Modifications to allow workflow to run to completion with GNU build o…

…n Hera (#526)

* Modifications to scripts to allow the workflow to run to completion
with the GNU build on Hera.  The python/miniconda3 module must be
unloaded prior to running the executable.

* "module" is not the best name for a variable, changed to a_module

* Address comments:

- Clarify message about why modules are being unloaded
- Remove print message if nothing is unloaded to reduce clutter in log file
- Rename "module_to_unload" to "modules_to_unload"
- Change "a_module" to "module_to_unload" for clarity

* Clarify purpose of the unload_python.sh function.

* Add the "why"

scripts/exregional_make_ics.sh

@@ -615,6 +615,13 @@ $settings"
 # of chgres_cube is nonzero.
 # A similar thing happens in the forecast task.
 #
+#-----------------------------------------------------------------------
+# Deactivate the conda environment to avoid conflicts between the 
+# environment used by the regional workflow (prepended to your $PATH)
+# and that used in the run environment.
+#-----------------------------------------------------------------------
+unload_python
+
 ${APRUN} ${exec_fp} || \
   print_err_msg_exit "\
 Call to executable (exec_fp) to generate surface and initial conditions

scripts/exregional_make_lbcs.sh

@@ -516,6 +516,13 @@ $settings"
 # of chgres_cube is nonzero.
 # A similar thing happens in the forecast task.
 #
+#-----------------------------------------------------------------------
+# Deactivate the conda environment to avoid conflicts between the 
+# environment used by the regional workflow (prepended to your $PATH)
+# and that used in the run environment.
+#-----------------------------------------------------------------------
+  unload_python
+
   ${APRUN} ${exec_fp} || \
     print_err_msg_exit "\
 Call to executable (exec_fp) to generate lateral boundary conditions (LBCs)

scripts/exregional_run_fcst.sh

@@ -539,6 +539,13 @@ fi
 #
 #-----------------------------------------------------------------------
 #
+#-----------------------------------------------------------------------
+# Deactivate the conda environment to avoid conflicts between the 
+# environment used by the regional workflow (prepended to your $PATH)
+# and that used in the run environment.
+#-----------------------------------------------------------------------
+unload_python
+
 $APRUN ${FV3_EXEC_FP} || print_err_msg_exit "\
 Call to executable to run FV3-LAM forecast returned with nonzero exit
 code."

ush/bash_utils/unload_python.sh

@@ -0,0 +1,97 @@
+#
+#-----------------------------------------------------------------------
+#
+# This file defines a function that detects if a python or miniconds3
+# module is loaded, and if so, unloads that module.  This may be
+# necessary on machines where the loaded python environment isn't
+# compatible with environment set for the compiler.
+#
+#-----------------------------------------------------------------------
+#
+function unload_python() {
+#
+#-----------------------------------------------------------------------
+#
+# Save current shell options (in a global array).  Then set new options
+# for this script/function.
+#
+#-----------------------------------------------------------------------
+#
+  { save_shell_opts; set -u +x; } > /dev/null 2>&1
+#
+#-----------------------------------------------------------------------
+#
+# Get the full path to the file in which this script/function is located 
+# (scrfunc_fp), the name of that file (scrfunc_fn), and the directory in
+# which the file is located (scrfunc_dir).
+#
+#-----------------------------------------------------------------------
+#
+  local scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+  local scrfunc_fn=$( basename "${scrfunc_fp}" )
+  local scrfunc_dir=$( dirname "${scrfunc_fp}" )
+#
+#-----------------------------------------------------------------------
+#
+# Get the name of this function.
+#
+#-----------------------------------------------------------------------
+#
+  local func_name="${FUNCNAME[0]}"
+#
+#-----------------------------------------------------------------------
+#
+# Check arguments.
+#
+#-----------------------------------------------------------------------
+#
+  if [ "$#" -ne 0 ]; then
+
+    print_err_msg_exit "
+Incorrect number of arguments specified:
+
+  Function name:  \"${func_name}\"
+  Number of arguments specified:  $#
+
+Usage:
+
+  ${func_name}
+
+"
+
+  fi
+#
+#-----------------------------------------------------------------------
+#
+# If the miniconda or python modules are loaded, unload them
+#
+#-----------------------------------------------------------------------
+#
+
+  modules_to_unload=( python miniconda3 )
+  loaded_modules=$(module list 2>&1)
+
+  for module_to_unload in ${modules_to_unload[@]}; do
+    if [[ "${loaded_modules}" =~ "${module_to_unload}" ]]; then
+  print_info_msg "\
+Unloading module ${module_to_unload} libraries needed for workflow generation but not for running the workflow... "
+      module unload ${module_to_unload}
+    fi
+  done
+
+  loaded_modules=$(module list 2>&1)
+  print_info_msg "\
+Loaded modules are: $loaded_modules "
+
+#
+#-----------------------------------------------------------------------
+#
+# Restore the shell options saved at the beginning of this script/func-
+# tion.
+#
+#-----------------------------------------------------------------------
+#
+  { restore_shell_opts; } > /dev/null 2>&1
+
+}
+

ush/source_util_funcs.sh

@@ -183,6 +183,12 @@ function source_util_funcs() {
 #
 #-----------------------------------------------------------------------
 #
+#  Unload python or miniconda3 if loaded
+#
+#-----------------------------------------------------------------------
+#
+  . ${bashutils_dir}/unload_python.sh
+#
 # Source the file containing the function that creates a symlink to a
 # file (including performing checks).
 #