.gitignore

-# configurations & testcases
+# configurations, testcases & tools
 
-*/work_cfgs.txt
+cfgs/work_cfgs.txt
 cfgs/*/BLD
 cfgs/*/EXP00
 cfgs/*/WORK
+cfgs/*/NEMOFILES
+cfgs/*/AGRIFLIB
 cfgs/*_ST
+
+tests/work_cfgs.txt
 tests/*/BLD
 tests/*/EXP00
 tests/*/WORK
+tests/*/NEMOFILES
+tests/*/AGRIFLIB
 tests/*_ST
 
+tools/*/BLD
+tools/*/*.exe
+tools/tools.txt
+
 # mk
-mk/arch*
-mk/cpp.*
 mk/full_key_list.txt
+
+# arch
+arch/arch-auto.fcm
+
+# sette param files
+sette/param*

.gitlab-ci.yml

+#----------#
+# SETTE CI #
+#----------#
+
+
+workflow:
+
+  name: "SETTE : $NEMO_HPC $NEMO_COMPILER $NEMO_COMPILATION - $NEMO_CONFIG cfg(s) - $SETTE_TEST test(s)"
+  rules:
+    - if: $CI_PIPELINE_SOURCE == 'web'
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event' && $CI_COMMIT_TITLE =~ /(?i).*\[ci\].*/
+    - if: $CI_PIPELINE_SOURCE == 'schedule'
+
+
+include:
+
+  # PIPELINE VARIABLES
+  - local: '.gitlab-ci/.VAR-SELECT.yml'
+
+  # SETTE TESTS
+  - local: '.gitlab-ci/.TEST-VAR.yml'
+  - local: '.gitlab-ci/.TEST-ALL.yml'
+    rules:
+      - if: $SETTE_TEST == "ALL"
+  - local: '.gitlab-ci/.TEST-RESTART.yml'
+    rules:
+      - if: $SETTE_TEST == "RESTART"
+  - local: '.gitlab-ci/.TEST-REPRO.yml'
+    rules:
+      - if: $SETTE_TEST == "REPRO"
+  - local: '.gitlab-ci/.TEST-CORRUPT.yml'
+    rules:
+      - if: $SETTE_TEST == "CORRUPT"
+  - local: '.gitlab-ci/.TEST-PHYOPTS.yml'
+    rules:
+      - if: $SETTE_TEST == "PHYOPTS"
+
+  # NEMO CONFIGURATIONS
+  - local: '.gitlab-ci/.CFG-ALL.yml'
+    rules:
+    - if: $NEMO_CONFIG == "ALL"
+  - local: '.gitlab-ci/.CFG-SELECT.yml'
+    rules:
+      - if: $NEMO_CONFIG != "ALL"
+
+  # HPC
+  - local: '.gitlab-ci/.HPC-MERCATOR.yml'
+
+
+# YAML ANCHORS
+
+.cache: &cache_CFG
+  key: ${CONFIG}_${CI_COMMIT_SHORT_SHA}_${CI_PIPELINE_ID}
+  paths:
+    - $CI_PROJECT_DIR/{cfgs,tests}/${CONFIG}_ST/EXP*
+    - $CI_PROJECT_DIR/{cfgs,tests}/${CONFIG}_ST/BLD/bin
+    - $CI_PROJECT_DIR/{cfgs,tests}/${CONFIG}_ST/cpp_${CONFIG}_ST.fcm
+
+.loop: &loop
+    matrix:
+      - CONFIG: !reference [.config, variables, CONFIG]
+
+.artifact_run: &artifact_run
+    paths:
+      - sette/sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+      - cfgs/${CONFIG}_ST/*/sette.*.out
+      - cfgs/${CONFIG}_ST/*/sette.*.err
+      - cfgs/${CONFIG}_ST/*/ocean.output*
+      - tests/${CONFIG}_ST/*/sette.*.out
+      - tests/${CONFIG}_ST/*/sette.*.err
+      - tests/${CONFIG}_ST/*/ocean.output*
+    when: always
+    expire_in: 30 days
+
+
+stages:
+  - compile
+  - run
+  - check
+
+
+before_script:
+# the following commands will be executed at the beginning of each job
+# they are needed to copy param.cfg to SETTE directory and to load the modules
+  - declare -A HOST_NAME=( ["aa"]="ECMWF" ["ab"]="ECMWF" ["ac"]="ECMWF" ["ad"]="ECMWF" ["lir"]="LIR"
+                           ["belenoslogin"]="MF" ["irene"]="IR" ["jean-zay"]="JZ" )
+  # modules should be loaded using .env files in NEMO arch directory
+  - SETTE_MOD=${HOST_NAME[${HOSTNAME//[-,.,0-9]*}]}_SETTE_MOD
+  - if [ -n "${!SETTE_MOD}" ]; then
+      if [ -d ${HOME}/modules ]; then module use ${HOME}/modules; fi;
+      module purge || true;
+      module load ${!SETTE_MOD};
+    fi
+  - set +x   # debug prints
+  # copy SETTE local param.cfg file
+  - SETTE_CFG=${HOST_NAME[${HOSTNAME//[-,.,0-9]*}]}_SETTE_CFG
+  - cp -aLv ${!SETTE_CFG} sette/param.cfg
+  - git config core.filemode false   # ignore git(lab) symlinks permissions changes when pushing then pulling cache ("old mode 100755 -> new mode 100644")
+  - SETTE_OPT="-u -w"   # no user interaction + wait for jobs to end options
+  - if [[ ${NEMO_COMPILATION} == "debug" ]]; then SETTE_OPT="${SETTE_OPT} -b"; fi
+
+
+# JOBS
+# sette_cmp : compile reference configurations / testcases
+# sette_run :     run reference configurations / testcases
+# sette_rpt :   check reference configurations / testcases results
+
+
+sette_cmp:
+  stage: compile
+  parallel:   # Parallelisation across the selected configuration(s)
+    <<: *loop
+  rules:      # Restriction to the configurations relevant for the selected test(s)
+    - if: ($CONFIG =~ $PATTERN || $NEMO_CONFIG =~ $PATTERN)
+  cache:
+    <<: *cache_CFG
+    policy: push
+  tags:
+    - $NEMO_HPC
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "COMPILE" | tee -a sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    - cd -
+  artifacts:
+    paths:
+      - sette/sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days
+
+
+sette_run:RESTART:
+  stage: run
+  needs:             # Dependency on the compilation of the configurations relevant for the 'RESTART' test
+    - job: sette_cmp
+      parallel:
+        matrix:
+          - CONFIG: !reference [.restart, variables, CONFIG]
+  parallel:          # Parallelisation across the selected configuration(s)
+    <<: *loop
+  rules:             # Dependency on the 'RESTART'-test selection, and restriction to the configurations relevant for the 'RESTART' test
+    - if: $SETTE_TEST =~ /ALL|RESTART/ && ($CONFIG =~ $PATTERN_RESTART || $NEMO_CONFIG =~ $PATTERN_RESTART)
+  dependencies: []   # No retrieval of previous artefacts
+  cache:
+    <<: *cache_CFG
+    policy: pull
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "RESTART" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    - cd -
+  artifacts:
+    <<: *artifact_run
+
+
+sette_run:REPRO:
+  stage: run
+  needs:
+    - job: sette_cmp
+      parallel:
+        matrix:
+          - CONFIG: !reference [.repro, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|REPRO/ && ($CONFIG =~ $PATTERN_REPRO || $NEMO_CONFIG =~ $PATTERN_REPRO)
+  parallel: 
+    <<: *loop
+  cache:
+    <<: *cache_CFG
+    policy: pull
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "REPRO" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    - cd -
+  artifacts:
+    <<: *artifact_run
+
+
+sette_run:CORRUPT:
+  stage: run
+  needs:
+    - job: sette_cmp
+      parallel:
+        matrix:
+          - CONFIG: !reference [.corrupt, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|CORRUPT/ && ($CONFIG =~ $PATTERN_CORRUPT || $NEMO_CONFIG =~ $PATTERN_CORRUPT)
+  parallel: 
+    <<: *loop
+  cache:
+    <<: *cache_CFG
+    policy: pull
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "CORRUPT" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    - cd -
+  artifacts:
+    <<: *artifact_run
+
+
+sette_run:PHYOPTS:
+  stage: run
+  needs:
+    - job: sette_cmp
+      parallel:
+        matrix:
+          - CONFIG: !reference [.phyopts, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|PHYOPTS/ && ($CONFIG =~ $PATTERN_PHYOPTS || $NEMO_CONFIG =~ $PATTERN_PHYOPTS)
+  parallel: 
+    <<: *loop
+  cache:
+    <<: *cache_CFG
+    policy: pull
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "PHYOPTS" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    - cd -
+  artifacts:
+    <<: *artifact_run
+
+
+sette_rpt:RESTART:
+  stage: check
+  needs:             # Dependency on the completion of the test runs relevant for the 'RESTART' test
+    - job: sette_run:RESTART
+      parallel:
+        matrix:
+          - CONFIG: !reference [.restart, variables, CONFIG]
+  parallel:          # Parallelisation across the selected configuration(s)
+    <<: *loop
+  rules:             # Dependency on the 'RESTART'-test selection, and restriction to the configurations relevant for the 'RESTART' test
+    - if: $SETTE_TEST =~ /ALL|RESTART/ && ($CONFIG =~ $PATTERN_RESTART || $NEMO_CONFIG =~ $PATTERN_RESTART)
+  dependencies: []   # No retrieval of previous artefacts
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "RESTART" ${SETTERPT_OPT} | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days
+
+
+sette_rpt:REPRO:
+  stage: check
+  needs:
+    - job: sette_run:REPRO
+      parallel:
+        matrix:
+          - CONFIG: !reference [.repro, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|REPRO/ && ($CONFIG =~ $PATTERN_REPRO || $NEMO_CONFIG =~ $PATTERN_REPRO)
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "REPRO" ${SETTERPT_OPT} | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days
+
+
+sette_rpt:CORRUPT:
+  stage: check
+  needs:
+    - job: sette_run:CORRUPT
+      parallel:
+        matrix:
+          - CONFIG: !reference [.corrupt, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|CORRUPT/ && ($CONFIG =~ $PATTERN_CORRUPT || $NEMO_CONFIG =~ $PATTERN_CORRUPT)
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "CORRUPT" ${SETTERPT_OPT} | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days
+
+
+sette_rpt:PHYOPTS:
+  stage: check
+  needs:
+    - job: sette_run:PHYOPTS
+      parallel:
+        matrix:
+          - CONFIG: !reference [.phyopts, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST =~ /ALL|PHYOPTS/ && ($CONFIG =~ $PATTERN_PHYOPTS || $NEMO_CONFIG =~ $PATTERN_PHYOPTS)
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "PHYOPTS" ${SETTERPT_OPT} | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days
+
+
+sette_rpt:COMPARE:
+  stage: check
+  needs:
+    - job: sette_run:RESTART
+      parallel:
+        matrix:
+          - CONFIG: !reference [.restart, variables, CONFIG]
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $NEMO_REFSHA != "" && ($CONFIG =~ $PATTERN_RESTART || $NEMO_CONFIG =~ $PATTERN_RESTART)
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "COMPARE" ${NEMO_REFSHA:+-S ${NEMO_REFSHA}} ${SETTERPT_OPT} | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${NEMO_HPC}.log
+    when: always
+    expire_in: 30 days

.gitlab-ci/.CFG-ALL.yml

+# CONFIG variable is used in '.config' template to define configurations parallel loops.
+# It contains the full list of nemo configurations and testcases by default.
+
+.config:
+  variables:
+    CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,AGRIF_DEMO,WED025,GYRE_PISCES,GYRE_GO,ORCA2_SAS_ICE,ORCA2_ICE_OBS,C1D_PAPA,
+             SWG,ICE_AGRIF,OVERFLOW,LOCK_EXCHANGE,VORTEX,ISOMIP+,IWAVE]
\ No newline at end of file

.gitlab-ci/.CFG-SELECT.yml

+# CONFIG variable is used in '.config' template to define parallel loops and in '.test' templates to define jobs dependencies.
+# If a specific configuration is selected manually, CONFIG is set here.
+
+.config:
+  variables:
+    CONFIG: [$NEMO_CONFIG]
+
+.restart:
+  variables:
+    CONFIG: [$NEMO_CONFIG]
+
+.repro:
+  variables:
+    CONFIG: [$NEMO_CONFIG]
+
+.corrupt:
+  variables:
+    CONFIG: [$NEMO_CONFIG]
+
+.phyopts:
+  variables:
+    CONFIG: [$NEMO_CONFIG]
\ No newline at end of file

.gitlab-ci/.HPC-MERCATOR.yml

+# SETTE 'param.cfg' file path for each HPC
+
+variables:
+  # METEO-FRANCE BELENOS (INTEL2018+INTELMPI)
+  MF_SETTE_CFG: "/home/ext/mr/smer/samsong/SRC/NEMO/main/sette/param_${NEMO_COMPILER}.ci"
+  # ECMWF AA/B/C/D (GCC13+OPENMPI & INTEL2021+OPENMPI)
+  ECMWF_SETTE_CFG: "/home/ar0s/SRC/NEMO/main/sette/param_${NEMO_COMPILER}.ci"
+  # MERCATOR LIR (GCC14+OPENMPI)
+  LIR_SETTE_CFG: "/home/gsamson/SRC/NEMO/main/sette/param_${NEMO_COMPILER}.ci"
\ No newline at end of file

.gitlab-ci/.TEST-ALL.yml

+variables:
+  #PATTERN: '$PATTERN_ALL'
+  PATTERN: '/ORCA2_ICE_PISCES|ORCA2_OFF_PISCES|AMM12|AGRIF_DEMO|WED025|GYRE_PISCES|GYRE_GO|ORCA2_SAS_ICE|ORCA2_ICE_OBS|C1D_PAPA|SWG|ICE_AGRIF|OVERFLOW|LOCK_EXCHANGE|VORTEX|ISOMIP+|IWAVE/'
\ No newline at end of file

.gitlab-ci/.TEST-CORRUPT.yml

+variables:
+  #PATTERN: $PATTERN_CORRUPT
+  PATTERN: '/AGRIF_DEMO/'
\ No newline at end of file

.gitlab-ci/.TEST-PHYOPTS.yml

+variables:
+  #PATTERN: $PATTERN_PHYOPTS
+  PATTERN: '/OVERFLOW|LOCK_EXCHANGE/'
\ No newline at end of file

.gitlab-ci/.TEST-REPRO.yml

+variables:
+  #PATTERN: $PATTERN_REPRO
+  PATTERN: '/ORCA2_ICE_PISCES|ORCA2_OFF_PISCES|AMM12|AGRIF_DEMO|WED025|GYRE_PISCES|GYRE_GO|ORCA2_SAS_ICE|ORCA2_ICE_OBS|SWG|ICE_AGRIF|VORTEX|ISOMIP+/'
\ No newline at end of file

.gitlab-ci/.TEST-RESTART.yml

+variables:
+  #PATTERN: $PATTERN_RESTART
+  PATTERN: '/ORCA2_ICE_PISCES|ORCA2_OFF_PISCES|AMM12|AGRIF_DEMO|WED025|GYRE_PISCES|GYRE_GO|ORCA2_SAS_ICE|ORCA2_ICE_OBS|C1D_PAPA|SWG|ICE_AGRIF|OVERFLOW|LOCK_EXCHANGE|VORTEX|ISOMIP+|IWAVE/'
\ No newline at end of file

.gitlab-ci/.TEST-VAR.yml

+# Regex patterns for each sette test to define jobs rules.
+# https://docs.gitlab.com/ci/jobs/job_rules/#store-a-regular-expression-in-a-variable
+
+variables:
+    PATTERN_RESTART: '/ORCA2_ICE_PISCES|ORCA2_OFF_PISCES|AMM12|AGRIF_DEMO|WED025|GYRE_PISCES|GYRE_GO|ORCA2_SAS_ICE|ORCA2_ICE_OBS|C1D_PAPA|SWG|ICE_AGRIF|OVERFLOW|LOCK_EXCHANGE|VORTEX|ISOMIP+|IWAVE/'
+    PATTERN_REPRO: '/ORCA2_ICE_PISCES|ORCA2_OFF_PISCES|AMM12|AGRIF_DEMO|WED025|GYRE_PISCES|GYRE_GO|ORCA2_SAS_ICE|ORCA2_ICE_OBS|SWG|ICE_AGRIF|VORTEX|ISOMIP+/'
+    PATTERN_CORRUPT: '/AGRIF_DEMO/'
+    PATTERN_PHYOPTS: '/OVERFLOW|LOCK_EXCHANGE/'
+
+
+# List of configurations for each type of tests to manage job dependencies.
+# It will be overwritten in '.CFG-SELECT.yml' if a specific configuration is selected manually.
+# https://docs.gitlab.com/ci/yaml/#needsparallelmatrix
+
+.restart:
+  variables:
+    CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,AGRIF_DEMO,WED025,GYRE_PISCES,GYRE_GO,ORCA2_SAS_ICE,ORCA2_ICE_OBS,C1D_PAPA,SWG,ICE_AGRIF,OVERFLOW,LOCK_EXCHANGE,VORTEX,ISOMIP+,IWAVE]
+
+.repro:
+  variables:
+    CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,AGRIF_DEMO,WED025,GYRE_PISCES,GYRE_GO,ORCA2_SAS_ICE,ORCA2_ICE_OBS,SWG,ICE_AGRIF,VORTEX,ISOMIP+]
+
+.corrupt:
+  variables:
+    CONFIG: [AGRIF_DEMO]
+
+.phyopts:
+  variables:
+    CONFIG: [OVERFLOW,LOCK_EXCHANGE]

.gitlab-ci/.VAR-SELECT.yml

+# pipelines variables that can be defined manually from https://forge.nemo-ocean.eu/nemo/nemo/-/pipelines/new
+
+variables:
+
+  NEMO_HPC:
+    # must correspond to runners tags
+    description: "Nemo HPC"   
+    value: "ecmwf"
+    options:
+      - "ecmwf"
+
+  NEMO_COMPILER:
+    description: "Nemo Fortran compiler"
+    value: "default"
+    options:
+      - "default"
+      - "intel"
+      - "gcc"
+
+  NEMO_COMPILATION:
+    description: "Nemo compilation mode"
+    value: "debug"
+    options:
+      - "debug"
+      - "normal"
+
+  NEMO_CONFIG:
+    description: "Nemo configuration(s)/testcase(s)"
+    value: "ALL"
+    options:
+      - "ALL"
+
+  SETTE_TEST:
+    description: "Sette test(s) to be executed"
+    value: ""
+    options:
+      - ""
+      - "ALL"
+      - "RESTART"
+      - "REPRO"
+      - "CORRUPT"
+      - "PHYOPTS"
+      - "TRANSFORM"
+      - "COMPARE"
+
+  NEMO_REFSHA:
+    description: "Nemo short SHA (8 digits) for results comparison (optional)"
+    value: ""
+    options:
+      - ""

.gitlab/issue_templates/Bug.md

+#### Context
+
+_Please provide informations on how to reproduce the bug:_
+
+- [x] Branches impacted: current release and/or main 
+- [x] Reference configuration/test case (chosen or used as template) ~AMM ~gyre ~orca ~papa or engines involved ~ABL ~NST ~OFF ~TOP ~SAO ~SAS ~"SI³" ~SWE
+- [x] Computing architecture: compiler, MPI & NetCDF libs (name and version)
+- [x] Dependencies: ~AGRIF ~BFM ~CICE ~OASIS ~XIOS (with known branch and hash/revision/version), ...
+- [ ] _Any other relevant information_
+
+#### Analysis
+
+_Please give your thoughts on the issue._
+
+#### Fix
+
+_Please share your proven solution or your recommendation on how to proceed._
+
+---
+
+_You can_
+- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or  diff outputs_ (\`\`\`diff ...\`\`\`)
+- :paperclip: _Include files_
+- :link:      _Add external links._
+
+:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:

.gitlab/issue_templates/Feature.md

+#### Context
+
+_Please provide informations on how to set the modelling environment_
+
+- [ ] Reference configuration/test case (to add, chosen or used as template)
+- [x] Modifications of versioned files: Fortran routines (`*.[Ffh]90`), namelists (`namelist\_*cfg`), outputs settings (`*.xml`), ...
+- [ ] Additional dependencies
+- [ ] New datasets
+- [ ] _Any other relevant information_
+
+#### Proposal
+
+_Please share your ideas or your wishes about modelling improvements for the NEMO model._  
+_In particular, express if you are willing to contribute personally to the implementation of this feature in NEMO._
+
+---
+
+_You can_
+- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or  diff outputs_ (\`\`\`diff ...\`\`\`)
+- :paperclip: _Include files_
+- :link:      _Add external links._
+
+:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:

.gitlab/issue_templates/Task_preview.md

+#### Development description
+
+_Describe the goal and the methodology._  
+_Add reference documents or publications if relevant._
+
+#### Code implementation
+
+_Describe flow chart of the changes in the code._  
+_List the Fortran modules and subroutines to be created/edited/deleted._  
+_Detailed list of new variables to be defined (including namelists), give for each the chosen name and description wrt coding rules._
+
+#### Documentation updates
+
+_Using previous parts, define the main changes to be done in the ~doc (manuals, guide, web pages, ...)._

.gitlab/merge_request_templates/.gitkeep

+

.gitlab/merge_request_templates/Task_review.md

+#### Tests
+
+Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.  
+This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
+
+**Regular checks**
+
+- [ ] Can this change be shown to produce expected impact (option activated)?
+- [ ] Can this change be shown to have a null impact (option not activated)?
+- [ ] Results of the required bit comparability tests been run: are there no differences when activating the development?
+- [ ] If some differences appear, is reason for the change valid/understood?
+- [ ] If some differences appear, is the impact as expected on model configurations?
+- [ ] Is this change expected to preserve all diagnostics?  
+  - [ ] If no, is reason for the change valid/understood?
+- [ ] Are there significant changes in run time/memory?
+
+#### Review
+
+A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
+
+**Assessments**
+
+- [ ] Is the proposed methodology now implemented?
+- [ ] Are the code changes in agreement with the flowchart defined at preview step?
+- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?  
+  - [ ] If, not, are the discrepancies acceptable?
+- [ ] Is the in-line documentation accurate and sufficient?
+- [ ] Do the code changes comply with NEMO coding standards?
+- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
+- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?

README.rst

-**Contents**
+NEMO
+====
 
-.. contents::
-   :local:
-
-
-
-
-.. _`Former web platform forge`: https://forge.ipsl.jussieu.fr/nemo
-.. _`NEMO users' guide`: https://sites.nemo-ocean.io/user-guide
-.. _`Migration Guide`: https://sites.nemo-ocean.io/user-guide/migration.html
-.. _`Change list`: https://sites.nemo-ocean.io/user-guide/changes.html
-.. _`Test case repository`: https://github.com/NEMO-ocean/NEMO-examples
-.. _`How to cite`: https://www.nemo-ocean.eu/bibliography/how-to-cite/
-.. _`NEMO forums`: https://nemo-ocean.discourse.group
-.. _`NEMO newsletter`: https://listes.ipsl.fr/sympa/subscribe/nemo-newsletter
-.. _`NEMO publications`: https://www.nemo-ocean.eu/bibliography/publications/add
-.. _`NEMO projects`: https://www.nemo-ocean.eu/projects/add
-.. _`Special Issue`: https://gmd.copernicus.org/articles/special_issue40.html
-.. _`NEMO System Team wiki`: https://forge.nemo-ocean.eu/developers/home/-/wikis/Home
-
-
-**Welcome to NEMO home page!**
-
-NEMO (*Nucleus for European Modelling of the Ocean*) is a state-of-the-art modelling
+*Nucleus for European Modelling of the Ocean* (NEMO) is a state-of-the-art modelling
 framework for research activities and forecasting services in ocean and climate sciences,
 developed in a sustainable way by the NEMO European consortium since 2008.
 
-This page intends to help you to get started using the NEMO platform and to introduce you
-to the different levels of information available. It starts here with NEMO release 4.2.0.
-
-Reminder: Our `Former web platform forge`_ (SVN+Trac) contains the previous documentation
-and releases made available from the beginning of the project up to of NEMO 4.0.
-
-Getting started
-===============
-
-Getting your hands on NEMO: the first steps are described in detail in the 
-`NEMO users' guide`_ . This explains how to download the code, build the environment, 
-create the executable, and perform a first integration.
-
-If you are already using a previous release of NEMO, please refer to the 
-`Migration Guide`_ which aims to help you to make the move to 4.2.0.
-
-The above users guides cover in detail what is available from gitlab and supported by NEMO
-System Team. Aside from this web platform, a set of test cases is also available from the
-`Test case repository`_ . These test cases can be useful for students, outreach, and
-exploring specific aspects of NEMO with light configurations. The web page also allows you
-to submit test cases you have developed and want to share with the community. Feel free to
-contribute!
-
-
-Project documentation
-=====================
-
-Reference manuals fully describing NEMO  for the three main component
-
-* |OCE| models the ocean {thermo}dynamics and solves the primitive equations (`./src/OCE <./src/OCE>`_)
-
-* |ICE| simulates sea-ice {thermo}dynamics, brine inclusions and subgrid-scale thickness 
-  variations (`./src/ICE <./src/ICE>`_)
-
-* |MBG| models the {on,off}line oceanic tracers transport and biogeochemical processes 
-  (`./src/TOP <./src/TOP>`_)
-are available from zenodo
-
-============ ==============================================   =============================================== 
- Component    Reference Manual (from zenondo, DOI to quote)   Reference manual (pdf on line version on gitlab)  
-============ ==============================================   ===============================================  
- |NEMO-OCE|   |https://zenodo.org/record/1464816|                 Final link to add 
- |NEMO-ICE|   |https://zenodo.org/record/1471689|             *Updated version will be online in  March 2022*
- |NEMO-MBG|   |https://zenodo.org/record/1471700|             *Updated version will be online in March 2022*
-============ ==============================================   ===============================================  
-
-These reference manuals are the publications that should be cited in your own
-publications. Please visit `How to cite`_? for details.
-
-New features of 4.2.0 release are described in the `Change list`_ section of the `NEMO users' guide`_
-
-
-Asking questions, and exchanging information
-============================================
-- Register once for all and use the `NEMO forums`_ on discourse to share and discuss with the NEMO community.
-
-- Register once for all and receive by mail the `NEMO newsletter`_ : recommended for all
-  users to receive the major announcements from the project (new releases, open meetings and
-  main informations). Low traffic: about ten messages a year.
-
-
-Contributing to NEMO visibility: projects and publications
-==========================================================
-Please help us justifying the NEMO development efforts by
-
--  Adding your publications using NEMO and its outputs to the `NEMO publications`_ page
-
--  Describing your project using NEMO on the `NEMO projects`_ page
-
-NEMO also has a `Special Issue`_ in the open-access journal
-Geoscientific Model Development (GMD) from the European Geosciences Union
-The main scope is to collect relevant manuscripts covering various topics and
-to provide a single portal to assess the model potential and evolution.
-
-
-
-Contributing to NEMO development
-================================
+For all information please refer to the `NEMO wiki <https://forge.nemo-ocean.eu/nemo/nemo/-/wikis/home>`_
 
-NEMO strives to be written in a way which allows the easy incorporation of developments.
-You are welcome to contribute to the development of the NEMO Shared reference.  NEMO
-development is driven by  NEMO Consortium planning and producing NEMO's sustainable
-development in order to keep a reliable evolving framework.  Development is organised and
-scheduled through a five years development strategy, Working groups and the activities of
-the development team (named NEMO System Team) in a yearly workplan. More information is
-available on the `NEMO System Team wiki`_
+How to cite
+===========
 
+To acknowledge the sustainable development efforts of the NEMO Consortium, please quote `these references <https://www.nemo-ocean.eu/bibliography/how-to-cite/>`_ in your publications and presentations using NEMO.
 
 Disclaimer
 ==========

arch/CMCC/arch-X64_JUNO.env

+
+module purge
+
+module load intel-2021.6.0/cmake/3.25.1-7wfsx
+module load oneapi-2022.1.0/compiler-rt/2022.1.0
+module load intel-2021.6.0/2021.6.0
+module load impi-2021.6.0/2021.6.0
+module load intel-2021.6.0/impi-2021.6.0/hdf5-threadsafe/1.13.3-zbgha
+module load intel-2021.6.0/impi-2021.6.0/netcdf-c-threadsafe/4.9.0-wpe4t
+module load intel-2021.6.0/impi-2021.6.0/netcdf-fortran-threadsafe/4.6.0-75oow
+module load intel-2021.6.0/impi-2021.6.0/parallel-netcdf/1.12.3-eshb5
+module load intel-2021.6.0/perl/5.36.0-jj4hw
+module load intel-2021.6.0/perl-uri/1.72-6at2i
+module load intel-2021.6.0/impi-2021.6.0/xios/2.5-36kwn
+
+# set linker path to 64-bit libraries
+export LD_LIBRARY_PATH="/lib64/":$LD_LIBRARY_PATH

arch/CMCC/arch-X64_JUNO.fcm

+# mpi ifort compiler options for ZEUS cluster + XIOS
+#
+#
+# NCDF_INC    netcdf4 include file
+# NCDF_LIB    netcdf4 library
+# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
+# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
+#
+# CPP         Pre-processor
+# FC          Fortran compiler command
+# FCFLAGS     Fortran compiler flags
+# FFLAGS      Fortran 77 compiler flags
+# LD          linker
+# FPPFLAGS    pre-processing flags
+# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
+# AR          assembler
+# ARFLAGS     assembler flags
+# MK          make (usually GNU make)
+# USER_INC    complete list of include files
+# USER_LIB    complete list of libraries to pass to the linker
+# CC          C compiler used to compile conv for AGRIF
+# CFLAGS      compiler flags used with CC
+#
+# Note that:
+#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
+#  - fcm variables are starting with a % (and not a $)
+#
+
+# Environment variables are set automatically when loading modules on JUNO cluster (see arch-X64_JUNO.env)
+
+%NCDF_INC            -I${NETCDF_FORTRAN}/include -I${NETCDF_C}/include -I${PARALLEL_NETCDF}/include
+%NCDF_LIB            -L${NETCDF_FORTRAN}/lib -lnetcdff -L${NETCDF_C}/lib -lnetcdf -L${PARALLEL_NETCDF}/lib -lpnetcdf
+%HDF5_INC            -I${HDF5}/include
+%HDF5_LIB            -L${HDF5}/lib -lhdf5_hl -lhdf5
+%XIOS_INC            -I${XIOS}/inc
+%XIOS_LIB            -L${XIOS}/lib -lxios
+
+%USER_INC            %XIOS_INC %NCDF_INC %HDF5_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB %HDF5_LIB
+
+%FC                  mpiifort
+%PROD_FCFLAGS        -r8 -O3 -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
+%DEBUG_FCFLAGS       -r8 -g -O0 -fp-model source -traceback -qmkl=cluster -march=icelake-client -mtune=icelake-client -qopt-zmm-usage=low -no-fma
+%FFLAGS              %FCFLAGS
+%CC                  mpiicc
+%CFLAGS              -O0
+
+%LD                  mpiifort
+%LDFLAGS             -lstdc++ -lgpfs
+%AR                  ar 
+%ARFLAGS             -r
+
+%CPP                 icc
+%FPPFLAGS            -E -P -traditional
+%MK                  gmake