Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…

…r-model into feature/chunked_array_support_use_it

.github/workflows/aux.yml

@@ -1,9 +1,12 @@
-name: Helpers
+name: Repo Check
 on:
-  workflow_run:
-    workflows: ["Pull Request Tests"]
-    types:
-      - requested
+  #workflow_run:
+  #  workflows: ["Pull Request Tests"]
+  #  types:
+  #    - requested
+  pull_request:
+    branches:
+      - develop
 env:
   app: Accept:application/vnd.github.v3+json
   base_url: $GITHUB_API_URL/repos/$GITHUB_REPOSITORY/actions/runs
@@ -30,24 +33,28 @@ jobs:
     steps:
     - name: Check up-to-dateness and post comment
       run: |
-        head_sha=${{ github.event.workflow_run.head_sha }}
-        git clone -q ${{ github.event.workflow_run.head_repository.html_url }} .
+        trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
+        head_sha=${{ github.event.pull_request.head.sha }}
+        head_brc=${{ github.event.pull_request.head.ref }}
+        head_url=${{ github.event.pull_request.head.repo.html_url }}
+        git clone -q -b $head_brc $head_url .
         git checkout -q $head_sha
         git submodule -q update --init --recursive
         cd ${{ github.workspace }}/tests/ci
         url=$GITHUB_API_URL/repos/$GITHUB_REPOSITORY
         pr_number=$(curl -sS -H $app $url/pulls \
           | jq -r '.[] | select(.head.sha == "'"$head_sha"'") | .number')
         echo "pr_number is $pr_number"
-        pr_uid=${{ github.event.workflow_run.head_repository.owner.login }}
+        pr_uid=${{ github.event.pull_request.head.repo.owner.login }}
         echo "pr_uid is $pr_uid"
-        comment="$(./repo_check.sh $pr_uid 2>/dev/null)"
-        echo "comment is $comment"
-        if [[ -n $comment ]]; then
-          curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-            $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
-          echo -n "failure" >~/repocheck_file
-        else
-          echo -n "success" >~/repocheck_file
-        fi
+        ./repo_check.sh
+        #comment="$(./repo_check.sh 2>/dev/null)"
+        #echo "comment is $comment"
+        #if [[ -n $comment ]]; then
+        #  curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+        #    $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
+        #  echo -n "failure" >~/repocheck_file
+        #else
+        #  echo -n "success" >~/repocheck_file
+        #fi
         

NOAHMP-interface/CMakeLists.txt

@@ -8,9 +8,10 @@ list(APPEND _noahmp_cap_files noahmp/drivers/nuopc/lnd_comp_kind.F90
                               noahmp/drivers/nuopc/lnd_comp_domain.F90
                               noahmp/drivers/nuopc/lnd_comp_import_export.F90
                               noahmp/drivers/nuopc/lnd_comp_nuopc.F90
-                              noahmp/drivers/nuopc/lnd_comp_driver.F90)
+                              noahmp/drivers/nuopc/lnd_comp_driver.F90
+			      noahmp/drivers/nuopc/lnd_comp_cplscalars.F90)
 
-# CCPP interface 
+# CCPP interface
 list(APPEND _noahmp_ccpp_files noahmp/drivers/ccpp/noahmpdrv.F90
                                noahmp/drivers/ccpp/sfc_diff.f
                                noahmp/drivers/ccpp/machine.F
@@ -25,7 +26,7 @@ list(APPEND _noahmp_files noahmp/src/module_sf_noahmplsm.F90
                           noahmp/src/module_sf_noahmp_glacier.F90)
 
 #------------------------------------------------------------------------------
-# Set CCPP flags for C/C++/Fortran preprocessor 
+# Set CCPP flags for C/C++/Fortran preprocessor
 add_definitions(-DCCPP)
 
 #------------------------------------------------------------------------------

cmake/GNU.cmake

@@ -5,10 +5,6 @@ endif()
 
 set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ggdb -fbacktrace -cpp -fcray-pointer -ffree-line-length-none -fno-range-check")
 
-if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
-endif()
-
 if(NOT 32BIT)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8 -fdefault-double-8")
 endif()

driver/UFS.F90

@@ -79,6 +79,9 @@ PROGRAM UFS
       TYPE(ESMF_Config) :: CF_MAIN                                         !<-- The Configure object
 !
       CHARACTER(ESMF_MAXSTR) :: MESSAGE_CHECK
+!
+      CHARACTER(len=MPI_MAX_LIBRARY_VERSION_STRING) :: library_version
+      INTEGER :: resultlen
 !
       INTEGER :: RC, RC_USER                                               !<-- The running error signal
 !
@@ -122,7 +125,12 @@ PROGRAM UFS
 !***  Print subversion version and other status information.
 !-----------------------------------------------------------------------
 !
-      if (mype==0) call w3tagb('ufs      ',0000,0000,0000,'np23   ')
+      if (mype == 0) then
+        call w3tagb('ufs-weather-model',0,0,0,'np23')
+        call MPI_Get_library_version(library_version, resultlen, rc)
+        write(*,'(A,A)')      'MPI Library = ', library_version(1:resultlen)
+        write(*,'(A,I0,A,I0)')'MPI Version = ', mpi_version,'.',mpi_subversion
+      endif
 !
 !-----------------------------------------------------------------------
 !***  Set up the default log.

modulefiles/ufs_hera.gnu.lua

@@ -2,9 +2,7 @@ help([[
 loads UFS Model prerequisites for Hera/GNU
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core")
--- for openmpi, need
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env-rocky8/install/modulefiles/Core")
 
 stack_gnu_ver=os.getenv("stack_gnu_ver") or "9.2.0"
 load(pathJoin("stack-gcc", stack_gnu_ver))

modulefiles/ufs_hera.intel.lua

@@ -2,7 +2,7 @@ help([[
 loads UFS Model prerequisites for Hera/Intel
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env-rocky8/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 load(pathJoin("stack-intel", stack_intel_ver))

modulefiles/ufs_noaacloud.intel.lua

@@ -3,7 +3,7 @@ loads UFS Model prerequisites for NOAA Parallelworks/Intel
 ]])
 
 
-prepend_path("MODULEPATH", "/contrib/EPIC/spack-stack/spack-stack-1.5.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.3.0"
 load(pathJoin("stack-intel", stack_intel_ver))

tests/atparse.bash

@@ -1,42 +1,106 @@
 #! /usr/bin/env bash
 function atparse {
-    local __set_x
-    [ -o xtrace ] && __set_x='set -x' || __set_x='set +x'
-    set +x
+    # Usage:
+    #     source atparse.bash # defines the "atparse" function; only do this once
+    #     atparse [ var1=value1 [ var2=value2 [...] ] ] < input_file > output_file
+    # This function filters text from stdin to stdout. It scans for text sequences like:
+    #    @[varname]
+    # And replaces them with the value of the corresponding ${varname} variable.
+    # You can provide variables that are not set in bash by providing them on the command line.
+    # If set -u is enabled, it will exit the process when a variable is empty or undefined via set -u.
+
     # Use __ in names to avoid clashing with variables in {var} blocks.
-    local __text __before __after __during
+    local __text # current line of text being parsed, or the current command-line argument being parsed
+    local __before # all text before the next @[...] option
+    local __after # all text after the next @[...] option
+    local __during # the contents of the @[...] option, including the @[ and ]
+    local __set_x=":" # will be "set -x" if the calling script had that option enabled
+    local __set_u=":" # will be "set -u" if the calling script had that option enabled
+    local __set_e=":" # will be "set -e" if the calling script had that option enabled
+    local __abort_on_undefined=NO # YES = script should abort if a variable is undefined, NO otherwise
+
+    # Ensure "set -x -e -u" are all inactive, but remember if they
+    # were active so we can reset them later.
+    if [[ -o xtrace ]] ; then
+        __set_x="set -x"
+    fi
+    if [[ -o errexit ]] ; then
+        __set_e="set -e"
+    fi
+    if [[ -o nounset ]] ; then
+        __set_u="set -u"
+        __abort_on_undefined=YES
+    fi
+    set +eux
+
+    # Allow setting variables on the atparse command line rather than the environment.
+    # They will be local variables in this function.
     for __text in "$@" ; do
         if [[ $__text =~ ^([a-zA-Z][a-zA-Z0-9_]*)=(.*)$ ]] ; then
             eval "local ${BASH_REMATCH[1]}"
             eval "${BASH_REMATCH[1]}="'"${BASH_REMATCH[2]}"'
         else
-            echo "ERROR: Ignoring invalid argument $__text\n" 1>&2
+            echo "ERROR: Ignoring invalid argument $__text" 1>&2
         fi
     done
-    while IFS= read -r __text ; do
+
+    # Loop over all lines of text.
+    while [[ 1 == 1 ]] ; do
+        # Read the next line of text. This will "fail" if no more text
+        # is left OR if the last line lacks an end-of-line character.
+        read -d '' -r __text
+
+        # Stop when "read" reports it is done ($? -ne 0) AND the text is
+        # non-empty (! -n "$__text"). This ensures we read the final line
+        # even if it lacks an end-of-line character.
+        if [[ $? -ne 0 ]] ; then
+            if [[ -n "$__text" ]] ; then
+                # Text remained, but it had no end-of-line.
+                :
+            else
+                break
+            fi
+        fi
+        # Search for strings like @[varname] or @['string'] or @[@]
         while [[ "$__text" =~ ^([^@]*)(@\[[a-zA-Z_][a-zA-Z_0-9]*\]|@\[\'[^\']*\'\]|@\[@\]|@)(.*) ]] ; do
             __before="${BASH_REMATCH[1]}"
             __during="${BASH_REMATCH[2]}"
             __after="${BASH_REMATCH[3]}"
-#            printf 'PARSE[%s|%s|%s]\n' "$__before" "$__during" "$__after"
             printf %s "$__before"
+            # @['string'] inserts string
             if [[ "$__during" =~ ^@\[\'(.*)\'\]$ ]] ; then
                 printf %s "${BASH_REMATCH[1]}"
+            # @[@] inserts @
             elif [[ "$__during" == '@[@]' ]] ; then
                 printf @
+            # @[varname] inserts $varname
             elif [[ "$__during" =~ ^@\[([a-zA-Z_][a-zA-Z_0-9]*)\] ]] ; then
+                # Flag unknown variables at this step only.
+                if [[ ${__abort_on_undefined} == YES ]] ; then
+                    set -u
+                fi
                 eval 'printf %s "$'"${BASH_REMATCH[1]}"'"'
+                if [[ ${__abort_on_undefined} == YES ]] ; then
+                    set +u
+                fi
+            # Unrecognized sequences are inserted verbatim.
             else
                 printf '%s' "$__during"
             fi
+            # Continue until we run out of text in this line.
             if [[ "$__after" == "$__text" ]] ; then
                 break
             fi
             __text="$__after"
         done
+        # Print the corrected text
         printf '%s\n' "$__text"
     done
+
+    # Restore the calling script's shell options.
     eval "$__set_x"
+    eval "$__set_u"
+    eval "$__set_e"
 }
 
 function test_atparse {
@@ -45,14 +109,18 @@ function test_atparse {
     testvar='[testvar]'
     var1='[var1]'
     var2='[var2]'
-    cat<<\EOF | atparse var3='**'
+    var4='[var4]'
+    ( cat<<\EOF ; echo -n "line with no end-of-line character [var4] = @[var4]" ) | atparse var3='**'
 Nothing special here. = @['Nothing special here.']
 [testvar] = @[testvar]
 [var1] [var2] = @[var1] @[var2]
 ** = @[var3]
+[var4] == @[var4]
 @ = @[@] = @['@']
+@[undefined_variable_that_should_exit_script_if_set_minus_u_is_used]
 -n
  eval "export PE$c=\${PE$c:-0}" = @[' eval "export PE$c=\${PE$c:-0}"']
 EOF
+    echo " ... this text should be on the same line as the line with no end-of-line character"
     echo "After block, \$var3 = \"$var3\" should be empty"
 }

tests/bl_date.conf

@@ -1 +1 @@
-export BL_DATE=20240301
+export BL_DATE=20240401

tests/ci/Jenkinsfile.combined

@@ -258,6 +258,8 @@ pipeline {
     agent none
     environment {
         ACCNR = 'epic'
+        AWS_PROD_ACCOUNT_ID = credentials('AWS_PROD_ACCOUNT_ID')
+        AWS_PROD_SNS_TOPIC = credentials('AWS_PROD_SNS_TOPIC')
         GITHUB_TOKEN = credentials('GithubJenkinsNew')
         GIT_URL = 'https://github.com/ufs-community/ufs-weather-model.git'
     }
@@ -285,15 +287,15 @@ pipeline {
              node('built-in') {
                 echo 'This will run only if successful.'
                 sh '''
-                  aws sns publish --topic-arn "arn:aws:sns:us-east-1:211527314271:Jenkins-CICD-Notifications" --region us-east-1 --message '{"version":"1.0","source":"custom","content":{"description":":sunny: Jenkins build *'"$JOB_NAME"' '"$BUILD_NUMBER"'* with *PR-'"$CHANGE_ID"'*  *succeeded*"}}'
+                  aws sns publish --topic-arn "arn:aws:sns:us-east-1:${AWS_PROD_ACCOUNT_ID}:${AWS_PROD_SNS_TOPIC}" --region us-east-1 --message '{"version":"1.0","source":"custom","content":{"description":":sunny: Jenkins build *'"$JOB_NAME"' '"$BUILD_NUMBER"'* with *PR-'"$CHANGE_ID"'*  *succeeded*"}}'
                '''
              }
          }
          failure {
              node('built-in') {
                 echo 'This will run only if the run was marked as unstable.'
                 sh '''
-                  aws sns publish --topic-arn "arn:aws:sns:us-east-1:211527314271:Jenkins-CICD-Notifications" --region us-east-1 --message '{"version":"1.0","source":"custom","content":{"description":":warning: Jenkins build *'"$JOB_NAME"' '"$BUILD_NUMBER"'* with *PR-'"$CHANGE_ID"'*  *failed!*"}}'
+                  aws sns publish --topic-arn "arn:aws:sns:us-east-1:${AWS_PROD_ACCOUNT_ID}:${AWS_PROD_SNS_TOPIC}" --region us-east-1 --message '{"version":"1.0","source":"custom","content":{"description":":warning: Jenkins build *'"$JOB_NAME"' '"$BUILD_NUMBER"'* with *PR-'"$CHANGE_ID"'*  *failed!*"}}'
                '''
              }
          }