custom metadata

azspiceEnv

@@ -3,18 +3,12 @@
 # `. azspiceEnv`
 
 # load Azure Spice Spack xios module
-module load xios
+module load csc/2025.3.20 gcc/12.2.0 mpich/4.2.3
+module load netcdf-c/4.9.2 netcdf-fortran/4.6.1
+module load xios/2701
 
-# provide specific sub_paths for the demonstration build
-export XIOS_INCDIR=$XIOS_ROOT/include
-export XIOS_LIBDIR=$XIOS_ROOT/lib
-export XIOS_BINDIR=$XIOS_ROOT/bin
-
-# ensure netcdf is on the LD path & flags
-export LD_LIBRARY_PATH=${NETCDFF_ROOT}/lib:$LD_LIBRARY_PATH
-export LDFLAGS="-L$XIOS_LIBDIR -lxios $(pkg-config --libs netcdf) $(pkg-config --libs netcdf-fortran) -lstdc++"
-
-export FCFLAGS="-g -I$XIOS_INCDIR $(pkg-config --cflags-only-I netcdf) $(pkg-config --cflags-only-I netcdf-fortran)"
+export FCFLAGS="-g $FFLAGS"
+export LDFLAGS="$LDFLAGS -lxios -lnetcdf -lnetcdff -lstdc++"
 export FC=mpif90
-
-export MVER=XIOS/trunk@2252
+export XIOS_BINDIR=`which xios_server.exe | xargs dirname`
+export MVER=XIOS2/trunk

xios_examples/basicUGrid/Makefile

@@ -0,0 +1,34 @@
+# 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/basicUGrid/Readme.md

@@ -0,0 +1,3 @@
+Demonstration of basic UGrid domain specification.
+
+Read mesh from file then create output mesh to add data to.

xios_examples/basicUGrid/actual_data_output.cdl

@@ -0,0 +1,299 @@
+netcdf data_output {
+dimensions:
+	axis_nbounds = 2 ;
+	Two = 2 ;
+	ncubedsphere_node = 8 ;
+	ncubedsphere_edge = 12 ;
+	ncubedsphere_face = 6 ;
+	ncubedsphere_vertex = 4 ;
+	nmain__domain_undef_id_8_node = 8 ;
+	nmain__domain_undef_id_8_edge = 12 ;
+	nmain__domain_undef_id_6_node = 8 ;
+	time_counter = UNLIMITED ; // (2 currently)
+variables:
+	int cubedsphere ;
+		cubedsphere:cf_role = "mesh_topology" ;
+		cubedsphere:long_name = "Topology data of 2D unstructured mesh" ;
+		cubedsphere:topology_dimension = 2 ;
+		cubedsphere:node_coordinates = "cubedsphere_node_x cubedsphere_node_y" ;
+		cubedsphere:edge_coordinates = "cubedsphere_edge_x cubedsphere_edge_y" ;
+		cubedsphere:edge_node_connectivity = "cubedsphere_edge_nodes" ;
+		cubedsphere:face_edge_connectivity = "cubedsphere_face_edges" ;
+		cubedsphere:edge_face_connectivity = "cubedsphere_edge_face_links" ;
+		cubedsphere:face_face_connectivity = "cubedsphere_face_links" ;
+		cubedsphere:face_coordinates = "cubedsphere_face_x cubedsphere_face_y" ;
+		cubedsphere:face_node_connectivity = "cubedsphere_face_nodes" ;
+	float cubedsphere_node_x(ncubedsphere_node) ;
+		cubedsphere_node_x:standard_name = "longitude" ;
+		cubedsphere_node_x:long_name = "Longitude of mesh nodes." ;
+		cubedsphere_node_x:units = "degrees_east" ;
+	float cubedsphere_node_y(ncubedsphere_node) ;
+		cubedsphere_node_y:standard_name = "latitude" ;
+		cubedsphere_node_y:long_name = "Latitude of mesh nodes." ;
+		cubedsphere_node_y:units = "degrees_north" ;
+	float cubedsphere_edge_x(ncubedsphere_edge) ;
+		cubedsphere_edge_x:standard_name = "longitude" ;
+		cubedsphere_edge_x:long_name = "Characteristic longitude of mesh edges." ;
+		cubedsphere_edge_x:units = "degrees_east" ;
+	float cubedsphere_edge_y(ncubedsphere_edge) ;
+		cubedsphere_edge_y:standard_name = "latitude" ;
+		cubedsphere_edge_y:long_name = "Characteristic latitude of mesh edges." ;
+		cubedsphere_edge_y:units = "degrees_north" ;
+	int cubedsphere_edge_nodes(ncubedsphere_edge, Two) ;
+		cubedsphere_edge_nodes:cf_role = "edge_node_connectivity" ;
+		cubedsphere_edge_nodes:long_name = "Maps every edge/link to two nodes that it connects." ;
+		cubedsphere_edge_nodes:start_index = 0 ;
+	float cubedsphere_face_x(ncubedsphere_face) ;
+		cubedsphere_face_x:standard_name = "longitude" ;
+		cubedsphere_face_x:long_name = "Characteristic longitude of mesh faces." ;
+		cubedsphere_face_x:units = "degrees_east" ;
+	float cubedsphere_face_y(ncubedsphere_face) ;
+		cubedsphere_face_y:standard_name = "latitude" ;
+		cubedsphere_face_y:long_name = "Characteristic latitude of mesh faces." ;
+		cubedsphere_face_y:units = "degrees_north" ;
+	int cubedsphere_face_nodes(ncubedsphere_face, ncubedsphere_vertex) ;
+		cubedsphere_face_nodes:cf_role = "face_node_connectivity" ;
+		cubedsphere_face_nodes:long_name = "Maps every face to its corner nodes." ;
+		cubedsphere_face_nodes:start_index = 0 ;
+	int cubedsphere_face_edges(ncubedsphere_face, ncubedsphere_vertex) ;
+		cubedsphere_face_edges:cf_role = "face_edge_connectivity" ;
+		cubedsphere_face_edges:long_name = "Maps every face to its edges." ;
+		cubedsphere_face_edges:start_index = 0 ;
+		cubedsphere_face_edges:_FillValue = 999999 ;
+	int cubedsphere_edge_face_links(ncubedsphere_edge, Two) ;
+		cubedsphere_edge_face_links:cf_role = "edge_face_connectivity" ;
+		cubedsphere_edge_face_links:long_name = "neighbor faces for edges" ;
+		cubedsphere_edge_face_links:start_index = 0 ;
+		cubedsphere_edge_face_links:_FillValue = -999 ;
+		cubedsphere_edge_face_links:comment = "missing neighbor faces are indicated using _FillValue" ;
+	int cubedsphere_face_links(ncubedsphere_face, ncubedsphere_vertex) ;
+		cubedsphere_face_links:cf_role = "face_face_connectivity" ;
+		cubedsphere_face_links:long_name = "Indicates which other faces neighbor each face" ;
+		cubedsphere_face_links:start_index = 0 ;
+		cubedsphere_face_links:_FillValue = 999999 ;
+		cubedsphere_face_links:flag_values = -1 ;
+		cubedsphere_face_links:flag_meanings = "out_of_mesh" ;
+	int main__domain_undef_id_8 ;
+		main__domain_undef_id_8:cf_role = "mesh_topology" ;
+		main__domain_undef_id_8:long_name = "Topology data of 2D unstructured mesh" ;
+		main__domain_undef_id_8:topology_dimension = 2 ;
+		main__domain_undef_id_8:node_coordinates = "main__domain_undef_id_8_node_x main__domain_undef_id_8_node_y" ;
+		main__domain_undef_id_8:edge_node_connectivity = "main__domain_undef_id_8_edge_nodes" ;
+		main__domain_undef_id_8:edge_coordinates = "main__domain_undef_id_8_edge_x main__domain_undef_id_8_edge_y" ;
+	float main__domain_undef_id_8_node_x(nmain__domain_undef_id_8_node) ;
+		main__domain_undef_id_8_node_x:standard_name = "longitude" ;
+		main__domain_undef_id_8_node_x:long_name = "Longitude of mesh nodes." ;
+		main__domain_undef_id_8_node_x:units = "degrees_east" ;
+	float main__domain_undef_id_8_node_y(nmain__domain_undef_id_8_node) ;
+		main__domain_undef_id_8_node_y:standard_name = "latitude" ;
+		main__domain_undef_id_8_node_y:long_name = "Latitude of mesh nodes." ;
+		main__domain_undef_id_8_node_y:units = "degrees_north" ;
+	float main__domain_undef_id_8_edge_x(nmain__domain_undef_id_8_edge) ;
+		main__domain_undef_id_8_edge_x:standard_name = "longitude" ;
+		main__domain_undef_id_8_edge_x:long_name = "Characteristic longitude of mesh edges." ;
+		main__domain_undef_id_8_edge_x:units = "degrees_east" ;
+	float main__domain_undef_id_8_edge_y(nmain__domain_undef_id_8_edge) ;
+		main__domain_undef_id_8_edge_y:standard_name = "latitude" ;
+		main__domain_undef_id_8_edge_y:long_name = "Characteristic latitude of mesh edges." ;
+		main__domain_undef_id_8_edge_y:units = "degrees_north" ;
+	int main__domain_undef_id_8_edge_nodes(nmain__domain_undef_id_8_edge, Two) ;
+		main__domain_undef_id_8_edge_nodes:cf_role = "edge_node_connectivity" ;
+		main__domain_undef_id_8_edge_nodes:long_name = "Maps every edge/link to two nodes that it connects." ;
+		main__domain_undef_id_8_edge_nodes:start_index = 0 ;
+	int main__domain_undef_id_6 ;
+		main__domain_undef_id_6:cf_role = "mesh_topology" ;
+		main__domain_undef_id_6:long_name = "Topology data of 2D unstructured mesh" ;
+		main__domain_undef_id_6:topology_dimension = 2 ;
+		main__domain_undef_id_6:node_coordinates = "main__domain_undef_id_6_node_x main__domain_undef_id_6_node_y" ;
+	float main__domain_undef_id_6_node_x(nmain__domain_undef_id_6_node) ;
+		main__domain_undef_id_6_node_x:standard_name = "longitude" ;
+		main__domain_undef_id_6_node_x:long_name = "Longitude of mesh nodes." ;
+		main__domain_undef_id_6_node_x:units = "degrees_east" ;
+	float main__domain_undef_id_6_node_y(nmain__domain_undef_id_6_node) ;
+		main__domain_undef_id_6_node_y:standard_name = "latitude" ;
+		main__domain_undef_id_6_node_y:long_name = "Latitude of mesh nodes." ;
+		main__domain_undef_id_6_node_y:units = "degrees_north" ;
+	double time_instant(time_counter) ;
+		time_instant:standard_name = "time" ;
+		time_instant:long_name = "Time axis" ;
+		time_instant:calendar = "gregorian" ;
+		time_instant:units = "seconds since 2022-02-02 12:00:00" ;
+		time_instant:time_origin = "2022-02-02 12:00:00" ;
+		time_instant:bounds = "time_instant_bounds" ;
+	double time_instant_bounds(time_counter, axis_nbounds) ;
+	double time_counter(time_counter) ;
+		time_counter:axis = "T" ;
+		time_counter:standard_name = "time" ;
+		time_counter:long_name = "Time axis" ;
+		time_counter:calendar = "gregorian" ;
+		time_counter:units = "seconds since 2022-02-02 12:00:00" ;
+		time_counter:time_origin = "2022-02-02 12:00:00" ;
+		time_counter:bounds = "time_counter_bounds" ;
+	double time_counter_bounds(time_counter, axis_nbounds) ;
+	double arbitrary_face_data(time_counter, ncubedsphere_face) ;
+		arbitrary_face_data:long_name = "Arbitrary data values" ;
+		arbitrary_face_data:units = "1" ;
+		arbitrary_face_data:mesh = "cubedsphere" ;
+		arbitrary_face_data:location = "face" ;
+		arbitrary_face_data:online_operation = "instant" ;
+		arbitrary_face_data:interval_operation = "1 h" ;
+		arbitrary_face_data:interval_write = "1 h" ;
+		arbitrary_face_data:cell_methods = "time: point" ;
+		arbitrary_face_data:coordinates = "time_instant cubedsphere_face_y cubedsphere_face_x" ;
+	double arbitrary_edge_data(time_counter, nmain__domain_undef_id_8_edge) ;
+		arbitrary_edge_data:long_name = "Arbitrary data values" ;
+		arbitrary_edge_data:units = "1" ;
+		arbitrary_edge_data:mesh = "main__domain_undef_id_8" ;
+		arbitrary_edge_data:location = "edge" ;
+		arbitrary_edge_data:online_operation = "instant" ;
+		arbitrary_edge_data:interval_operation = "1 h" ;
+		arbitrary_edge_data:interval_write = "1 h" ;
+		arbitrary_edge_data:cell_methods = "time: point" ;
+		arbitrary_edge_data:coordinates = "time_instant main__domain_undef_id_8_edge_y main__domain_undef_id_8_edge_x" ;
+	double arbitrary_node_data(time_counter, nmain__domain_undef_id_6_node) ;
+		arbitrary_node_data:long_name = "Arbitrary data values" ;
+		arbitrary_node_data:units = "1" ;
+		arbitrary_node_data:mesh = "main__domain_undef_id_6" ;
+		arbitrary_node_data:location = "node" ;
+		arbitrary_node_data:online_operation = "instant" ;
+		arbitrary_node_data:interval_operation = "1 h" ;
+		arbitrary_node_data:interval_write = "1 h" ;
+		arbitrary_node_data:cell_methods = "time: point" ;
+		arbitrary_node_data:coordinates = "time_instant main__domain_undef_id_6_node_y main__domain_undef_id_6_node_x" ;
+
+// global attributes:
+		:name = "data_output" ;
+		:description = "Created by xios" ;
+		:title = "Created by xios" ;
+		:Conventions = "UGRID" ;
+		:timeStamp = "2025-May-07 14:23:04 GMT" ;
+		:uuid = "02f24392-2446-494f-a1a7-d482900beb2b" ;
+data:
+
+ cubedsphere = _ ;
+
+ cubedsphere_node_x = -45, 45, 135, -135, 45, -45, 135, -135 ;
+
+ cubedsphere_node_y = 35.26439, 35.26439, 35.26439, 35.26439, -35.26439, 
+    -35.26439, -35.26439, -35.26439 ;
+
+ cubedsphere_edge_x = 0, -45, 0, 90, 45, 90, 0, 135, 0, -90, -135, -90 ;
+
+ cubedsphere_edge_y = 35.26439, 0, -35.26439, 35.26439, 0, -35.26439, 
+    35.26439, 0, -35.26439, 35.26439, 0, -35.26439 ;
+
+ cubedsphere_edge_nodes =
+  0, 1,
+  5, 0,
+  4, 5,
+  1, 2,
+  4, 1,
+  6, 4,
+  2, 3,
+  6, 2,
+  7, 6,
+  3, 0,
+  7, 3,
+  5, 7 ;
+
+ cubedsphere_face_x = 2.754441e-15, 90, -180, -90, 0, 0 ;
+
+ cubedsphere_face_y = -5.508882e-15, -5.508882e-15, -5.508882e-15, 
+    -5.508882e-15, 90, -90 ;
+
+ cubedsphere_face_nodes =
+  5, 4, 1, 0,
+  4, 6, 2, 1,
+  7, 3, 2, 6,
+  5, 0, 3, 7,
+  0, 1, 2, 3,
+  5, 7, 6, 4 ;
+
+ cubedsphere_face_edges =
+  2, 4, 0, 1,
+  5, 7, 3, 4,
+  10, 6, 7, 8,
+  1, 9, 10, 11,
+  0, 3, 6, 9,
+  11, 8, 5, 2 ;
+
+ cubedsphere_edge_face_links =
+  0, 4,
+  0, 3,
+  0, 5,
+  1, 4,
+  0, 1,
+  1, 5,
+  2, 4,
+  1, 2,
+  2, 5,
+  3, 4,
+  2, 3,
+  3, 5 ;
+
+ cubedsphere_face_links =
+  5, 1, 4, 3,
+  5, 2, 4, 0,
+  3, 4, 1, 5,
+  0, 4, 2, 5,
+  0, 1, 2, 3,
+  3, 2, 1, 0 ;
+
+ main__domain_undef_id_8 = _ ;
+
+ main__domain_undef_id_8_node_x = -45, 45, 135, -135, 45, -45, 135, -135 ;
+
+ main__domain_undef_id_8_node_y = 35.26439, 35.26439, 35.26439, 35.26439, 
+    -35.26439, -35.26439, -35.26439, -35.26439 ;
+
+ main__domain_undef_id_8_edge_x = 0, -45, 0, 90, 45, 90, 0, 135, 0, -90, 
+    -135, -90 ;
+
+ main__domain_undef_id_8_edge_y = 35.26439, 0, -35.26439, 35.26439, 0, 
+    -35.26439, 35.26439, 0, -35.26439, 35.26439, 0, -35.26439 ;
+
+ main__domain_undef_id_8_edge_nodes =
+  0, 1,
+  5, 0,
+  4, 5,
+  1, 2,
+  4, 1,
+  6, 4,
+  2, 3,
+  6, 2,
+  7, 6,
+  3, 0,
+  7, 3,
+  5, 7 ;
+
+ main__domain_undef_id_6 = _ ;
+
+ main__domain_undef_id_6_node_x = -45, 45, 135, -135, 45, -45, 135, -135 ;
+
+ main__domain_undef_id_6_node_y = 35.26439, 35.26439, 35.26439, 35.26439, 
+    -35.26439, -35.26439, -35.26439, -35.26439 ;
+
+ time_instant = 27133200, 27136800 ;
+
+ time_instant_bounds =
+  27133200, 27133200,
+  27136800, 27136800 ;
+
+ time_counter = 27133200, 27136800 ;
+
+ time_counter_bounds =
+  27133200, 27133200,
+  27136800, 27136800 ;
+
+ arbitrary_face_data =
+  10, 10, 10, 10, 10, 10,
+  20, 20, 20, 20, 20, 20 ;
+
+ arbitrary_edge_data =
+  100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100,
+  200, 200, 200, 200, 200, 200, 200, 200, 200, 200, 200, 200 ;
+
+ arbitrary_node_data =
+  1, 1, 1, 1, 1, 1, 1, 1,
+  2, 2, 2, 2, 2, 2, 2, 2 ;
+}