failing to interface to planar ugrid

xios_examples/ugrid_projected/Makefile

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+# Make file for the write demonstartion XIOS programme
+# Targets provided our detailed below...
+#
+# all: (default) Build the write programme
+# clean: Delete all final products and working files
+# run: run the programme
+#
+# Environment Variables expected by this MakeFile:
+#
+# FC: mpif90
+# FCFLAGS: -g & include files for netcdf & xios
+# LD_FLAGS: for xios, netcdf, netcdff, stfc++
+# LD_LIBRARY_PATH: for netCDF & XIOS libs
+# XIOS_BINDIR: The directory for XIOS binary files
+
+.PHONY: all, clean, run
+
+all: write
+
+# fortran compilation
+%.o: %.F90
+	$(FC) $(FCFLAGS) -c $<
+
+# fortran linking
+write: write.o
+	$(FC) -o write.exe write.o $(LDFLAGS) \
+		&& ln -fs $(XIOS_BINDIR)/xios_server.exe .
+
+run:
+	mpiexec -n 1 ./write.exe : -n 1 ./xios_server.exe
+
+# cleanup
+clean:
+	rm -f *.exe *.o *.mod *.MOD *.out *.err

xios_examples/ugrid_projected/Readme.md

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+Demonstration of basic UGrid domain specification.
+
+Read mesh from file then create output mesh to add data to.

xios_examples/ugrid_projected/axis_check.xml

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+<context>
+
+  <calendar type="Gregorian"/>
+
+  <domain_definition>
+
+    <domain id="mesh_node_domain" type="unstructured"  nvertex="1">
+      <generate_rectilinear_domain/>
+    </domain>
+
+    <domain id="mesh_face_domain" type="unstructured"  nvertex="4">
+      <generate_rectilinear_domain/>
+    </domain>
+
+    <domain id="mesh_edge_domain" type="unstructured"  nvertex="2">
+      <generate_rectilinear_domain/>
+    </domain>
+
+  </domain_definition>
+
+  <grid_definition>
+    <grid id="mfng" >
+      <axis id="fv" />
+      <domain domain_ref="mesh_face_domain" />
+      <!-- <axis id="nf" /> -->
+    </grid>
+    <grid id="meng" >
+      <axis id="ev" />
+      <domain domain_ref="mesh_edge_domain" />
+      <!-- <axis id="ne" /> -->
+    </grid>
+  </grid_definition>
+
+
+  <file_definition type="one_file">
+    <file id="din" name="cubedsphere_mesh" output_freq="1ts" mode="read" enabled=".true." convention="UGRID">
+      <field id="cndata" name="node_empty_data_container" domain_ref="mesh_node_domain" operation="once" read_access=".true." />
+      <field id="cfdata" name="face_empty_data_container" domain_ref="mesh_face_domain" operation="instant" read_access=".true." />
+      <field id="cedata" name="edge_empty_data_container" domain_ref="mesh_edge_domain" operation="instant" read_access=".true." />
+      <field id="mesh_face_nodes" grid_ref="mfng" name="mesh_face_nodes"  operation="instant" read_access=".true." prec="2" />
+      <field id="mesh_edge_nodes" grid_ref="meng" name="mesh_edge_nodes"  operation="instant" read_access=".true." prec="2" />
+    </file>
+  </file_definition>
+
+</context>

xios_examples/ugrid_projected/iodef.xml

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+<?xml version="1.0"?>
+<simulation>
+
+<context id="main" src="main.xml"/>
+<context id="axis_check" src="axis_check.xml"/>
+
+<context id="xios" src="xios.xml"/>
+
+</simulation>

xios_examples/ugrid_projected/main.xml

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+<context>
+
+  <calendar type="Gregorian"/>
+
+  <domain_definition>
+
+    <domain id="node_domain" name="cubedsphere" type="unstructured" nvertex="1">
+      <generate_rectilinear_domain/>
+    </domain>
+
+    <domain id="face_domain" name="cubedsphere" type="unstructured" nvertex="4">
+      <generate_rectilinear_domain/>
+    </domain>
+
+    <domain id="edge_domain" name="cubedsphere" type="unstructured" nvertex="2">
+      <generate_rectilinear_domain/>
+    </domain>
+
+  </domain_definition>
+
+
+  <field_definition prec="8" enabled=".TRUE." >
+    <field id="ndata" name="arbitrary_node_data" domain_ref="node_domain" long_name="Arbitrary data values" unit="1" />
+    <field id="fdata" name="arbitrary_face_data" domain_ref="face_domain" long_name="Arbitrary data values" unit="1" />
+    <field id="edata" name="arbitrary_edge_data" domain_ref="edge_domain" long_name="Arbitrary data values" unit="1" />
+  </field_definition>
+
+
+  <file_definition type="one_file">
+    <file id="data_output" convention="UGRID" enabled=".TRUE." output_freq="1ts">
+      <field_group operation="instant">
+        <field field_ref="ndata" >
+        </field>
+        <field field_ref="fdata" >
+        </field>
+        <field field_ref="edata" >
+        </field>
+
+      </field_group>
+
+
+    </file>
+  </file_definition>
+
+</context>

xios_examples/ugrid_projected/planar_mesh.cdl

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+netcdf planar_mesh {
+dimensions:
+	One = 1 ;
+	Two = 2 ;
+	Four = 4 ;
+	nmesh_node = 21 ;
+	nmesh_edge = 32 ;
+	nmesh_face = 12 ;
+variables:
+	int mesh ;
+		mesh:cf_role = "mesh_topology" ;
+		mesh:geometry = "planar" ;
+		mesh:topology = "non_periodic" ;
+		mesh:coord_sys = "xyz" ;
+		mesh:periodic_x = "F" ;
+		mesh:periodic_y = "F" ;
+		mesh:constructor_inputs = "geometry=planar;topology=non_periodic;coord_sys=xyz;edge_cells_x=6;edge_cells_y=2;periodic_x=F;periodic_y=F;domain_size=[6.00,2.00];domain_centre=[9000.00,7000.00]" ;
+		mesh:max_stencil_depth = 0 ;
+		mesh:n_mesh_maps = 0 ;
+		mesh:long_name = "Topology data of 2D unstructured mesh" ;
+		mesh:topology_dimension = 2 ;
+		mesh:node_coordinates = "mesh_node_x mesh_node_y" ;
+		mesh:face_coordinates = "mesh_face_x mesh_face_y" ;
+		mesh:face_node_connectivity = "mesh_face_nodes" ;
+		mesh:edge_node_connectivity = "mesh_edge_nodes" ;
+		mesh:face_edge_connectivity = "mesh_face_edges" ;
+		mesh:face_face_connectivity = "mesh_face_links" ;
+		mesh:domain_extents = "mesh_domain_extents" ;
+		mesh:npanels = 1 ;
+	int mesh_face_nodes(nmesh_face, Four) ;
+		mesh_face_nodes:cf_role = "face_node_connectivity" ;
+		mesh_face_nodes:long_name = "Maps every quadrilateral face to its four corner nodes." ;
+		mesh_face_nodes:start_index = 1 ;
+	int mesh_face_edges(nmesh_face, Four) ;
+		mesh_face_edges:cf_role = "face_edge_connectivity" ;
+		mesh_face_edges:long_name = "Maps every quadrilateral face to its four edges." ;
+		mesh_face_edges:start_index = 1 ;
+	int mesh_face_links(nmesh_face, Four) ;
+		mesh_face_links:cf_role = "face_face_connectivity" ;
+		mesh_face_links:long_name = "Indicates which other faces neighbour each face." ;
+		mesh_face_links:start_index = 1 ;
+		mesh_face_links:_FillValue = -9999 ;
+	int mesh_edge_nodes(nmesh_edge, Two) ;
+		mesh_edge_nodes:cf_role = "edge_node_connectivity" ;
+		mesh_edge_nodes:long_name = "Maps every edge to the two nodes that it connects." ;
+		mesh_edge_nodes:start_index = 1 ;
+	double mesh_node_x(nmesh_node) ;
+		mesh_node_x:standard_name = "projection_x_coordinate" ;
+		mesh_node_x:long_name = "x coordinate of 2D mesh nodes." ;
+		mesh_node_x:units = "m" ;
+	double mesh_node_y(nmesh_node) ;
+		mesh_node_y:standard_name = "projection_y_coordinate" ;
+		mesh_node_y:long_name = "y coordinate of 2D mesh nodes." ;
+		mesh_node_y:units = "m" ;
+	double mesh_face_x(nmesh_face) ;
+		mesh_face_x:standard_name = "projection_x_coordinate" ;
+		mesh_face_x:long_name = "x coordinate of 2D face centres" ;
+		mesh_face_x:units = "m" ;
+	double mesh_face_y(nmesh_face) ;
+		mesh_face_y:standard_name = "projection_y_coordinate" ;
+		mesh_face_y:long_name = "y coordinate of 2D face centres" ;
+		mesh_face_y:units = "m" ;
+	double mesh_domain_extents(Four, Two) ;
+	double node_empty_data_container(nmesh_node) ;
+	       node_empty_data_container:coordinates = "mesh_node_y mesh_node_x" ;
+	double face_empty_data_container(nmesh_face) ;
+	       face_empty_data_container:coordinates = "mesh_face_y mesh_face_x" ;
+	double edge_empty_data_container(nmesh_edge) ;
+
+// global attributes:
+                :Conventions = "CF-1.6 UGRID-1.0" ;
+
+data:
+
+ mesh = _ ;
+
+ mesh_face_nodes =
+  1, 2, 3, 4,
+  2, 5, 6, 3,
+  5, 7, 8, 6,
+  7, 9, 10, 8,
+  9, 11, 12, 10,
+  11, 13, 14, 12,
+  15, 16, 2, 1,
+  16, 17, 5, 2,
+  17, 18, 7, 5,
+  18, 19, 9, 7,
+  19, 20, 11, 9,
+  20, 21, 13, 11 ;
+
+ mesh_face_edges =
+  1, 2, 3, 4,
+  3, 5, 6, 7,
+  6, 8, 9, 10,
+  9, 11, 12, 13,
+  12, 14, 15, 16,
+  15, 17, 18, 19,
+  20, 21, 22, 2,
+  22, 23, 24, 5,
+  24, 25, 26, 8,
+  26, 27, 28, 11,
+  28, 29, 30, 14,
+  30, 31, 32, 17 ;
+
+ mesh_face_links =
+  _, 7, 2, _,
+  1, 8, 3, _,
+  2, 9, 4, _,
+  3, 10, 5, _,
+  4, 11, 6, _,
+  5, 12, _, _,
+  _, _, 8, 1,
+  7, _, 9, 2,
+  8, _, 10, 3,
+  9, _, 11, 4,
+  10, _, 12, 5,
+  11, _, _, 6 ;
+
+ mesh_edge_nodes =
+  4, 1,
+  1, 2,
+  3, 2,
+  4, 3,
+  2, 5,
+  6, 5,
+  3, 6,
+  5, 7,
+  8, 7,
+  6, 8,
+  7, 9,
+  10, 9,
+  8, 10,
+  9, 11,
+  12, 11,
+  10, 12,
+  11, 13,
+  14, 13,
+  12, 14,
+  1, 15,
+  15, 16,
+  2, 16,
+  16, 17,
+  5, 17,
+  17, 18,
+  7, 18,
+  18, 19,
+  9, 19,
+  19, 20,
+  11, 20,
+  20, 21,
+  13, 21 ;
+
+ mesh_node_x = 8997, 8998, 8998, 8997, 8999, 8999, 9000, 9000, 9001, 9001, 
+    9002, 9002, 9003, 9003, 8997, 8998, 8999, 9000, 9001, 9002, 9003 ;
+
+ mesh_node_y = 7000, 7000, 7001, 7001, 7000, 7001, 7000, 7001, 7000, 7001, 
+    7000, 7001, 7000, 7001, 6999, 6999, 6999, 6999, 6999, 6999, 6999 ;
+
+ mesh_face_x = 8997.5, 8998.5, 8999.5, 9000.5, 9001.5, 9002.5, 8997.5, 
+    8998.5, 8999.5, 9000.5, 9001.5, 9002.5 ;
+
+ mesh_face_y = 7000.5, 7000.5, 7000.5, 7000.5, 7000.5, 7000.5, 6999.5, 
+    6999.5, 6999.5, 6999.5, 6999.5, 6999.5 ;
+
+ mesh_domain_extents =
+  8997, 6999,
+  9003, 6999,
+  9003, 7001,
+  8997, 7001 ;
+}

xios_examples/ugrid_projected/test_write_metadata.py

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+import copy
+import glob
+import netCDF4
+import numpy as np
+import os
+import subprocess
+import unittest
+
+import xios_examples.shared_testing as xshared
+
+this_path = os.path.realpath(__file__)
+this_dir = os.path.dirname(this_path)
+
+class TestWriteMetadata(xshared._TestCase):
+    test_dir = this_dir
+    transient_inputs = ['cubedsphere_mesh.nc']
+    transient_outputs = ['data_output.nc']
+    executable = './write.exe'
+    mesh_file_cdl = 'planar_mesh.cdl'
+
+    @classmethod
+    def make_a_write_test(cls, inf, nclients=1, nservers=1):
+        """
+        this function makes a test case and returns it as a test function,
+        suitable to be dynamically added to a TestCase for running.
+
+        """
+        # always copy for value, don't pass by reference.
+        infcp = copy.copy(inf)
+        # expected by the fortran XIOS program's main.xml
+        inputfile = cls.transient_inputs[0]
+        outputfile = cls.transient_outputs[0]
+        @unittest.skipIf(os.environ.get('MVER', '') != 'XIOS3/trunk',
+                         "skipping for XIOS2 as XIOS3 syntax used")
+        def test_write_metadata(self):
+            # create a netCDF file using nc_method
+            cls.make_netcdf(infcp, inputfile)
+            cls.run_mpi_xios(nclients=nclients, nservers=nservers)
+
+            # load the result netCDF file
+            runfile = '{}/{}'.format(cls.test_dir, outputfile)
+            assert(os.path.exists(runfile))
+        return test_write_metadata
+
+f = f'{this_dir}/planar_mesh.cdl'
+# 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
+
+# !!! remove this limit on success
+if os.environ.get('MVER', '').startswith('XIOS3/trunk'):
+    setattr(TestWriteMetadata, tname,
+            TestWriteMetadata.make_a_write_test(f, nclients=1))