Convert machine scripts to yaml format. (#388)

* Make machine files yaml.

* Remove redundant SR_WX dir

* Remove some duplicate derived types.

* Convert constants to yaml.

* Bug fix GFDL grid.

* Bug fix machine lower/upper case.

* Fix unittest to capture exit code.

* Gaea lmod setup fix with tcsh.

* Add missing gaea commands.

* Remove obsolete module-setup scripts.

* Fix linux modulefile name.

docs/UsersGuide/source/WE2Etests.rst

@@ -70,12 +70,12 @@ The examples below demonstrate several common ways that ``run_WE2E_tests.sh`` ca
 
       ./run_WE2E_tests.sh tests_file="my_tests.txt" machine="hera" account="rtrr"
 
-   This will create the experiment subdirectories for the two sample WE2E tests in the directory ``${SR_WX_APP_TOP_DIR}/../expt_dirs``, where ``SR_WX_APP_TOP_DIR`` is the top-level directory for the ufs-srweather-app repository (usually set to something like ``/path/to/ufs-srweather-app``). Thus, the following two experiment directories will be created:
+   This will create the experiment subdirectories for the two sample WE2E tests in the directory ``${HOMEdir}/../expt_dirs``, where ``HOMEdir`` is the top-level directory for the ufs-srweather-app repository (usually set to something like ``/path/to/ufs-srweather-app``). Thus, the following two experiment directories will be created:
 
    .. code-block::
 
-      ${SR_WX_APP_TOP_DIR}/../expt_dirs/custom_ESGgrid
-      ${SR_WX_APP_TOP_DIR}/../expt_dirs/grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
+      ${HOMEdir}/../expt_dirs/custom_ESGgrid
+      ${HOMEdir}/../expt_dirs/grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
 
    In addition, by default, cron jobs will be added to the user's cron table to relaunch the workflows of these experiments every 2 minutes.
 
@@ -95,7 +95,7 @@ The examples below demonstrate several common ways that ``run_WE2E_tests.sh`` ca
    In this case, the user will have to go into each test's experiment directory and either manually call the ``launch_FV3LAM_wflow.sh`` script or use the Rocoto commands described in :numref:`Chapter %s <RocotoInfo>` to (re)launch the workflow. Note that if using the Rocoto commands directly, the log file ``log.launch_FV3LAM_wflow`` will not be created; in this case, the status of the workflow can be checked using the ``rocotostat`` command (see :numref:`Section %s <RocotoManualRun>` or :numref:`Section %s <RocotoStatCmd>`).
 
 #. To place the experiment subdirectories in a subdirectory named ``test_set_01`` under 
-   ``${SR_WX_APP_TOP_DIR}/../expt_dirs`` (instead of immediately under ``expt_dirs``), use:
+   ``${HOMEdir}/../expt_dirs`` (instead of immediately under ``expt_dirs``), use:
 
    .. code-block::
 
@@ -105,8 +105,8 @@ The examples below demonstrate several common ways that ``run_WE2E_tests.sh`` ca
 
    .. code-block::
 
-      ${SR_WX_APP_TOP_DIR}/../expt_dirs/test_set_01/custom_ESGgrid
-      ${SR_WX_APP_TOP_DIR}/../expt_dirs/test_set_01/grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
+      ${HOMEdir}/../expt_dirs/test_set_01/custom_ESGgrid
+      ${HOMEdir}/../expt_dirs/test_set_01/grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
 
    This is useful for grouping various sets of tests.
 

etc/lmod-setup.csh

@@ -20,17 +20,24 @@ if ( "$L_MACHINE" == macos ) then
 
    module purge
 
+else if ( "$L_MACHINE" == linux ) then
+   setenv ENV "/usr/share/lmod/lmod/init/csh"
+   source $ENV
+
+   module purge
+
 else if ( "$L_MACHINE" == singularity ) then
    set ENV="/usr/share/lmod/lmod/init/csh"
    source $ENV
 
    module purge
 
 else if ( "$L_MACHINE" == gaea ) then
-   export LMOD_SYSTEM_DEFAULT_MODULES=modules/3.2.11.4
-   export BASH_ENV=/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/profile
-   source $BASH_ENV
-   module --initial_load restore
+   set ENV="/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/csh"
+   source $ENV
+
+   setenv LMOD_SYSTEM_DEFAULT_MODULES "modules/3.2.11.4"
+   module --initial_load --no_redirect restore
 
 else if ( "$L_MACHINE" == odin ) then
    module unload modules

etc/lmod-setup.sh

@@ -21,18 +21,24 @@ if [ "$L_MACHINE" = macos ]; then
 
    module purge
 
+elif [ "$L_MACHINE" = linux ]; then
+   export BASH_ENV="/usr/share/share/lmod/init/bash"
+   source $BASH_ENV
+
+   module purge
+
 elif [ "$L_MACHINE" = singularity ]; then
    export BASH_ENV="/usr/share/lmod/lmod/init/bash"
    source $BASH_ENV
 
    module purge
 
 elif [ "$L_MACHINE" = gaea ]; then
-   export LMOD_SYSTEM_DEFAULT_MODULES=modules/3.2.11.4
-   export BASH_ENV=/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/profile
+   export BASH_ENV="/lustre/f2/dev/role.epic/contrib/apps/lmod/lmod/init/bash"
    source $BASH_ENV
-   module --initial_load restore
 
+   export LMOD_SYSTEM_DEFAULT_MODULES="modules/3.2.11.4"
+   module --initial_load --no_redirect restore
 elif [ "$L_MACHINE" = odin ]; then
    module unload modules
    unset -f module

modulefiles/wflow_noaacloud

@@ -13,9 +13,12 @@ module load rocoto
 module use /contrib/GST/miniconda3/modulefiles
 module load miniconda3/4.10.3
 
+setenv PROJ_LIB "/contrib/GST/miniconda/envs/regional_workflow/share/proj"
+setenv OPT "/contrib/EPIC/hpc-modules"
+append-path PATH "/contrib/GST/miniconda/envs/regional_workflow/bin"
+
 if { [module-info mode load] } {
   puts stderr "Please do the following to activate conda:
        > conda activate regional_workflow"
 }
 
-

scripts/exregional_make_grid.sh

@@ -60,7 +60,6 @@ This is the ex-script for the task that generates grid files.
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 if [ -z "${RUN_CMD_SERIAL:-}" ] ; then

scripts/exregional_make_ics.sh

@@ -63,7 +63,6 @@ export OMP_STACKSIZE=${OMP_STACKSIZE_MAKE_ICS}
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 nprocs=$(( NNODES_MAKE_ICS*PPN_MAKE_ICS ))

scripts/exregional_make_lbcs.sh

@@ -63,7 +63,6 @@ export OMP_STACKSIZE=${OMP_STACKSIZE_MAKE_LBCS}
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 nprocs=$(( NNODES_MAKE_LBCS*PPN_MAKE_LBCS ))

scripts/exregional_make_orog.sh

@@ -65,7 +65,6 @@ export OMP_STACKSIZE=${OMP_STACKSIZE_MAKE_OROG}
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 if [ -z "${RUN_CMD_SERIAL:-}" ] ; then

scripts/exregional_make_sfc_climo.sh

@@ -106,7 +106,6 @@ EOF
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 nprocs=$(( NNODES_MAKE_SFC_CLIMO*PPN_MAKE_SFC_CLIMO ))

scripts/exregional_run_fcst.sh

@@ -62,7 +62,6 @@ export OMP_STACKSIZE=${OMP_STACKSIZE_RUN_FCST}
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 nprocs=$(( NNODES_RUN_FCST*PPN_RUN_FCST ))

scripts/exregional_run_post.sh

@@ -62,7 +62,6 @@ export OMP_STACKSIZE=${OMP_STACKSIZE_RUN_POST}
 #
 #-----------------------------------------------------------------------
 #
-. ${MACHINE_FILE}
 eval ${PRE_TASK_CMDS}
 
 nprocs=$(( NNODES_RUN_POST*PPN_RUN_POST ))

test/README.md

@@ -21,9 +21,9 @@ The CMake build is done in the ``build_${compiler}`` directory.
 The executables for each build are installed under the ``bin_${compiler}`` directory.
 
 NOTE:  To run the regional workflow using these executables, the ``EXECDIR`` variable in the
-``${SR_WX_APP_TOP_DIR}/regional_workflow/ush/setup.sh`` file must be set to the
-appropiate directory, for example:  ``EXECDIR="${SR_WX_APP_TOP_DIR}/bin_intel/bin"``,
-where ``${SR_WX_APP_TOP_DIR}`` is the top-level directory of the cloned ufs-srweather-app repository.
+``${HOMEdir}/ush/setup.py`` file must be set to the
+appropiate directory, for example:  ``EXECDIR="${HOMEdir}/bin_intel/bin"``,
+where ``${HOMEdir}`` is the top-level directory of the cloned ufs-srweather-app repository.
 
 ## Usage
 
@@ -36,4 +36,4 @@ cd test
 ./build.sh cheyenne >& build.out &
 ```
 
-Check the ``${SR_WX_APP_TOP_DIR}/test/build_test$PID.out`` file for PASS/FAIL.
+Check the ``${HOMEdir}/test/build_test$PID.out`` file for PASS/FAIL.

tests/WE2E/get_WE2Etest_names_subdirs_descs.sh

@@ -256,6 +256,14 @@ function get_WE2Etest_names_subdirs_descs() {
 #
 #-----------------------------------------------------------------------
 #
+# Source constant files.
+#
+#-----------------------------------------------------------------------
+#
+  source_config $USHdir/constants.yaml
+#
+#-----------------------------------------------------------------------
+#
 # Specify the set of valid argument names for this script or function.  
 # Then process the arguments provided to it on the command line (which 
 # should consist of a set of name-value pairs of the form arg1="value1", 
@@ -411,14 +419,6 @@ function get_WE2Etest_names_subdirs_descs() {
 #
 #-----------------------------------------------------------------------
 #
-# Source files.
-#
-#-----------------------------------------------------------------------
-#
-  . $USHdir/constants.sh
-#
-#-----------------------------------------------------------------------
-#
 # Set variables associated with the CSV (comma-separated value) file that 
 # this function may generate.  The conditions under which such a file is 
 # generated are described above in the description of this function.
@@ -1136,9 +1136,6 @@ configuration files of the primary WE2E tests...
 params=$(\
   PREDEF_GRID_NAME="${PREDEF_GRID_NAME}" \
   QUILTING="FALSE" \
-  RADIUS_EARTH=${RADIUS_EARTH} \
-  DEGS_PER_RADIAN=${DEGS_PER_RADIAN} \
-  NH4=${NH4} \
     $USHdir/calculate_cost.py -c "${test_configs_basedir}/$subdir/${config_fn}")
 
 read dta nxny dta_r nxny_r <<< "${params}"