Updates on the test cases and minor fixes in the rt* scripts

README-ufs_weather.md

@@ -0,0 +1,56 @@
+[![Read The Docs Status](https://readthedocs.org/projects/ufs-weather-model/badge/?badge=latest)](http://ufs-weather-model.readthedocs.io/)
+
+# ufs-weather-model
+
+This is the UFS weather model source code
+
+# Where to find information
+
+Start at the [wiki](https://github.com/ufs-community/ufs-weather-model/wiki) which has quick start instructions.
+
+[User's reference guide](http://ufs-weather-model.readthedocs.io/) is hosted on read the docs.
+
+# What files are what
+
+The top level directory structure groups source code and input files as follow:
+
+| File/directory            | Purpose |
+| --------------            | ------- |
+| ```LICENSE.md```          | A copy of the GNU Lesser General Public License, Version 3. |
+| ```README.md```           | This file with basic pointers to more information. |
+| ```NEMS/```               | Contains NOAA Environmental Modeling System source code and nems compset run scripts. |
+| ```CMEPS-interface/```    | Contains CMEPS mediator |
+| ```FV3/```                | Contains FV3 atmosphere model component including FV3 dynamical core, dynamics to physics driver, physics and IO. |
+| ```DATM/```               | Contains Data Atmosphere model component |
+| ```WW3/```                | Contains community wave modeling framework WW3. |
+| ```MOM6-interface/```     | Contains MOM6 ocean model component |
+| ```CICE-interface/```     | Contains CICE sea-ice model component including CICE6 and Icepack |
+| ```stochastic_physics/``` | Contains the stochastic physics source code. |
+| ```cmake/```              | Contains compile option files on various platforms. |
+| ```modulefiles/```        | Contains module files on various platforms. |
+| ```tests/```              | Regression and unit testing framework scripts. |
+| ```build.sh```            | Script to build the model executable. (also used by `tests/`) |
+
+E.g. use of `build.sh` to build the coupled model with `FV3_GFS_v15p2` as the CCPP suite.
+```
+$> CMAKE_FLAGS="-DAPP=S2S" CCPP_SUITES="FV3_GFS_v15p2" ./build.sh
+```
+The build system is regularly tested with [Tier-1 and Tier-2 platforms](
+https://github.com/ufs-community/ufs-weather-model/wiki/Regression-Test-Policy-for-Weather-Model-Platforms-and-Compilers).
+Configurations for other platforms that are available with UFS should be used with the understanding that they are not regularly
+tested and users will have to adapt those to make it work.
+
+# Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is provided
+on an "as is" basis and the user assumes responsibility for its use. DOC has
+relinquished control of the information and no longer has responsibility to
+protect the integrity, confidentiality, or availability of the information. Any
+claims against the Department of Commerce stemming from the use of its GitHub
+project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation or favoring by the Department of Commerce. The
+Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
+shall not be used in any manner to imply endorsement of any commercial product
+or activity by DOC or the United States Government.

tests/parm/ufs.configure.coastal_datm_ocn_wav.IN

@@ -59,7 +59,7 @@ WAV_attributes::
   DumpFields = false
   ProfileMemory = false
   merge_import = .false.
-  mesh_wav = mesh.shinnecock.cdf5.nc
+  mesh_wav = @[MESH_WAV]
   multigrid = false
   gridded_netcdfout = true
   diro = "."

tests/parm/ufs.configure.coastal_datm_wav.IN

@@ -45,7 +45,7 @@ WAV_attributes::
   DumpFields = false
   ProfileMemory = false
   merge_import = .false.
-  mesh_wav = mesh.shinnecock.cdf5.nc
+  mesh_wav = @[MESH_WAV]
   multigrid = false
   gridded_netcdfout = true
   diro = "."

tests/parm/ufs.configure.coastal_wav.IN

@@ -21,7 +21,7 @@ WAV_attributes::
   DumpFields = false
   ProfileMemory = false
   merge_import = .false.
-  mesh_wav = mesh.shinnecock.cdf5.nc
+  mesh_wav = @[MESH_WAV]
   multigrid = false
   gridded_netcdfout = true
   diro = "."

tests/rt.sh

@@ -391,8 +391,8 @@ elif [[ $MACHINE_ID = hercules ]]; then
   ECFLOW_START=/work/noaa/epic/role-epic/spack-stack/hercules/ecflow-5.8.4/bin/ecflow_start.sh
   ECF_PORT=$(( $(id -u) + 1500 ))
 
-  QUEUE=windfall
-  COMPILE_QUEUE=windfall
+  QUEUE=batch
+  COMPILE_QUEUE=batch
   PARTITION=hercules
   dprefix=/work2/noaa/stmp/${USER}
   DISKNM=/work/noaa/epic/hercules/UFS-WM_RT
@@ -652,8 +652,8 @@ if [[ $ROCOTO == true ]]; then
     COMPILE_QUEUE=batch
     ROCOTO_SCHEDULER=slurm
   elif [[ $MACHINE_ID = hercules ]]; then
-    QUEUE=windfall
-    COMPILE_QUEUE=windfall
+    QUEUE=batch
+    COMPILE_QUEUE=batch
     ROCOTO_SCHEDULER=slurm
   elif [[ $MACHINE_ID = s4 ]]; then
     QUEUE=s4
@@ -744,7 +744,7 @@ EOF
   elif [[ $MACHINE_ID = orion ]]; then
     QUEUE=batch
   elif [[ $MACHINE_ID = hercules ]]; then
-    QUEUE=windfall
+    QUEUE=batch
   elif [[ $MACHINE_ID = jet ]]; then
     QUEUE=batch
   elif [[ $MACHINE_ID = s4 ]]; then

tests/rt_coastal.conf

@@ -24,60 +24,66 @@
 ##########
 ### ADCIRC tests: 1-5
 COMPILE | 1 | intel | -DAPP=CSTLA -DADCIRC_CONFIG=PADCIRC -DCOUPLED=ON | | fv3 |
-RUN | coastal_florence_hsofs_atm2adc | | baseline |
-RUN | coastal_ike_shinnecock_atm2adc | | baseline |
+RUN | coastal_florence_hsofs_atm2adc           | | baseline |
+RUN | coastal_idealized_shinnecock_atm2adc     | | baseline |
+RUN | coastal_sandy_shinnecock_atm2adc         | | baseline |
 
 COMPILE | 2 | intel | -DAPP=CSTLAW -DADCIRC_CONFIG=PADCIRC -DCOUPLED=ON | | fv3 |
-RUN | coastal_florence_hsofs.atm2adc2ww3 | | baseline |
-RUN | coastal_ike_shinnecock.atm2adc2ww3 | | baseline |
+RUN | coastal_florence_hsofs_atm2adc2ww3       | | baseline |
+RUN | coastal_idealized_shinnecock_atm2adc2ww3 | | baseline |
+RUN | coastal_sandy_shinnecock_atm2adc2ww3     | | baseline |
 
 COMPILE | 3 | intel | -DAPP=CSTLPA -DADCIRC_CONFIG=PADCIRC -DCOUPLED=ON | | fv3 |
-RUN | coastal_florence_hsofs.pam2adc   | | baseline |
-RUN | coastal_sandy_shinnecock.pam2adc | | baseline |
+RUN | coastal_florence_hsofs_pam2adc           | | baseline |
+RUN | coastal_sandy_shinnecock_pam2adc         | | baseline |
 
 COMPILE | 4 | intel | -DAPP=CSTLPAW -DADCIRC_CONFIG=PADCIRC -DCOUPLED=ON | | fv3 |
-RUN | coastal_florence_hsofs.pam2adc2ww3   | | baseline |
-RUN | coastal_sandy_shinnecock.pam2adc2ww3 | | baseline |
+RUN | coastal_florence_hsofs_pam2adc2ww3       | | baseline |
+RUN | coastal_sandy_shinnecock_pam2adc2ww3     | | baseline |
 
 ##########
 ### FVCOM tests: 6-10
 COMPILE | 6 | intel | -DAPP=CSTLF -DCOORDINATE_TYPE=SPHERICAL -DWET_DRY=ON | | fv3 |
-RUN | coastal_scituateharbor_atm2fvc | | baseline |
+RUN | coastal_scituateharbor_atm2fvc           | | baseline |
 
 ##########
 ### SCHISM tests: 11-15
 COMPILE | 11 | intel | -DAPP=CSTLS -DUSE_ATMOS=ON -DNO_PARMETIS=OFF -DOLDIO=ON | | fv3 |
-RUN | coastal_florence_hsofs.atm2sch | | baseline |
-RUN | coastal_ike_shinnecock_atm2sch | | baseline |
+RUN | coastal_florence_hsofs_atm2sch           | | baseline |
+RUN | coastal_idealized_shinnecock_sch         | | baseline |
+RUN | coastal_idealized_shinnecock_atm2sch     | | baseline |
+RUN | coastal_sandy_shinnecock_sch             | | baseline |
+RUN | coastal_sandy_shinnecock_atm2sch         | | baseline |
 
 #P.V We might need test cases to use the internal wave model (WWM: -DUSE_WWM=ON)
-#P.V It might be simpler to setup a test case using WWM
 COMPILE | 12 | intel | -DAPP=CSTLSW -DUSE_ATMOS=ON -DUSE_WW3=ON -DNO_PARMETIS=OFF -DOLDIO=ON -DPDLIB=ON | | fv3 |
-RUN | coastal_florence_hsofs.atm2sch2ww3 | | baseline |
-RUN | coastal_ike_shinnecock_atm2sch2ww3 | | baseline |
+RUN | coastal_florence_hsofs_atm2sch2ww3       | | baseline |
+RUN | coastal_florence_hsofs_atm2sch2ww3_nobc  | | baseline |
+RUN | coastal_idealized_shinnecock_atm2sch2ww3 | | baseline |
+RUN | coastal_sandy_shinnecock_atm2sch2ww3     | | baseline |
 
 COMPILE | 13 | intel | -DAPP=CSTLS -DUSE_PAHM=ON -DNO_PARMETIS=OFF -DOLDIO=ON | | fv3 |
-RUN | coastal_florence_hsofs_sch_pam     | | baseline |
-RUN | coastal_sandy_shinnecock.sch_pam   | | baseline |
+RUN | coastal_florence_hsofs_sch_pam           | | baseline |
+RUN | coastal_sandy_shinnecock_sch_pam         | | baseline |
 
 COMPILE | 14 | intel | -DAPP=CSTLPS -DUSE_ATMOS=ON -DNO_PARMETIS=OFF -DOLDIO=ON | | fv3 |
-RUN | coastal_florence_hsofs.pam2sch   | | baseline |
-RUN | coastal_sandy_shinnecock_pam2sch | | baseline |
+RUN | coastal_florence_hsofs_pam2sch           | | baseline |
+RUN | coastal_sandy_shinnecock_pam2sch         | | baseline |
 
 COMPILE | 15 | intel | -DAPP=CSTLPSW -DUSE_ATMOS=ON -DUSE_WW3=ON -DNO_PARMETIS=OFF -DOLDIO=ON | | fv3 |
-RUN | coastal_florence_hsofs.pam2sch2ww3   | | baseline |
-RUN | coastal_sandy_shinnecock_pam2sch2ww3 | | baseline |
+RUN | coastal_florence_hsofs_pam2sch2ww3       | | baseline |
+RUN | coastal_sandy_shinnecock_pam2sch2ww3     | | baseline |
 
 ##########
 ### ROMS tests: 16-20
 COMPILE | 16 | intel | -DAPP=CSTLR -DMY_CPP_FLAGS=BULK_FLUXES | | fv3 |
-RUN | coastal_irene_atm2roms | | baseline |
+RUN | coastal_irene_atm2roms                   | | baseline |
 
 ##########
 ### PAHM tests: 21-25
 
 ##########
 ### WW3 tests: 26-30
 COMPILE | 26 | intel | -DAPP=CSTLW -DPDLIB=ON | | fv3 |
-RUN | coastal_ike_shinnecock_ww3     | | baseline |
-RUN | coastal_ike_shinnecock_atm2ww3 | | baseline |
+RUN | coastal_idealized_shinnecock_ww3         | | baseline |
+RUN | coastal_idealized_shinnecock_atm2ww3     | | baseline |

tests/tests/coastal_florence_hsofs_atm2adc

@@ -1,6 +1,6 @@
 ###############################################################################
 #
-# ADCIRC standalone florence_shinnecock_atm2adc configuration
+# ADCIRC coupled florence_shinnecock_atm2adc configuration
 #
 ###############################################################################
 

tests/tests/coastal_florence_hsofs_atm2adc2ww3

@@ -0,0 +1,107 @@
+###############################################################################
+#
+# ADCIRC coupled florence_hsofs_atm2adc2ww3 configuration
+#
+###############################################################################
+
+export TEST_DESCR="Compare florence_hsofs_atm2adc2ww3 results with previous trunk version"
+
+export CNTL_DIR=coastal_florence_hsofs_atm2adc2ww3
+
+export LIST_FILES="fort.74.nc \
+                   fort.73.nc \
+                   fort.64.nc \
+                   fort.63.nc \
+                   fort.61.nc \
+                   ufs.cpld.cpl.hi.2018-09-10-00000.nc \
+                   ufs.cpld.cpl.hi.2018-09-11-00000.nc \
+                   ufs.cpld.cpl.hi.2018-09-12-00000.nc"
+
+# deafult options
+export_coastal
+
+# model_configure
+export SYEAR=2018
+export SMONTH=09
+export SDAY=10
+export SHOUR=00
+export FHMAX=1
+#export FHMAX=7
+export FHROT=0
+# not used
+export DT_ATMOS=720
+export RESTART_INTERVAL=0
+export QUILTING=.true.
+export QUILTING_RESTART=.false.
+export WRITE_GROUP=1
+export WRTTASK_PER_GROUP=6
+export ITASKS=1
+export OUTPUT_HISTORY=.true.
+export WRITE_DOPOST=.false.
+export NUM_FILES=2
+export FILENAME_BASE="'atm' 'sfc'"
+export OUTPUT_GRID="'cubed_sphere_grid'"
+export OUTPUT_FILE="'netcdf'"
+export IDEFLATE=0
+export NBITS=0
+export ICHUNK2D=0
+export JCHUNK2D=0
+export ICHUNK3D=0
+export JCHUNK3D=0
+export KCHUNK3D=0
+export IMO=384
+export JMO=190
+export WRITE_NSFLIP=.false.
+export OUTPUT_FH="12 -1"
+export IAU_OFFSET=0
+if [[ " hera orion hercules gaea jet " =~ " ${MACHINE_ID} " ]] ; then
+  ZSTANDARD_LEVEL=5
+fi
+
+# datm
+export DATM_CDEPS=true
+export DATM_STREAM_CONFIGURE=datm.streams.coastal.IN
+export atm_datamode="ATMMESH"
+export MESH_ATM="Wind_Pressure_HWRF_Florence_ExtendedSmooth_ESMFmesh.nc"
+export ATM_NX_GLB=3241
+export ATM_NY_GLB=2761
+export EXPORT_ALL=.true.
+export FILENAME_BASE='atmmesh.'
+export STREAM_VECTORS="null"
+export stream_files="\"INPUT/Wind_Pressure_HWRF_Florence_ExtendedSmooth.nc\""
+export stream_variables="\"uwnd Sa_u10m\" \"vwnd Sa_v10m\" \"P Sa_pslv\""
+export mapalgo=redist
+export dtlimit=1.5
+export STREAM_OFFSET=0
+
+# datm/ocean
+export HURR="Florence"
+export CPL_CONF="atm2adc2ww3"
+
+# pes
+export ATM_compute_tasks=20
+export OCN_tasks=240
+export WAV_tasks=480
+
+export WLCLK=120
+
+# configuration
+export MODEL_CONFIGURE=model_configure.IN
+export UFS_CONFIGURE=ufs.configure.coastal_datm_ocn_wav.IN
+export med_model=cmeps
+export med_omp_num_threads=1
+export atm_model=datm
+export atm_omp_num_threads=1
+export ocn_model=adcirc
+export ocn_omp_num_threads=1
+export wav_model=ww3
+export wav_omp_num_threads=1
+export MESH_WAV="HSOFS_ESMFmesh.nc"
+export coupling_interval_slow_sec=3600
+export RESTART_N=12
+export RUNTYPE=startup
+export CPLMODE=coastal
+export meshloc=element
+
+# input files
+export FV3_RUN="coastal_datm_atmmesh.IN coastal_schism_run.IN coastal_ww3_run.IN"