Updates to the NCO mode (#443)

* Add a move step to binaries for NCO purposes.

* Pass COMROOT to setpdy.

* Correct path of post dependency on forecat.

* Remove DATA_SHARED directory.

* Remove symlinks and use unique id for run_fcst instead.

* Remove forecast directory after post is done.

* Use raw workflow_id

* Add templated data paths to wcoss2 that use compath.py.

* Remove cron relaunch from config.nco

* Undo for_ICS/LBCS stuff in NCO mode.

* Remove RESTART symlinking because DATAFCST is accessible to all other tasks.

* Undo cyc addition to COMIN.

* Update devclean.

* Follow symlinks when tarring log files in Jenkins.

* Add memory otpion for get_extrn_ics/lbcs.

* Optimize fundamental test coverage.

* Reduce work load on orion.

* Add minimum memory requirement to all serial tasks.

* Simplify set_predef_grid_params.

* Simplify generate_FV3LAM_wflow.

* Simplify link_fix.

* Simplify to get rid of export_vars from setup.

* Import only necessary variables from environment.

* Use `eval echo` or `eval` depending on situation.

* Add cyc back to COMIN.

* Fix calculate_cost.

* Fix gaea test list.

* Remove a test case from cheyenne that is taking extremely long.

* Reduce memory requirement for serial job to 1G.

* Create COMINaws ics/lbcs staging directory.

* Also symlink gfs ics/lbcs if on disk and in community mode.

* Remove failing tests on orion.

* Exclude gaea from --mem specification.

* Add a run_vx modulefile for orion.

* Add separate fundamental list for cheyenne GNU runs.

* Bug fix for wcoss2 GFS version

* Load prod_util on wcoss2.

* Rename AWSROOT to EXTROOT.

* Remove leftover COMINaws.

.cicd/Jenkinsfile

@@ -173,7 +173,7 @@ pipeline {
                         post {
                             always {
                                 // Archive the test log files
-                                sh 'cd "${SRW_WE2E_EXPERIMENT_BASE_DIR}" && tar --create --gzip --verbose --file "${WORKSPACE}/we2e_test_logs-${SRW_PLATFORM}-${SRW_COMPILER}.tgz" */log.generate_FV3LAM_wflow */log.launch_FV3LAM_wflow */log/*'
+                                sh 'cd "${SRW_WE2E_EXPERIMENT_BASE_DIR}" && tar --create --gzip --verbose --dereference --file "${WORKSPACE}/we2e_test_logs-${SRW_PLATFORM}-${SRW_COMPILER}.tgz" */log.generate_FV3LAM_wflow */log.launch_FV3LAM_wflow */log/*'
                                 // Remove the data sets from the experiments directory to conserve disk space
                                 sh 'find "${SRW_WE2E_EXPERIMENT_BASE_DIR}" -regextype posix-extended -regex "^.*(orog|[0-9]{10})$" -type d | xargs rm -rf'
                                 s3Upload consoleLogLevel: 'INFO', dontSetBuildResultOnFailure: false, dontWaitForConcurrentBuildCompletion: false, entries: [[bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: 'we2e_test_results-*-*.txt', storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false], [bucket: 'woc-epic-jenkins-artifacts', excludedFile: '', flatten: false, gzipFiles: false, keepForever: false, managedArtifacts: true, noUploadOnFailure: false, selectedRegion: 'us-east-1', showDirectlyInBrowser: false, sourceFile: 'we2e_test_logs-*-*.tgz', storageClass: 'STANDARD', uploadFromSlave: false, useServerSideEncryption: false]], pluginFailureResultConstraint: 'FAILURE', profileName: 'main', userMetadata: []

devbuild.sh

@@ -33,6 +33,8 @@ OPTIONS
       does a "make clean"
   --build
       does a "make" (build only)
+  --move
+      move binaries to final location.
   --build-dir=BUILD_DIR
       build directory
   --install-dir=INSTALL_DIR
@@ -125,6 +127,7 @@ BUILD_RRFS_UTILS="off"
 # Make options
 CLEAN=false
 BUILD=false
+MOVE=false
 USE_SUB_MODULES=false #change default to true later
 
 # process required arguments
@@ -155,6 +158,7 @@ while :; do
     --continue=?*|--continue=) usage_error "$1 argument ignored." ;;
     --clean) CLEAN=true ;;
     --build) BUILD=true ;;
+    --move) MOVE=true ;;
     --build-dir=?*) BUILD_DIR=${1#*=} ;;
     --build-dir|--build-dir=) usage_error "$1 requires argument." ;;
     --install-dir=?*) INSTALL_DIR=${1#*=} ;;
@@ -398,18 +402,31 @@ module list
 mkdir -p ${BUILD_DIR}
 cd ${BUILD_DIR}
 
-printf "... Generate CMAKE configuration ...\n"
-cmake ${SRW_DIR} ${CMAKE_SETTINGS} 2>&1 | tee log.cmake
-
 if [ "${CLEAN}" = true ]; then
-    printf "... Clean executables ...\n"
-    make ${MAKE_SETTINGS} clean 2>&1 | tee log.make
+    if [ -f $PWD/Makefile ]; then
+       printf "... Clean executables ...\n"
+       make ${MAKE_SETTINGS} clean 2>&1 | tee log.make
+    fi
 elif [ "${BUILD}" = true ]; then
+    printf "... Generate CMAKE configuration ...\n"
+    cmake ${SRW_DIR} ${CMAKE_SETTINGS} 2>&1 | tee log.cmake
+
     printf "... Compile executables ...\n"
     make ${MAKE_SETTINGS} build 2>&1 | tee log.make
 else
+    printf "... Generate CMAKE configuration ...\n"
+    cmake ${SRW_DIR} ${CMAKE_SETTINGS} 2>&1 | tee log.cmake
+
     printf "... Compile and install executables ...\n"
     make ${MAKE_SETTINGS} install 2>&1 | tee log.make
+
+    if [ "${MOVE}" = true ]; then
+       if [[ ! ${SRW_DIR} -ef ${INSTALL_DIR} ]]; then
+           printf "... Moving executables to final locations ...\n"
+           mkdir -p ${SRW_DIR}/${BIN_DIR}
+           mv ${INSTALL_DIR}/${BIN_DIR}/* ${SRW_DIR}/${BIN_DIR}
+       fi
+    fi
 fi
 
 exit 0

devclean.sh

@@ -119,9 +119,11 @@ elif [ "${CLEAN}" = true ]; then
   printf '%s\n' " from the installation directory = ${INSTALL_DIR} "
   [[ -d "${BUILD_DIR}" ]] && rm -rf ${BUILD_DIR}  && printf '%s\n' "rm -rf ${BUILD_DIR}"
   [[ -d "${INSTALL_DIR}/${BIN_DIR}" ]] && ( rm -rf ${INSTALL_DIR}/${BIN_DIR}  && printf '%s\n' "rm -rf ${INSTALL_DIR}/${BIN_DIR}" )
-  [[ -d "${INSTALL_DIR}/lib" ]] && ( rm -rf ${INSTALL_DIR}/share  && printf '%s\n' "rm -rf ${INSTALL_DIR}/share" )
+  [[ -d "${SRW_DIR}/${BIN_DIR}" ]] && ( rm -rf ${SRW_DIR}/${BIN_DIR}  && printf '%s\n' "rm -rf ${SRW_DIR}/${BIN_DIR}" )
+  [[ -d "${INSTALL_DIR}/share" ]] && ( rm -rf ${INSTALL_DIR}/share  && printf '%s\n' "rm -rf ${INSTALL_DIR}/share" )
   [[ -d "${INSTALL_DIR}/include" ]] && ( rm -rf ${INSTALL_DIR}/include  && printf '%s\n' "rm -rf ${INSTALL_DIR}/include" )
   [[ -d "${INSTALL_DIR}/lib" ]] && rm -rf ${INSTALL_DIR}/lib  && printf '%s\n' "rm -rf ${INSTALL_DIR}/lib"
+  [[ -d "${INSTALL_DIR}/lib64" ]] && rm -rf ${INSTALL_DIR}/lib  && printf '%s\n' "rm -rf ${INSTALL_DIR}/lib64"
   [[ -d "${SRW_DIR}/manage_externals/manic" ]] && rm -f ${SRW_DIR}/manage_externals/manic/*.pyc  && printf '%s\n' "rm -f ${SRW_DIR}/manage_externals/manic/*.pyc"
   echo " "
 fi

jobs/JREGIONAL_GET_EXTRN_MDL_FILES

@@ -209,7 +209,7 @@ esac
 #-----------------------------------------------------------------------
 #
 if [ $RUN_ENVIR = "nco" ]; then
-    export EXTRN_MDL_STAGING_DIR="${COMIN}/for_${ICS_OR_LBCS}"
+    export EXTRN_MDL_STAGING_DIR="${COMINext}"
     mkdir_vrfy -p "${EXTRN_MDL_STAGING_DIR}"
 else
     export EXTRN_MDL_STAGING_DIR="${COMIN}/${EXTRN_MDL_NAME}/for_${ICS_OR_LBCS}"

jobs/JREGIONAL_RUN_FCST

@@ -19,7 +19,7 @@
 #
 . ${GLOBAL_VAR_DEFNS_FP}
 . $USHdir/source_util_funcs.sh
-. $USHdir/job_preamble.sh
+. $USHdir/job_preamble.sh "TRUE"
 #
 #-----------------------------------------------------------------------
 #

modulefiles/tasks/orion/run_vx.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/wcoss2/get_extrn_ics.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/get_extrn_lbcs.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/get_obs.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/make_grid.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/make_ics.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/make_lbcs.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/make_sfc_climo.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/python_regional_workflow.lua

@@ -0,0 +1,3 @@
+load(pathJoin("intel", os.getenv("intel_ver")))
+load(pathJoin("python", os.getenv("python_ver")))
+load(pathJoin("prod_util", os.getenv("prod_util_ver")))

modulefiles/tasks/wcoss2/run_fcst.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")

modulefiles/tasks/wcoss2/run_vx.local.lua

@@ -1,2 +1 @@
-load(pathJoin("intel", os.getenv("intel_ver")))
-load(pathJoin("python", os.getenv("python_ver")))
+load("python_regional_workflow")