc
@@ -95,13 +95,13 @@ CASE("test  interpolator") {
         oops::Variable{"sea_surface_foundation_temperature"}}};
     settings_map["ORCA2_T"].surf_values = std::vector<double>{
         1,             missing_value, 0,
-        18.4888916016, missing_value, 18.1592999503};
+        18.4888877869, missing_value, 18.1592998505};
 
     settings_map["ORCA2_T"].vol_vars = oops::Variables{
         {oops::Variable{"sea_water_potential_temperature"}}};
     settings_map["ORCA2_T"].vol_values = std::vector<double>{
-        18.4888916016, missing_value, 18.1592999503,
-        17.9419364929, missing_value, 17.75000288,
+        18.4888877869, missing_value, 18.1592998505,
+        18           , missing_value, 17.7500019073,
         missing_value, missing_value, missing_value};
   }
 

diff --git a/src/tests/testoutput/test_hofx3d_nc_potm.ref b/src/tests/testoutput/test_hofx3d_nc_potm.ref
@@ -1,12 +1,12 @@
-Test     : State: 
-Test     : Model state valid at time: 2021-06-30T00:00:00Z
-Test     :     3 variables: sea_water_potential_temperature, depthBelowWaterSurface, sea_water_potential_temperature_background_error
+Test     : State:
+Test     :  Model state valid at time: 2021-06-30T00:00:00Z
+Test     :     3 variables: sea_water_potential_temperature, sea_water_potential_temperature_background_error, depth
 Test     :     atlas field norms:
 Test     :         sea_water_potential_temperature: 9.73262e-02
 Test     :         sea_water_potential_temperature_background_error: 3.54309e-04
-Test     :         depthBelowWaterSurface: 2.05581e-01
+Test     :         depth: 2.05581e-01
 
-Test     : H(x): 
+Test     : H(x):
 Test     : Sea Temperature nobs= 6 Min=1.80417e+01, Max=1.81944e+01, RMS=1.81181e+01
 
 Test     : End H(x)
diff --git a/src/tests/testoutput/test_hofx3d_nc_prof_2vars.ref b/src/tests/testoutput/test_hofx3d_nc_prof_2vars.ref
@@ -1,14 +1,14 @@
-Test     : State: 
-Test     : Model state valid at time: 2021-06-30T00:00:00Z
-Test     :     5 variables: sea_water_potential_temperature, sea_water_potential_temperature_background_error, depthBelowWaterSurface, salinity, salinity_background_error
+Test     : State:
+Test     :  Model state valid at time: 2021-06-30T00:00:00Z
+Test     :     5 variables: sea_water_potential_temperature, sea_water_potential_temperature_background_error, depth, salinity, salinity_background_error
 Test     :     atlas field norms:
 Test     :         sea_water_potential_temperature: 9.73262e-02
 Test     :         sea_water_potential_temperature_background_error: 3.54309e-04
-Test     :         depthBelowWaterSurface: 2.05581e-01
+Test     :         depth: 2.05581e-01
 Test     :         salinity: 1.89413e-01
 Test     :         salinity_background_error: 3.54309e-04
 
-Test     : H(x): 
+Test     : H(x):
 Test     : ARGO profiles nobs= 12 Min=1.81028e+01, Max=3.52000e+01, RMS=2.79784e+01
 
 Test     : End H(x)
diff --git a/src/tests/testoutput/test_hofx3d_nc_sst.ref b/src/tests/testoutput/test_hofx3d_nc_sst.ref
@@ -1,13 +1,12 @@
-Test     : State: 
+Test     : State:
 Test     :  Model state valid at time: 2021-06-30T00:00:00Z
 Test     :     2 variables: sea_surface_temperature, sea_surface_temperature_background_error
 Test     :     atlas field norms:
 Test     :         sea_surface_temperature: 1.37607e-01
 Test     :         sea_surface_temperature_background_error: 6.13682e-04
 
-Test     : H(x): 
-Test     : Sea Surface Temperature nobs= 7 Min=17.6445, Max=18.4389, RMS=18.0723
-
-Test     : End H(x)
+Test     : H(x):
 
+Test     : Sea Surface Temperature nobs= 7 Min=1.76445e+01, Max=1.84389e+01, RMS=1.80723e+01
 
+Test     : End H(x)
diff --git a/src/tests/testoutput/test_hofx_nc_ice.ref b/src/tests/testoutput/test_hofx_nc_ice.ref
@@ -1,18 +1,18 @@
-Test     : Initial state: 
+Test     : Initial state:
 Test     :  Model state valid at time: 2021-06-28T23:00:00Z
 Test     :     2 variables: ice_area_fraction, ice_area_fraction_background_error
 Test     :     atlas field norms:
 Test     :         ice_area_fraction: 0.00000e+00
 Test     :         ice_area_fraction_background_error: 3.06841e-03
 
-Test     : Final state: 
+Test     : Final state:
 Test     :  Model state valid at time: 2021-06-30T23:00:00Z
 Test     :     2 variables: ice_area_fraction, ice_area_fraction_background_error
 Test     :     atlas field norms:
 Test     :         ice_area_fraction: 3.16981e-03
 Test     :         ice_area_fraction_background_error: 3.06841e-03
 
-Test     : H(x): 
-Test     : Sea Ice nobs= 7 Min=0.00000e+00, Max=5.41667e-01, RMS=2.04731e-01'
+Test     : H(x):
+Test     : Sea Ice nobs= 7 Min=0.00000e+00, Max=5.41667e-01, RMS=2.04731e-01
 
 Test     : End H(x)
diff --git a/src/tests/testoutput/test_hofx_nc_sst.ref b/src/tests/testoutput/test_hofx_nc_sst.ref
@@ -1,18 +1,19 @@
-Test     : Initial state: 
+Test     : Initial state:
 Test     :  Model state valid at time: 2021-06-28T23:00:00Z
 Test     :     2 variables: sea_surface_temperature, sea_surface_temperature_background_error
 Test     :     atlas field norms:
 Test     :         sea_surface_temperature: 1.37673e-01
 Test     :         sea_surface_temperature_background_error: 6.13682e-04
 
-Test     : Final state: 
+Test     : Final state:
 Test     :  Model state valid at time: 2021-06-30T23:00:00Z
 Test     :     2 variables: sea_surface_temperature, sea_surface_temperature_background_error
 Test     :     atlas field norms:
 Test     :         sea_surface_temperature: 1.37683e-01
 Test     :         sea_surface_temperature_background_error: 6.13682e-04
 
-Test     : H(x): 
+Test     : H(x):
+
 Test     : Sea Surface Temperature nobs= 7 Min=1.76544e+01, Max=1.84389e+01, RMS=1.80765e+01
 
 Test     : End H(x)
diff --git a/src/tests/testoutput/test_ostia_seaice_obs_hofx3d.ref b/src/tests/testoutput/test_ostia_seaice_obs_hofx3d.ref
@@ -1,11 +1,11 @@
-Test     : State: 
+Test     : State:
 Test     :  Model state valid at time: 2021-06-30T00:00:00Z
 Test     :     2 variables: ice_area_fraction, ice_area_fraction_background_error
 Test     :     atlas field norms:
 Test     :          ice_area_fraction: 3.20183e-03
 Test     :          ice_area_fraction_background_error: 3.06841e-03
 
-Test     : H(x): 
+Test     : H(x):
 Test     : Sea Ice nobs= 4 Min=0, Max=0, RMS=0
 
 Test     : End H(x)