pack data with missing value (#27)

* pack data with missing value * use XIOS int conversion * skip notImplemented * ipsl domain * skip notImplemented * restore skip
MetOffice · Oct 25, 2024 · 5f31386 · 5f31386
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commit 5f31386
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Showing 7 changed files with 56 additions and 19 deletions.
diff --git a/.github/workflows/buildTest.yml b/.github/workflows/buildTest.yml
@@ -23,7 +23,7 @@ jobs:
             sudo apt -yq install $(<dependencies)
       - name: clone and build XIOS
         run: |
-          svn co http://forge.ipsl.jussieu.fr/ioserver/svn/${{ matrix.version }} XIOS
+          svn co http://forge.ipsl.fr/ioserver/svn/${{ matrix.version }} XIOS
           cp arch/* XIOS/arch/
           cd XIOS
           if [ ${{ matrix.version }} == 'XIOS3/trunk' ]; then

diff --git a/xios_examples/packing_scale_offset/axis_check.xml b/xios_examples/packing_scale_offset/axis_check.xml
@@ -2,23 +2,17 @@
 
   <calendar type="Gregorian"/>
 
-  <axis_definition>
-    <axis id="x" unit="1" long_name="original x coordinate" />
-    <axis id="y" unit="1" long_name="original y coordinate" />
-
-  </axis_definition>
-
   <grid_definition>
     <grid id="oax_grid">
-      <axis axis_ref="x" />
-      <axis axis_ref="y" />
+      <axis id="x" />
+      <axis id="y" />
     </grid>
 
   </grid_definition>
 
   <file_definition type="one_file">
     <file id="din" name="domain_input" output_freq="1ts" mode="read" enabled=".true.">
-      <field id="odatax" name="original_data" grid_ref="oax_grid" operation="instant" />
+      <field id="odatax" name="original_data" grid_ref="oax_grid" operation="instant" read_access=".true." />
     </file>
   </file_definition>
 

diff --git a/xios_examples/packing_scale_offset/main.xml b/xios_examples/packing_scale_offset/main.xml
@@ -3,8 +3,8 @@
   <calendar type="Gregorian"/>
 
   <domain_definition>
-
     <domain id="original_domain" type="rectilinear" />
+    <generate_rectilinear_domain/>
 
   </domain_definition>
 
@@ -24,10 +24,10 @@
 
   <file_definition type="one_file">
     <file id="domain_input" output_freq="1ts" mode="read" enabled=".true.">
-      <field id="odatain" name="original_data" grid_ref="original_grid" operation="instant" />
+      <field id="odatain" name="original_data" grid_ref="original_grid" operation="instant" read_access=".true." />
     </file>
     <file id="domain_output" output_freq="1ts">
-      <field_group operation="once">
+      <field_group operation="once" conversion_by_netcdf=".false.">
         <field field_ref="odata" />
         <field field_ref="pdata" />
       </field_group>

diff --git a/xios_examples/packing_scale_offset/pack.F90 b/xios_examples/packing_scale_offset/pack.F90
@@ -28,6 +28,8 @@ subroutine initialise()
     integer :: mpi_error
     integer :: lenx
     integer :: leny
+    double precision, dimension (:), allocatable :: latvals, lonvals
+    double precision, dimension (:,:), allocatable :: latb, lonb
 
     ! Arbitrary datetime setup, required for XIOS but unused
     origin = xios_date(2022, 2, 2, 12, 0, 0)
@@ -54,14 +56,23 @@ subroutine initialise()
     call xios_get_axis_attr('x', n_glo=lenx)
     call xios_get_axis_attr('y', n_glo=leny)
 
-    ! initialize the main context for interacting with the data.
+    allocate ( lonvals(lenx) )
+    allocate ( latvals(leny) )
+    allocate ( lonb(2, lenx) )
+    allocate ( latb(2, leny) )
+
+    call xios_get_axis_attr('x', value=lonvals)
+    call xios_get_axis_attr('y', value=latvals)
+
+    ! ! initialize the main context for interacting with the data.
     call xios_context_initialize('main', comm)
 
     call xios_set_time_origin(origin)
     call xios_set_start_date(start)
     call xios_set_timestep(tstep)
 
-    call xios_set_domain_attr("original_domain", ni=lenx, nj=leny, ibegin=0, jbegin=0)
+    call xios_set_domain_attr("original_domain", ni_glo=lenx, nj_glo=leny, ni=lenx, nj=leny, ibegin=0, jbegin=0)
+    call xios_set_domain_attr("original_domain", lonvalue_1d=lonvals, latvalue_1d=latvals)
 
     call xios_close_context_definition()
 
@@ -76,7 +87,7 @@ subroutine finalise()
     call xios_context_finalize()
     call xios_set_current_context('main')
     call xios_context_finalize()
-    call MPI_Comm_free(comm, mpi_error)
+    ! call MPI_Comm_free(comm, mpi_error)
     call xios_finalize()
     call MPI_Finalize(mpi_error)
 
@@ -93,6 +104,7 @@ subroutine simulate()
     ! Allocatable arrays, size is taken from input file
     double precision, dimension (:,:), allocatable :: inodata
 
+    print *, "simulate"
     call xios_get_domain_attr('original_domain', ni_glo=lenx)
     call xios_get_domain_attr('original_domain', nj_glo=leny)
 

diff --git a/...ale_offset/domain_input_simple_linear.cdl → ...packing_scale_offset/pack_data_thirds.cdl b/...ale_offset/domain_input_simple_linear.cdl → ...packing_scale_offset/pack_data_thirds.cdl
diff --git a/xios_examples/packing_scale_offset/pack_data_thirds_missing.cdl b/xios_examples/packing_scale_offset/pack_data_thirds_missing.cdl
@@ -0,0 +1,31 @@
+netcdf domain_input {
+dimensions:
+        x = 5 ;
+        y = 5 ;
+variables:
+        float x(x) ;
+                x:long_name = "original x coordinate" ;
+                x:units = "1";
+        float y(y) ;
+                y:long_name = "original y coordinate" ;
+                y:units = "1";
+        double original_data(y,x) ;
+                original_data:long_name = "input data values" ;
+                original_data:units = "1";
+
+// global attributes:
+                :title = "Input data for XIOS Domain resampling; data is a sum of the x & y coordinates each multiplied by 1/3; x/3 + y/3 ." ;
+
+data:
+
+ x = 0, 2, 4, 6, 8 ;
+
+ y = 0, 2, 4, 6, 8 ;
+
+ original_data =  0,  0.6666666666666666,  1.3333333333333333,  2,  2.6666666666666665,
+                  0.6666666666666666,  1.3333333333333333,  2,  2.6666666666666665, 3.3333333333333335,
+                  1.3333333333333333,  2,  2.6666666666666665, 3.3333333333333335, 4,
+                  2,  2.6666666666666665, 3.3333333333333335, 4, 4.666666666666667,
+                  2.6666666666666665, 3.3333333333333335, 4, 4.666666666666667, _ ;
+
+}
diff --git a/xios_examples/packing_scale_offset/test_packing_cases.py b/xios_examples/packing_scale_offset/test_packing_cases.py
@@ -75,9 +75,9 @@ def test_pack(self):
     # unique name for the test
     tname = 'test_{}'.format(os.path.splitext(os.path.basename(f))[0])
     # add the test as an attribute (function) to the test class
-    if os.environ.get('MVER', '').startswith('XIOS3/trunk'):
-        # these tests are hitting exceptions with XIOS3
-        # but not XIOS2, so skip for XIOS3 runner
+    if os.environ.get('MVER', '') == 'XIOS/trunk@2252':
+        # this test is hitting exceptions with XIOS2@2252
+        # notImplemented "conversion_by_netcdf" , so skip for XIOS2@2252 runner
         setattr(TestPackDomain, tname,
                 unittest.skip(TestPackDomain.make_a_pack_test(f)))
     elif tname in known_failures: