Merge pull request #464 from NCAR/WRF_tutorial

Add DART input.nml to template in WRF Tutorial

CHANGELOG.rst

@@ -22,6 +22,11 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**April 11 2023 :: Bug-fixes for WRF Tutorial and developer test quickbuilds. Tag v10.6.5**
+
+- Fixes the developer_tests quickbuild.sh files
+- Fixes the broken link to WRF DART tutorial input.nml.template
+
 **February 22 2023 :: Bug-fix release. Tag v10.6.4**
 
 - Removes unused and uninitialized argument to adaptive_inflate_init.

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.6.4'
+release = '10.6.5'
 master_doc = 'README'
 
 # -- General configuration ---------------------------------------------------

developer_tests/forward_operators/work/quickbuild.sh

@@ -10,10 +10,11 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
-LOCATION="threed_sphere"
+MODEL="none"
+EXTRA=$DART/models/template/threed_model_mod.f90
 dev_test=1
 TEST="forward_operators"
+LOCATION="threed_sphere"
 
 programs=(
 rttov_test

developer_tests/io/work/quickbuild.sh

@@ -10,10 +10,11 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
-LOCATION="threed_sphere"
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
 dev_test=1
 TEST="io"
+LOCATION="threed_sphere"
 
 programs=(
 test_cf_conventions

developer_tests/obs_sequence/work/quickbuild.sh

@@ -10,7 +10,8 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
+MODEL="none"
+EXTRA="$DART"/models/template/oned_model_mod.f90
 LOCATION="oned"
 dev_test=1
 TEST="obs_sequence"

developer_tests/quad_interpolate/work/quickbuild.sh

@@ -5,11 +5,11 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL=template
-LOCATION=threed_sphere
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
 TEST=quad_interpolate
 dev_test=1
-
+LOCATION="threed_sphere"
 
 programs=(
 )

developer_tests/random_seq/work/quickbuild.sh

@@ -10,10 +10,11 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
-LOCATION="threed_sphere"
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
 dev_test=1
 TEST="random_seq"
+LOCATION="threed_sphere"
 
 serial_programs=(
 test_corr

developer_tests/time_manager/work/quickbuild.sh

@@ -10,10 +10,11 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
-LOCATION="threed_sphere"
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
 dev_test=1
 TEST="time_manager"
+LOCATION="threed_sphere"
 
 serial_programs=(
 timetest

developer_tests/utilities/work/quickbuild.sh

@@ -10,7 +10,8 @@ main() {
 export DART=$(git rev-parse --show-toplevel)
 source "$DART"/build_templates/buildfunctions.sh
 
-MODEL="template"
+MODEL="none"
+EXTRA="$DART"/models/template/threed_model_mod.f90
 LOCATION="threed_sphere"
 dev_test=1
 TEST="utilities"

models/wrf/shell_scripts/diagnostics_obs.csh

@@ -17,7 +17,7 @@
   source $paramfile
 
   cd $OBS_DIAG_DIR
-  ${COPY} ${TEMPLATE_DIR}/input.nml.template input.nml
+  ${COPY} ${RUN_DIR}/input.nml input.nml
   set gdate  = (`echo $datea 0 -g | ${DART_DIR}/models/wrf/work/advance_time`)
   set yyyy2  = `echo $datea | cut -b1-4`
   set mm2    = `echo $datea | cut -b5-6`
@@ -57,7 +57,7 @@
      set datef = `echo $datef $ASSIM_INT_HOURS | ${DART_DIR}/models/wrf/work/advance_time`
 
   end
-  ls -1 obs_seq.final_* >! flist
+  readlink -f obs_seq.final_* >! flist
 
   cat >! script.sed << EOF
   /obs_sequence_name/c\
@@ -95,7 +95,7 @@
 EOF
 
 
-  sed -f script.sed ${TEMPLATE_DIR}/input.nml.template >! input.nml
+  sed -f script.sed ${RUN_DIR}/input.nml >! input.nml
 
   # create the state-space diagnostic summary
 

models/wrf/shell_scripts/driver.csh

@@ -372,6 +372,13 @@ while ( 1 == 1 )
 
    echo "ready to integrate ensemble members"
 
+   # Removing old start_member and done_member diagnostics
+   if ( -e ${RUN_DIR}/start_member_1) then
+      ${REMOVE} ${RUN_DIR}/start_member_*  \
+                ${RUN_DIR}/done_member_*
+   endif
+
+
    set n = 1
    while ( $n <= $NUM_ENS )
 

models/wrf/shell_scripts/gen_retro_icbc.csh

@@ -58,7 +58,7 @@ while ( 1 == 1 )
    if ( ! -d ${OUTPUT_DIR}/${datea} )  mkdir -p ${OUTPUT_DIR}/${datea}
 
    cd ${ICBC_DIR}
-   ${LINK} ${TEMPLATE_DIR}/input.nml.template input.nml
+   ${LINK} ${RUN_DIR}/input.nml input.nml
    ${REMOVE} gfs*pgrb2* *grib2
 
    #  prepare to run WPS ungrib and metgrid

models/wrf/shell_scripts/init_ensemble_var.csh

@@ -50,7 +50,6 @@ set dd     = `echo $initial_date | cut -b7-8`
 set hh     = `echo $initial_date | cut -b9-10`
 
 ${COPY} ${TEMPLATE_DIR}/namelist.input.meso namelist.input
-${COPY} ${TEMPLATE_DIR}/input.nml.template input.nml
 ${REMOVE} ${RUN_DIR}/WRF
 ${LINK} ${OUTPUT_DIR}/${initial_date} WRF
 
@@ -61,11 +60,8 @@ while ( $n <= $NUM_ENS )
 
    mkdir -p ${RUN_DIR}/advance_temp${n}
 
-   # TJH why does the run_dir/*/input.nml come from the template_dir and not the rundir?
-   # TJH furthermore, template_dir/input.nml.template and rundir/input.nml are identical. SIMPLIFY.
-
    ${LINK} ${RUN_DIR}/WRF_RUN/* ${RUN_DIR}/advance_temp${n}/.
-   ${LINK} ${TEMPLATE_DIR}/input.nml.template ${RUN_DIR}/advance_temp${n}/input.nml
+   ${LINK} ${RUN_DIR}/input.nml ${RUN_DIR}/advance_temp${n}/input.nml
 
    ${COPY} ${OUTPUT_DIR}/${initial_date}/wrfinput_d01_${gdate[1]}_${gdate[2]}_mean \
            ${RUN_DIR}/advance_temp${n}/wrfvar_output.nc

models/wrf/shell_scripts/new_advance_model.csh

@@ -219,11 +219,12 @@ while($state_copy <= $num_states)     # MULTIPLE DOMAINS - we don't expect advan
 #   endif
 
    # link WRF-runtime files (required) and be.dat (if using WRF-Var)
-     ${LN} ${CENTRALDIR}/WRF_RUN/*       .
-
-   # link DART namelist
-   ${COPY} ${CENTRALDIR}/input.nml       .
+   ${LN} ${CENTRALDIR}/WRF_RUN/*       .
 
+   # Copy DART namelist if necessary
+   if ( ! -e input.nml) then
+      ${COPY} ${CENTRALDIR}/input.nml       .
+   endif
    # append LSM data from previous cycle
    if ( -e ${CENTRALDIR}/append_lsm_data ) then
       ${LN} ${CENTRALDIR}/LSM/lsm_data_${ensemble_member}.nc lsm_data.nc

models/wrf/shell_scripts/setup.csh

@@ -89,7 +89,7 @@ ${COPY} ${SHELL_SCRIPTS_DIR}/add_bank_perts.ncl    ${RUN_DIR} || exit 8
 ${COPY} ${SHELL_SCRIPTS_DIR}/new_advance_model.csh ${RUN_DIR} || exit 9
 
 # Edit input.nml.template so that its ens_size is set to the same value as $NUM_ENS in param.csh
-sed "s/ens_size.*/ens_size                 =$NUM_ENS,/g" ${DART_DIR}/models/wrf/tutorial/template/input.nml.template > ${RUN_DIR}/input.nml || exit 8
+sed "s/ens_size.*/ens_size                 =  $NUM_ENS,/g" ${DART_DIR}/models/wrf/tutorial/template/input.nml.template > ${RUN_DIR}/input.nml || exit 8
 
 echo "$myname complete at "`date`
 echo 

models/wrf/tutorial/README.rst

@@ -237,9 +237,8 @@ bash  ``export BASE_DIR=<path_to_your_working_directory>``
        cp $DART_DIR/models/wrf/tutorial/template/namelist.input.meso   $BASE_DIR/template/.
        cp $DART_DIR/models/wrf/tutorial/template/namelist.wps.template $BASE_DIR/template/.
 
-3. You will also need the scripting to run a WRF/DART experiment. Copy
-   the contents of ``$DART_DIR/models/wrf/shell_scripts`` to the
-   ``$BASE_DIR/scripts`` directory.
+3. You will also need scripting to run a WRF/DART experiment. Copy the contents of 
+   ``$DART_DIR/models/wrf/shell_scripts`` to the ``$BASE_DIR/scripts`` directory.
 
    ::
 
@@ -457,7 +456,7 @@ changes:
 +====================+======================================+=========================================================================================================================================================================================================================================================+
 | driver.csh         | datefnl = 2017042712                 | Change to the final target date; here the final date is already set correctly for this tutorial.                                                                                                                                                        |
 +--------------------+--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| gen_retro_icbc.csh | datefnl = 2017043000                 | This is the final date to create WRF initial/boundary conditions for. This is set to the last date that files are included in the tutorial.                                                                                                             |
+| gen_retro_icbc.csh | datefnl = 2017042712                 | Set to the final target date of the tutorial.  However, it is possible (not necessary) to create WRF initial/boundary conditions to 2017043000. This is the latest date that files are included in the tutorial.                                        |
 +--------------------+--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | gen_retro_icbc.csh | paramfile = <full path to param.csh> | The full path to param.csh. Change this on the line after the comment. While these two files are in the same directory here, in general it is helpful to have one param.csh for each experiment.                                                        |
 +--------------------+--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -557,6 +556,11 @@ and look near the end. You will need to modify the lines staring with
 also want to modify this script to test running a single member first —
 just in case you have some debugging to do.
 
+However, be warned that to successfully complete the tutorial, including
+running the *driver.csh* script in Step 5, using a smaller ensemble 
+(e.g. < 20 members) can lead to spurious updates during the analysis step,
+causing the WRF simulation to fail. 
+
 When complete for the full ensemble, you should find 50 new files in the
 directory ``output/2017042700/PRIORS`` with names like *prior_d01.0001*,
 *prior_d01.0002*, etc... You may receive an e-mail to helpfully inform