Convert to running the interpolation on CETO

app/regrid_domain_ceto/file/add_FillValue.sh

+#!/bin/sh
+vars_str=$1
+vars_list=$(echo $vars_str | tr "," "\n")
+for v in $vars_list; do
+ncatted -a _FillValue,$v,o,f,"-32768" output.nc
+done
+

app/regrid_domain_ceto/file/grid_interp.py

@@ -65,45 +65,50 @@ if rank == 0:
         collected_interp_data[this_var] = np.ma.masked_invalid(np.vstack(output_list))
 
     # write to cmems format
-    output_file = 'output.nc'
     fvcom = pf.read.FileReader(fvcom_file)
 
     dims = {'time':len(fvcom.time.datetime), 'depth':len(worker.regular_grid.dep_lays), 'lon':len(worker.regular_grid.lons),
                                 'lat':len(worker.regular_grid.lats), 'DateStrLen': 26} 
 
-    all_attributes = {'lon':{'standard_name':'longitude', 'units':'degrees_east'},
-            'lat':{'standard_name':'latitude', 'units':'degrees_north'},
-            'depth':{'standard_name':'depth', 'units':'m'},
-            'temp':{'standard_name':'sea_water_potential_temperature','units':'C','missing_value':-32768} ,
-            'salinity':{'standard_name':'sea_water_salinity','units':'psu', 'missing_value':-32768},
-            'u':{'standard_name':'eastward_sea_water_velocity','units':'m s-1', 'missing_value':32768},
-            'v':{'standard_name':'northward_sea_water_velocity','units':'m s-1', 'missing_value':-32768},
-            'zeta':{'standard_name':'sea_surface_height_above_geoid','units':'m', 'missing_value':-32768}}
+    output_file_name = 'output.nc'
+
+    all_attributes = {'lon':{'standard_name':'longitude', 'units':'degrees_east', 'long_name':'longitude'},
+            'lat':{'standard_name':'latitude', 'units':'degrees_north', 'long_name':'latitude'},
+            'depth':{'standard_name':'depth', 'units':'m', 'long_name':'depth, measured downwards from free surface', 'axis':'Z', 'positive':'down'},
+            'temp':{'standard_name':'sea_water_potential_temperature','units':'C','missing_value':-32768, 'long_name':'Sea Water Potential Temperature'} ,
+            'salinity':{'standard_name':'sea_water_salinity','units':'psu', 'missing_value':-32768, 'long_name':'Sea Water Salinity'},
+            'u':{'standard_name':'eastward_sea_water_velocity','units':'m s-1', 'missing_value':-32768, 'long_name':'Eastward Current Velocity'},
+            'v':{'standard_name':'northward_sea_water_velocity','units':'m s-1', 'missing_value':-32768, 'long_name':'Northward Current Velocity'},
+            'zeta':{'standard_name':'sea_surface_height_above_geoid','units':'m', 'missing_value':-32768,'long_name':'Sea surface height above geoid'}}
 
     globals = {'type': 'OPERATIONAL MODEL REGULAR GRID OUTPUT',
-                   'title': 'Regularly gridded data interpolated from FVCOM output',
-                   'history': 'File created using PyFVCOM',
-                   'filename': str(output_file),
-                   'Conventions': 'CF-1.0'}
+                    'title': 'Regularly gridded data interpolated from FVCOM output',
+                    'history': 'File created using PyFVCOM',
+                    'filename': str(output_file_name),
+                    'Conventions': 'CF-1.0',
+                    '_FillValue':-32768}
 
     for this_val in collected_interp_data.values():
         np.ma.set_fill_value(this_val, -32768)
     ncopts = {}
 
-    with pf.preproc.WriteForcing(output_file, dims, global_attributes=globals, clobber=True, format='NETCDF4') as outfile:
+    #for this_var, this_mode in varlist.items():
+    #    this_output_file_name = 'output_{}.nc'.format(this_var)
+    
+    with pf.preproc.WriteForcing(output_file_name, dims, global_attributes=globals, clobber=True, format='NETCDF4') as outfile:
         # Add the variables.
+        outfile.write_fvcom_time(fvcom.time.datetime)
         outfile.add_variable('lon', worker.regular_grid.lons, ['lon'], attributes=all_attributes['lon'])
         outfile.add_variable('lat', worker.regular_grid.lats, ['lat'], attributes=all_attributes['lat'])
         outfile.add_variable('depth', worker.regular_grid.dep_lays, ['depth'], attributes=all_attributes['depth'])
-        
+    
         for this_var, this_mode in varlist.items():
             if this_mode == 'surface':
                 outfile.add_variable(this_var, collected_interp_data[this_var], ['time', 'lon', 'lat'],
-                                 attributes=all_attributes[this_var], ncopts=ncopts)
+                                         attributes=all_attributes[this_var], ncopts=ncopts)
             else:
                 outfile.add_variable(this_var, collected_interp_data[this_var], ['time', 'lon', 'lat', 'depth'],
-                                 attributes=all_attributes[this_var], ncopts=ncopts)
-        
-        outfile.write_fvcom_time(fvcom.time.datetime)
+                                         attributes=all_attributes[this_var], ncopts=ncopts)
+            
 else:
     print('Rank {} process finished'.format(rank))

app/regrid_domain_ceto/rose-app.conf

@@ -15,4 +15,8 @@ default =
 	export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so;
 
 	srun -n $np python3 grid_interp.py ${FVCOM_GRID_NAME}_0001.nc ${GRID_LOWER_LEFT} ${GRID_UPPER_RIGHT} ${HORIZ_RES} ${DEPTH_LAYERS} ${VARS};
+
+	module purge;
+	module load nco;	
+	bash ./add_FillValue.sh ${VARS};
 	mv output.nc ${ROSE_DATAC}

app/softlink_to_portal/rose-app.conf

+[command]
+default =       src_file=/${OUTPUT_DIR}/${FORECAST_DAY}/${OUTPUT_FILENAME}.nc;
+		mkdir -p /${PORTAL_BASEDIR}/${FORECAST_YEAR}/${FORECAST_MONTH}/
+		dst_file=/${PORTAL_BASEDIR}/${FORECAST_YEAR}/${FORECAST_MONTH}/${OUTPUT_FILENAME}_hrly_${FORECAST_DAY}.nc
+
+		ln -sf ${src_file} ${dst_file}

app/transfer_from_remote/rose-app.conf

@@ -2,5 +2,4 @@
 default =       dst=/pml${OUTPUT_DIR}/${FORECAST_DAY};
 		mkdir -p $dst;
                 src=${ROSE_DATAC}/output.nc;
-                ssh ceto6 -t "rsync -aph --no-o --no-g $src $dst/${OUTPUT_FILENAME}";
-
+                ssh ceto6 -t "rsync -aph --no-o --no-g $src $dst/${OUTPUT_FILENAME}.nc";

rose-suite.conf

 [jinja2:suite.rc]
 ## Run properties
-INITIAL_START_DATE='2019-03-18T00:00:00Z'
+INITIAL_START_DATE='2019-05-04T00:00:00Z'
 FINAL_CYCLE_POINT='NONE'
 MAIL_TO='mbe@pml.ac.uk'
 NPROCS=12
@@ -16,8 +16,10 @@ FVCOM_OUTPUT_DIR='data/sthenno1/scratch/modop/Model/FVCOM_tamar/output'
 GRID_LOWER_LEFT='-4.3,50.24'
 GRID_UPPER_RIGHT='-4.05,50.55'
 HORIZ_RES=0.001
-DEPTH_LAYERS='0,2,5,10,15,25,40'
+DEPTH_LAYERS='0,3,5,10,15,20,25,30,40'
 VARS='temp,salinity,u,v,zeta'
 
 OUTPUT_DIR='data/sthenno1/scratch/modop/Model/FVCOM_tamar/estuary_output'
-OUTPUT_FILENAME='tamar_estuary_0001.nc'
+OUTPUT_FILENAME='tamar_estuary_001'
+
+PORTAL_BASEDIR='data/sthenno1/scratch/modop/Portal/Model/TAMAR_ESTUARY_FORECAST_PHY_001/tamar_estuary_forecast_phy_001_hourly_t_s_u_v_ssh'

suite.rc

@@ -15,7 +15,7 @@
 			graph = """
 {% if USE_CETO %}
 					regrid_domain_ceto[-P1D]:finish => start_cycle => suite_trigger <{{TRIGGER_SUITE}}::{{TRIGGER_TASK}}> => transfer_to_remote
-					transfer_to_remote => regrid_domain_ceto => transfer_from_remote
+					transfer_to_remote => regrid_domain_ceto => transfer_from_remote => softlink_to_portal
 {% else %}
 					regrid_domain[-P1D]:finish => start_cycle => suite_trigger <{{TRIGGER_SUITE}}::{{TRIGGER_TASK}}> => regrid_domain
 {% endif %}
@@ -43,8 +43,11 @@
 			OUTPUT_DIR={{OUTPUT_DIR}}
 			OUTPUT_FILENAME={{OUTPUT_FILENAME}}
 			FORECAST_DAY=$(rose date --print-format='%Y-%m-%d' $CYLC_TASK_CYCLE_POINT)
-			
+			FORECAST_YEAR=$(rose date --print-format='%Y' $CYLC_TASK_CYCLE_POINT)
+			FORECAST_MONTH=$(rose date --print-format='%m' $CYLC_TASK_CYCLE_POINT)
+	
 			FVCOM_FILE={{FVCOM_OUTPUT_DIR}}/${FORECAST_DAY}/${FVCOM_GRID_NAME}_0001.nc
+			PORTAL_BASEDIR={{PORTAL_BASEDIR}}
 
         [[start_cycle]]
                 script = """
@@ -86,6 +89,7 @@
 		inherit = remote_job
 	[[regrid_domain_ceto]]
 		inherit = slurm_job
+	[[softlink_to_portal]]
 {% else %}
 
 	[[regrid_domain]]