Remove ENV_INIT_SCRIPT and avoid dependency on system python

etc/lmod-setup.csh

@@ -12,6 +12,8 @@ EOF_USAGE
 else
    set L_MACHINE=$1
 endif
+
+source /etc/csh.login
 
 if ( "$L_MACHINE" == macos ) then
    set ENV="/opt/homebrew/opt/lmod/init/csh"

etc/lmod-setup.sh

@@ -14,6 +14,14 @@ else
    L_MACHINE=$1
 fi
 
+[[ ${SHELLOPTS} =~ nounset ]] && has_mu=true || has_mu=false
+[[ ${SHELLOPTS} =~ errexit ]] && has_me=true || has_me=false
+$has_mu && set +u
+$has_me && set +e
+source /etc/profile
+$has_mu && set -u
+$has_me && set -e
+
 if [ "$L_MACHINE" = macos ]; then
    export BASH_ENV="/opt/homebrew/opt/lmod/init/bash"
    # export BASH_ENV="/usr/local/opt/lmod/init/bash"

tests/WE2E/setup_WE2E_tests.sh

@@ -82,24 +82,7 @@ exec_subdir="install_${compiler}/exec"
 #-----------------------------------------------------------------------
 
 # Load Python Modules
-env_path="${SRW_APP_DIR}/modulefiles"
-env_file="wflow_${machine}"
-echo "-- Load environment =>" $env_file
-source ${SRW_APP_DIR}/etc/lmod-setup.sh ${machine}
-module use ${env_path}
-module load ${env_file}
-
-if [[ "${machine}" == 'cheyenne' ]]; then
-    conda activate /glade/p/ral/jntp/UFS_SRW_app/conda/regional_workflow
-else
-    if [[ "${machine}" == 'noaacloud' && -z "${PROJ_LIB-}" ]]; then
-        PROJ_LIB=''
-    fi
-
-    conda activate regional_workflow
-fi
-
-module list
+source ${SRW_APP_DIR}/ush/load_modules_wflow.sh ${machine}
 
 # Run the E2E Workflow tests
 ./run_WE2E_tests.sh \

ush/config_defaults.yaml

@@ -322,10 +322,9 @@ platform:
   DOMAIN_PREGEN_BASEDIR: ""
   #
   #-----------------------------------------------------------------------
-  # Scripts and commands needed by workflow and tasks
+  # Pre task commands such as "ulimit" needed by tasks
   #-----------------------------------------------------------------------
   #
-  ENV_INIT_SCRIPTS_FPS: []
   PRE_TASK_CMDS: ""
   #
   #-----------------------------------------------------------------------
@@ -1103,6 +1102,7 @@ task_make_orog:
   OMP_NUM_THREADS_MAKE_OROG: 6
   OMP_STACKSIZE_MAKE_OROG: "2048m"
   OROG_DIR: ""
+  TOPO_DIR: ""
 
 #----------------------------
 # MAKE SFC CLIMO config parameters
@@ -1117,6 +1117,7 @@ task_make_sfc_climo:
   OMP_NUM_THREADS_MAKE_SFC_CLIMO: 1
   OMP_STACKSIZE_MAKE_SFC_CLIMO: "1024m"
   SFC_CLIMO_DIR: ""
+  SFC_CLIMO_INPUT_DIR: ""
 
 #----------------------------
 # EXTRN ICS config parameters
@@ -1628,14 +1629,6 @@ task_run_fcst:
   # FIXlut:
   # System directory where the lookup tables for optics properties are located
   #
-  # TOPO_DIR:
-  # The location on disk of the static input files used by the make_orog
-  # task (orog.x and shave.x). Can be the same as FIXgsm.
-  #
-  # SFC_CLIMO_INPUT_DIR:
-  # The location on disk of the static surface climatology input fields, used by 
-  # sfc_climo_gen. These files are only used if RUN_TASK_MAKE_SFC_CLIMO=TRUE
-  #
   # FNGLAC, ..., FNMSKH:
   # Names of (some of the) global data files that are assumed to exist in 
   # a system directory specified (this directory is machine-dependent; 
@@ -1691,8 +1684,6 @@ task_run_fcst:
   FIXgsm: ""
   FIXaer: ""
   FIXlut: ""
-  TOPO_DIR: ""
-  SFC_CLIMO_INPUT_DIR: ""
 
   FNGLAC: &FNGLAC "global_glacier.2x2.grb"
   FNMXIC: &FNMXIC "global_maxice.2x2.grb"

ush/launch_FV3LAM_wflow.sh

@@ -96,7 +96,6 @@ fi
 #
 . $exptdir/var_defns.sh
 . $USHdir/source_util_funcs.sh
-. $USHdir/init_env.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -122,16 +121,6 @@ called_from_cron=$(boolify "${called_from_cron}")
 #
 #-----------------------------------------------------------------------
 #
-# Initialize the environment, e.g. by making the "module" command as well
-# as others available.
-#
-#-----------------------------------------------------------------------
-#
-env_init_scripts_fps_str="( "$(printf "\"%s\" " "${ENV_INIT_SCRIPTS_FPS[@]}")")"
-init_env env_init_scripts_fps="${env_init_scripts_fps_str}"
-#
-#-----------------------------------------------------------------------
-#
 # Set the name of the experiment.  We take this to be the name of the 
 # experiment subdirectory (i.e. the string after the last "/" in the 
 # full path to the experiment directory).
@@ -146,31 +135,9 @@ expt_name="${EXPT_SUBDIR}"
 #
 #-----------------------------------------------------------------------
 #
-# source version file (run) only if it is specified in versions directory
-VERSION_FILE="${HOMEdir}/versions/${RUN_VER_FN}"
-if [ -f ${VERSION_FILE} ]; then
-  . ${VERSION_FILE}
-fi  
-module use "${HOMEdir}/modulefiles"
-module load "${WFLOW_MOD_FN}" > /dev/null 2>&1 || print_err_msg_exit "\
-Loading of platform-specific module file (WFLOW_MOD_FN) for the workflow 
-task failed:
-  WFLOW_MOD_FN = \"${WFLOW_MOD_FN}\""
+machine=$(echo_lowercase $MACHINE)
 
-#
-#-----------------------------------------------------------------------
-#
-# Hack for Cheyenne since system python3 version is 3.4.10.
-# SRW app requires at least 3.6 so crontab deletion doesn't work with it.
-# Here we switch to using the python3 in conda that satisfies the requirement.
-# In the future, we could do conda activate on all systems here, to get rid
-# of the system python requirement.
-#
-#-----------------------------------------------------------------------
-#
-if [ "$MACHINE" = "CHEYENNE" ]; then
-    conda activate /glade/p/ral/jntp/UFS_SRW_app/conda/regional_workflow
-fi
+. ${USHdir}/load_modules_wflow.sh ${machine}
 
 #
 #-----------------------------------------------------------------------

ush/load_modules_run_task.sh

@@ -9,7 +9,6 @@
 #
 . ${GLOBAL_VAR_DEFNS_FP}
 . $USHdir/source_util_funcs.sh
-. $USHdir/init_env.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -66,16 +65,6 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-# Initialize the environment, e.g. by making available the "module" 
-# command as well as others.
-#
-#-----------------------------------------------------------------------
-#
-env_init_scripts_fps_str="( "$(printf "\"%s\" " "${ENV_INIT_SCRIPTS_FPS[@]}")")"
-init_env env_init_scripts_fps="${env_init_scripts_fps_str}"
-#
-#-----------------------------------------------------------------------
-#
 # Get the task name and the name of the J-job script.
 #
 #-----------------------------------------------------------------------
@@ -195,6 +184,10 @@ module list
 if [ -n "${SRW_ENV:-}" ] ; then
   set +u
   conda activate ${SRW_ENV}
+  if [ $machine = "gaea" ]; then
+     conda deactivate
+     conda activate ${SRW_ENV}
+  fi
   set -u
 fi
 

ush/load_modules_wflow.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+#
+#-----------------------------------------------------------------------
+#
+# This script loads the workflow modulefile for a given machine.
+# It is a central place for all other scripts so that this is the only
+# place workflow module loading can be modified.
+#
+#-----------------------------------------------------------------------
+#
+
+function usage() {
+  cat << EOF_USAGE
+Usage: source $0 PLATFORM
+
+OPTIONS:
+   PLATFORM - name of machine you are on
+      (e.g. cheyenne | hera | jet | orion | wcoss2 )
+EOF_USAGE
+}
+
+# Make sure machine name is passed as first argument
+if [ $# -eq 0 ]; then
+  usage
+  exit 1
+fi
+
+# help message
+if [ "$1" == "--help" ] || [ "$1" == "-h" ]; then
+  usage
+  exit 0
+fi
+
+# Set machine name to lowercase
+machine=${1,,}
+
+# Get home directory
+scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_dir=$( dirname "${scrfunc_fp}" )
+HOMEdir=$( dirname "${scrfunc_dir}" )
+
+# source version file (run) only if it is specified in versions directory
+RUN_VER_FN="run_ver.${machine}"
+VERSION_FILE="${HOMEdir}/versions/${RUN_VER_FN}"
+if [ -f ${VERSION_FILE} ]; then
+  . ${VERSION_FILE}
+fi
+
+# Source modulefile for this machine
+WFLOW_MOD_FN="wflow_${machine}"
+source "${HOMEdir}/etc/lmod-setup.sh" ${machine}
+module use "${HOMEdir}/modulefiles"
+module load "${WFLOW_MOD_FN}" > /dev/null 2>&1 || { echo "ERROR:
+Loading of platform-specific module file (WFLOW_MOD_FN) for the workflow 
+task failed:
+  WFLOW_MOD_FN = \"${WFLOW_MOD_FN}\""; exit 1; }
+
+# Activate conda
+[[ ${SHELLOPTS} =~ nounset ]] && has_mu=true || has_mu=false
+
+$has_mu && set +u
+if [[ "${machine}" == 'cheyenne' ]]; then
+    conda activate /glade/p/ral/jntp/UFS_SRW_app/conda/regional_workflow
+else
+    if [ ! -z $(command -v conda) ]; then
+        conda activate regional_workflow
+    fi
+fi
+$has_mu && set -u
+
+# List loaded modulefiles
+module list
+

ush/machine/cheyenne.yaml

@@ -16,18 +16,18 @@ platform:
   RUN_CMD_POST: mpirun -np $nprocs
   RUN_CMD_SERIAL: time
   RUN_CMD_UTILS: mpirun -np $nprocs
-  ENV_INIT_SCRIPTS_FPS:
-    - /etc/profile
   PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
   TEST_EXTRN_MDL_SOURCE_BASEDIR: /glade/p/ral/jntp/UFS_SRW_App/develop/input_model_data
   TEST_PREGEN_BASEDIR: /glade/p/ral/jntp/UFS_SRW_App/develop/FV3LAM_pregen
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /glade/p/ral/jntp/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /glade/p/ral/jntp/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
+task_make_orog:
+  TOPO_DIR: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_orog
+task_make_sfc_climo:
+  SFC_CLIMO_INPUT_DIR: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_sfc_climo
 task_run_fcst:
   FIXaer: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_aer
   FIXgsm: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_am
   FIXlut: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_lut
-  TOPO_DIR: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_orog
-  SFC_CLIMO_INPUT_DIR: /glade/p/ral/jntp/UFS_SRW_App/develop/fix/fix_sfc_climo
 data:
   FV3GFS: /glade/p/ral/jntp/UFS_CAM/COMGFS/gfs.${yyyymmdd}/${hh}

ush/machine/gaea.yaml

@@ -16,19 +16,18 @@ platform:
   RUN_CMD_SERIAL: time
   RUN_CMD_UTILS: srun --mpi=pmi2 -n $nprocs
   SCHED_NATIVE_CMD: -M c3
-  ENV_INIT_SCRIPTS_FPS:
-    - /etc/profile
-    - /lustre/f2/dev/role.epic/contrib/Lmod_init.sh
   PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
   TEST_EXTRN_MDL_SOURCE_BASEDIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/input_model_data
   TEST_PREGEN_BASEDIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/FV3LAM_pregen
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/dummy_FV3GFS_sys_dir
+task_make_orog:
+  TOPO_DIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_orog
+task_make_sfc_climo:
+  SFC_CLIMO_INPUT_DIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_sfc_climo
 task_run_fcst:
   FIXaer: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_aer
   FIXgsm: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_am
   FIXlut: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_lut
-  TOPO_DIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_orog
-  SFC_CLIMO_INPUT_DIR: /lustre/f2/pdata/ncep_shared/UFS_SRW_App/develop/fix/fix_sfc_climo
 data:
   FV3GFS: /lustre/f2/dev/Mark.Potts/EPIC/SRW/model_data/FV3GFS/${yyyymmdd}${hh}

ush/machine/hera.yaml

@@ -19,13 +19,15 @@ platform:
   RUN_CMD_POST: srun
   RUN_CMD_SERIAL: time
   RUN_CMD_UTILS: srun
-  ENV_INIT_SCRIPTS_FPS:
-    - /etc/profile
   PRE_TASK_CMDS: '{ ulimit -s unlimited; ulimit -a; }'
   TEST_EXTRN_MDL_SOURCE_BASEDIR: /scratch2/BMC/det/UFS_SRW_App/develop/input_model_data
   TEST_PREGEN_BASEDIR: /scratch2/BMC/det/UFS_SRW_App/develop/FV3LAM_pregen
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS: /scratch2/BMC/det/UFS_SRW_app/develop/dummy_FV3GFS_sys_dir
   TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS: /scratch2/BMC/det/UFS_SRW_app/develop/dummy_FV3GFS_sys_dir
+task_make_orog:
+  TOPO_DIR: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_orog
+task_make_sfc_climo:
+  SFC_CLIMO_INPUT_DIR: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_sfc_climo
 task_get_extrn_ics:
   EXTRN_MDL_DATA_STORES: hpss aws nomads
 task_get_extrn_lbcs:
@@ -34,5 +36,3 @@ task_run_fcst:
   FIXaer: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_aer
   FIXgsm: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_am
   FIXlut: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_lut
-  TOPO_DIR: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_orog
-  SFC_CLIMO_INPUT_DIR: /scratch2/BMC/det/UFS_SRW_App/develop/fix/fix_sfc_climo