Add ncml conversion step

app/write_ncml/file/write_ncml_file.py

@@ -21,7 +21,8 @@ all_attributes = {'lon':{'var_name':'longitude','standard_name':'longitude', 'un
             'v':{'var_name':'vo','standard_name':'northward_sea_water_velocity','units':'m s-1', 'missing_value':-32768, 'long_name':'Northward Current Velocity', 'shape':'time depth latitude longitude'},
             'zeta':{'var_name':'zos','standard_name':'sea_surface_height_above_geoid','units':'m', 'missing_value':-32768,'long_name':'Sea surface height above geoid', 'shape':'time latitude longitude'},
             'mask':{'standard_name':'sea_binary_mask','units':'1', 'long_name':'Land-sea mask: sea = 1 ; land = 0', 'shape':'depth latitude longitude'},
-            'h':{'standard_name':'h', 'units':'m', 'long_name':'model bathymetry depth, measured downwards from geoid', 'axis':'Z', 'positive':'down', 'shape':'depth latitude longitude' }
+            'h':{'standard_name':'h', 'units':'m', 'long_name':'model bathymetry depth, measured downwards from geoid', 'axis':'Z', 'positive':'down', 'shape':'latitude longitude' },
+            'ww':{'var_name':'wo', 'standard_name':'upward_sea_water_velocity','units':'m s-1', 'missing_value':-32768, 'long_name':'Upward Current Velocity', 'shape':'time depth latitude longitude'}
             }
 
 all_type = {'add_offset':'float', 'scale_factor':'float', '_FillValue':'double'}

app/write_ncml/rose-app.conf

 [command]
 default =
 	base_file=/${PORTAL_BASEDIR}/${FORECAST_YEAR}/${FORECAST_MONTH}/${OUTPUT_FILENAME}_hrly_${FORECAST_DAY}.nc
-	mkdir -p /${PORTAL_NCML_BASEDIR}/${FORECAST_YEAR}/${FORECAST_MONTH}/
-	dst_file=/${PORTAL_NCML_BASEDIR}/${FORECAST_YEAR}/${FORECAST_MONTH}/${OUTPUT_FILENAME}_hrly_${FORECAST_DAY}.ncml
+	dst_file=/${PORTAL_NCML_BASEDIR}/${NCML_FILE_PRE}${NCML_DATE}${NCML_FILE_POST}.ncml
 	rm ${dst_file} || true
 	python3 write_ncml_file.py ${base_file} ${dst_file} ${VARS}

rose-suite.conf

 [jinja2:suite.rc]
 ## Run properties
-INITIAL_START_DATE='2020-01-01T00:00:00Z'
+INITIAL_START_DATE='2020-03-27T00:00:00Z'
 FINAL_CYCLE_POINT='NONE'
 MAIL_TO='mbe@pml.ac.uk'
-NPROCS=12
+NPROCS=20
 USE_CETO=True
 REMOTE_USER='modop'
 NODES=3
@@ -16,11 +16,14 @@ 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='0,3,5,10,15,20,25,30,40'
-VARS='temp,salinity,u,v,zeta'
+DEPTH_LAYERS='0,3,5,10,15,20,25,30,45'
+VARS='temp,salinity,u,v,ww,zeta'
 
 OUTPUT_DIR='data/sthenno1/scratch/modop/Model/FVCOM_tamar/estuary_output'
 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'
-PORTAL_NCML_BASEDIR='data/sthenno1/scratch/modop/Portal/Model/test_ncml/tamar_estuary_forecast_phy_001_hourly_t_s_u_v_ssh'
+PORTAL_NCML_BASEDIR='data/sthenno1/scratch/modop/Portal/Model/FVCOM/tamar'
+NCML_FILE_PRE='MyCOAST_V0_PML_FVCOM_tamar_01hr_'
+NCML_FILE_DATEFMT='%Y%m%d%H'
+NCML_FILE_POST='_ANPR'

suite.rc

@@ -27,7 +27,7 @@
 		env-script = eval $(rose task-env --cycle-offset=P1D)
 		script = rose task-run --verbose
 		[[[job]]]
-			execution time limit = PT3H
+			execution time limit = PT6H
 		[[[events]]]
 			mail events = submission timeout, execution timeout, failed
 			mail to = {{MAIL_TO}}
@@ -42,13 +42,17 @@
 			VARS={{VARS}}
 			OUTPUT_DIR={{OUTPUT_DIR}}
 			OUTPUT_FILENAME={{OUTPUT_FILENAME}}
+			NCML_FILE_DATEFMT={{NCML_FILE_DATEFMT}}
 			FORECAST_DAY=$(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' $CYLC_TASK_CYCLE_POINT)
+			NCML_DATE=$(rose date --print-format=${NCML_FILE_DATEFMT} $CYLC_TASK_CYCLE_POINT)
 	
 			FVCOM_FILE={{FVCOM_OUTPUT_DIR}}/${FORECAST_DAY}/${FVCOM_GRID_NAME}_0001.nc
 			PORTAL_BASEDIR={{PORTAL_BASEDIR}}
 			PORTAL_NCML_BASEDIR={{PORTAL_NCML_BASEDIR}}
+			NCML_FILE_PRE={{NCML_FILE_PRE}}
+			NCML_FILE_POST={{NCML_FILE_POST}}
 
         [[start_cycle]]
                 script = """