Temporary fix to new atlas error about non-linear interpolation. Add

some input data to the repo so the tests work.

Author: frld

src/orca-jedi/geometry/Geometry.cc

@@ -363,8 +363,6 @@ void Geometry::set_gmask(atlas::Field & field) const {
     auto field_viewgm = atlas::array::make_view<int32_t, 2>(gmask);
 //    auto lonlat_view = atlas::array::make_view<double, 2>(funcSpace_.lonlat());
 
-    
-
     if (has_mv) {
       for (atlas::idx_t j = 0; j < field_viewgm.shape(0); ++j) {
         for (atlas::idx_t k = 0; k < field_viewgm.shape(1); ++k) {

src/tests/Data/CMakeLists.txt

@@ -27,6 +27,8 @@ amm1r_atlas_grid_spec.yaml
 hofx_potm_amm1r_obs.nc
 hofx_ssh_amm_obs.nc
 sic_obs_ideal.nc
+orca2_nicas_grids_local_000001-000001.nc
+orca2_nicas_local_000001-000001.nc
 )
 
 foreach(FILENAME ${orcajedi_test_data})

src/tests/Data/orca2_nicas_grids_local_000001-000001.nc

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c1dff50df912f216a92eb301a79153d69e344a4ef77cfeaf0b3f2533750f8c35
+size 376391

src/tests/Data/orca2_nicas_local_000001-000001.nc

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cc41eb63fcf58e99c02d8167dfff3b8e384429a9a203d7b3b2dee008dab0d3eb
+size 7963989

src/tests/testinput/3dvar_sic.yaml

@@ -14,8 +14,8 @@ cost function:
           testing: true
         io:
           data directory: Data
-          files prefix: dirac_bump_nicas/test
-          overriding nicas file: test_nicas
+          files prefix: dirac_bump_nicas/orca2
+          overriding nicas file: orca2_nicas
         drivers:
           multivariate strategy: univariate
           read local nicas: true
@@ -38,7 +38,7 @@ cost function:
           testing: true
         io:
           data directory: Data
-          files prefix: test
+          files prefix: orca2
         drivers:
           compute variance: true
         variance:
@@ -89,7 +89,7 @@ cost function:
         time interpolation: linear
         atlas-interpolator:
           type: unstructured-bilinear-lonlat
-          non_linear: missing-if-all-missing
+#          non_linear: missing-if-all-missing
           max_fraction_elems_to_try: 0.0
           adjoint: true
       obs operator:

src/tests/testinput/bump_nicas_setup.yaml

@@ -8,9 +8,8 @@ background error:
         testing: true
         universe length-scale: 40000.0e3
       io:
-#        data directory: Data
         data directory: testoutput
-        files prefix: test
+        files prefix: orca2
       drivers:
         compute covariance: false
         compute correlation: false
@@ -19,17 +18,7 @@ background error:
         write diagnostics: true
         compute nicas: true
         write local nicas: true
-    #    write global nicas: true
         write nicas grids: true
-    #  sampling:
-    #    computation grid size: 500
-    #    diagnostic grid size: 250
-    #    distance classes: 10
-    #    angular sectors: 4
-    #    distance class width: 800.0e3
-    #    reduced levels: 2
-    #  ensemble sizes:
-    #    total ensemble size: 50
       model:
         do not cross mask boundaries: true
       nicas:

src/tests/testinput/dirac.yaml

@@ -8,8 +8,8 @@ background error:
         testing: true
       io:
         data directory: Data
-        files prefix: dirac_bump_nicas/test
-        overriding nicas file: test_nicas
+        files prefix: dirac_bump_nicas/orca2
+        overriding nicas file: orca2_nicas
       drivers:
         multivariate strategy: univariate
         read local nicas: true
@@ -33,7 +33,7 @@ background error:
         testing: true
       io:
         data directory: Data
-        files prefix: test
+        files prefix: orca2
       drivers:
         compute variance: true
       variance:

src/tests/testoutput/test_3dvar_sic.ref

@@ -1,26 +1,26 @@
        Independent levels:  1[1]
-          Subset Sc0 size:            26136
+          Subset Sc0 size:            26460
           Domain area (% of Earth area): 0.100E+03%
              Level   1 ~> 100.0%
              Level   1 ~>  0.100E+01 vert. coord.
        Independent levels:  1[1]
-          Subset Sc0 size:            26136
+          Subset Sc0 size:            26460
           Domain area (% of Earth area): 0.100E+03%
              Level   1 ~> 100.0%
              Level   1 ~>  0.100E+01 vert. coord.
 CostJb   : Nonlinear Jb = 0.0000000000000000e+00
-CostJo   : Nonlinear Jo(Sea Ice) = 1.5000000000000000e+00, nobs = 48, Jo/n = 3.1250000000000000e-02, err = 2.0000000000000000e+00
-CostFunction: Nonlinear J = 1.5000000000000000e+00
-DRPCGMinimizer: reduction in residual norm = 1.2748291035575463e+02
+CostJo   : Nonlinear Jo(Sea Ice) = 1.0178967056984216e+08, nobs = 48, Jo/n = 2.1206181368717118e+06, err = 2.0000000000000000e+00
+CostFunction: Nonlinear J = 1.0178967056984216e+08
+DRPCGMinimizer: reduction in residual norm = 3.8373920435826797e+01
 CostFunction::addIncrement: Analysis: 
  Model state valid at time: 2021-06-29T12:00:00Z
     1 variables: ice_area_fraction
     atlas field norms:
-        ice_area_fraction: 3.21124e-03
+        ice_area_fraction: 2.64715e-01
 
 
 
 
-CostJb   : Nonlinear Jb = 0.00000e+00
-CostJo   : Nonlinear Jo(Sea Ice) = 8.72908e-01, nobs = 48, Jo/n = 1.81856e-02, err = 2.00000e+00
-CostFunction: Nonlinear J = 8.72908e-01
+CostJb   : Nonlinear Jb = -2.51949e-03
+CostJo   : Nonlinear Jo(Sea Ice) = 1.00960e+08, nobs = 48, Jo/n = 2.10333e+06, err = 2.00000e+00
+CostFunction: Nonlinear J = 1.00960e+08

src/tests/testoutput/test_dirac.ref

@@ -4,17 +4,17 @@ Input Dirac increment:Increment valid at time: 2021-06-30T12:00:00Z
         ice_area_fraction num: 26553 mean: 3.76605e-05 rms: 6.13682e-03 min: 0.00000e+00 max: 1.00000e+00
 
        Independent levels:  1[1]
-          Subset Sc0 size:            26136
-          Domain area (% of Earth area): 0.643E+02%
-             Level   1 ~>  64.3%
+          Subset Sc0 size:            26460
+          Domain area (% of Earth area): 0.642E+02%
+             Level   1 ~>  64.2%
              Level   1 ~>  0.100E+01 vert. coord.
        Independent levels:  1[1]
-          Subset Sc0 size:            26136
-          Domain area (% of Earth area): 0.643E+02%
-             Level   1 ~>  64.3%
+          Subset Sc0 size:            26460
+          Domain area (% of Earth area): 0.642E+02%
+             Level   1 ~>  64.2%
              Level   1 ~>  0.100E+01 vert. coord.
 Covariance(SABER) * Increment:Increment valid at time: 2021-06-30T12:00:00Z
     1 variables: ice_area_fraction
     atlas field:
-        ice_area_fraction num: 26553 mean: -1.17187e+38 rms: 1.97685e+38 min: -3.33477e+38 max: 1.00000e+00
+        ice_area_fraction num: 17074 mean: 9.21018e-03 rms: 7.51883e-02 min: 0.00000e+00 max: 1.00000e+00