.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_${CONFIG}_ST.fcm
+
+.loop: &loop
+    matrix:
+      - CONFIG: !reference [.config, variables, CONFIG]
+
+.artifact_run: &artifact_run
+    paths:
+      - sette/$LOG_FILE
+      - 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: 1 week
+
+.artifact_rpt: &artifact_rpt
+    paths: ['sette/$LOG_FILE']
+    when: always
+    expire_in: 1 week
+
+
+stages:
+  - compile
+  - run
+  - check
+  - report
+
+
+before_script:
+# the following commands will be executed at the beginning of each job
+# they are needed to copy param.cfg to SETTE directory and to load the modules
+  - declare -A HOST_NAME=( ["aa"]="ECMWF" ["ab"]="ECMWF" ["ac"]="ECMWF" ["ad"]="ECMWF" ["lir"]="LIR"
+                           ["belenoslogin"]="MF" ["irene"]="IR" ["jean-zay"]="JZ" )
+  # modules should be loaded using .env files in NEMO arch directory
+  - SETTE_MOD=${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}_${NEMO_HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_cmp_${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:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'RESTART'
+    LOG_FILE: 'sette_run_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n "${CONFIG}" -x "${TEST_TYPE}" | tee -a ${LOG_FILE}
+  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:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'REPRO'
+    LOG_FILE: 'sette_run_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n "${CONFIG}" -x "${TEST_TYPE}" | tee -a ${LOG_FILE}
+  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:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'CORRUPT'
+    LOG_FILE: 'sette_run_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n "${CONFIG}" -x "${TEST_TYPE}" | tee -a ${LOG_FILE}
+  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:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'PHYOPTS'
+    LOG_FILE: 'sette_run_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n "${CONFIG}" -x "${TEST_TYPE}" | tee -a ${LOG_FILE}
+  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)
+      when: delayed
+      start_in: 5 seconds
+  dependencies: []   # No retrieval of previous artefacts
+  tags:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'RESTART'
+    LOG_FILE: 'sette_rpt_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "${TEST_TYPE}" -s ${CI_COMMIT_SHORT_SHA} | tee -a ${LOG_FILE}
+  artifacts:
+    <<: *artifact_rpt
+
+
+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)
+      when: delayed
+      start_in: 5 seconds
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'REPRO'
+    LOG_FILE: 'sette_rpt_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "${TEST_TYPE}" -s ${CI_COMMIT_SHORT_SHA} | tee -a ${LOG_FILE}
+  artifacts:
+    <<: *artifact_rpt
+
+
+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)
+      when: delayed
+      start_in: 5 seconds
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'CORRUPT'
+    LOG_FILE: 'sette_rpt_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "${TEST_TYPE}" -s ${CI_COMMIT_SHORT_SHA} | tee -a ${LOG_FILE}
+  artifacts:
+    <<: *artifact_rpt
+
+
+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)
+      when: delayed
+      start_in: 5 seconds
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'PHYOPTS'
+    LOG_FILE: 'sette_rpt_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "${TEST_TYPE}" -s ${CI_COMMIT_SHORT_SHA} | tee -a ${LOG_FILE}
+  artifacts:
+    <<: *artifact_rpt
+
+
+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)
+      when: delayed
+      start_in: 5 seconds
+  parallel: 
+    <<: *loop
+  tags:
+    - $NEMO_HPC
+  variables:
+    TEST_TYPE: 'COMPARE'
+    LOG_FILE: 'sette_rpt_${TEST_TYPE}_${CONFIG}_${NEMO_HPC}_${CI_COMMIT_SHORT_SHA}.log'
+    GIT_STRATEGY: none
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -n "${CONFIG}" -x "${TEST_TYPE}" -s ${CI_COMMIT_SHORT_SHA} ${NEMO_REFSHA:+-S ${NEMO_REFSHA}} | tee -a ${LOG_FILE}
+  artifacts:
+    <<: *artifact_rpt
+
+
+sette_rpt:FULL:
+  stage: report
+  dependencies: []   # do not retrieve previous artifacts
+  rules:
+    - if: $SETTE_TEST == "ALL" && $NEMO_CONFIG == "ALL"
+  tags:
+    - $NEMO_HPC
+  script:
+    - cd sette
+    - ./sette_rpt.sh ${SETTE_OPT/" -w"} -s ${CI_COMMIT_SHORT_SHA} > sette_rpt.log
+  artifacts:
+    expose_as: 'SETTE report'
+    paths: ['sette/sette_rpt.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?

CHANGES.rst

-*******
-Changes
-*******
-
-.. todo::
-
-   List the main additions of the the new release

CONTRIBUTING.rst

-************
-Contributing
-************
-
-.. todo::
-
-
-
-.. contents::
-   :local:
-
-Sending feedbacks
-=================
-
-|  Sending feedbacks is a useful way to contribute to NEMO efficency and reliability. Before doing so,
-   please check here :forge:`search <search on the developement platform>` in wiki, tickets, forum and online
-   documentation if the subject has already been discussed. You can either contribute to an existing
-   discussion, or
-| Create an entry for the discussion online, according to your needs
-
-- You have a question: create a topic in the appropriate :forge:`discussion <forum>`
-- You would like to raise and issue: open a new ticket of the right type depending of its severity
-
-  - "Unavoidable" :forge:`newticket?type=Bug       <bug>`
-
-  - "Workable"    :forge:`newticket?type=Defect <defect>`
-
-Please follow the guidelines and try to be as specific as possible in the ticket description.
-
-New development
-===============
-
-You have build a development relevant for NEMO shared reference: an addition of the source code,
-a full fork of the reference, ...
-
-You may want to share it with the community (see Hack below) or to propose it for implementation in the future
-NEMO release (see Proposal / Task below).
-
-The proposals for developments to be included in the shared NEMO reference are first examined by NEMO Developers
-Committee / Scientific Advisory Board.
-The implementation of a new development requires some additionnal work from the intial developer.
-These tasks will need to be scheduled with NEMO System Team.
-
-
-Hack
-----
-
-You only would like to inform NEMO community about your developments.
-You can promote your work on NEMO forum gathering  the contributions fromof the community by creating
-a specific topic here :forge:`discussion/forum/5 <dedicated forum>`
-
-
-Proposal / Task
----------------
-
-| Your development is quite small, and you would only like to offer it as a possible enhancement. Please suggest it
-  as an enhancement here :forge:`newticket?type=Enhancement <enhancement>` . It will be taken in account, if
-  feasible, by NEMO System Team. To ease the process, it is suggested, rather than attaching the modified
-  routines to the ticket, to highlight the proposed changes by adding to the ticket the output of ``svn diff``
-  or ``svn patch`` from your working copy.
-
-| Your development seems relevant for addition into the future release of NEMO shared reference.
-  Implementing it into NEMO shared reference following the usual quality control will require some additionnal work
-  from you and also from the NEMO System Team in charge of NEMO development. In order to evaluate the work,
-  your suggestion should be send as a proposed enhancement here :forge:`newticket?type=Enhancement <enhancement>`
-  including description of the development, its implementation, and the existing validations.
-
-  The proposed enhancement will be examined  by NEMO Developers Committee / Scientific Advisory Board.
-  Once approved by the  Committee, the assicated development task can be scheduled in NEMO development work plan,
-  and tasks distributed between you as initial developer and PI of this development action, and the NEMO System Team.
-
-  Once sucessful (meeting the usual quality control steps) this action will allow the merge of these developments with
-  other developments of the year, building the future NEMO.

INSTALL.rst

-*******************
-Build the framework
-*******************
-
-.. todo::
-
-   TBD
-
-.. contents::
-   :local:
-
-Prerequisites
-=============
-
-| The NEMO source code is written in *Fortran 95* and
-  some of its prerequisite tools and libraries are already included in the download.
-| It contains the AGRIF_ preprocessing program ``conv``; the FCM_ build system and
-  the IOIPSL_ library for parts of the output.
-
-System dependencies
--------------------
-
-In the first place the other requirements should be provided natively by your system or
-can be installed from the official repositories of your Unix-like distribution:
-
-- *Perl* interpreter
-- *Fortran* compiler (``ifort``, ``gfortran``, ``pgfortran``, ...),
-- *Message Passing Interface (MPI)* implementation (e.g. |OpenMPI|_ or |MPICH|_).
-- |NetCDF|_ library with its underlying |HDF|_
-
-**NEMO, by default, takes advantage of some MPI features introduced into the MPI-3 standard.**
-
-.. hint::
-
-   The MPI implementation is not strictly essential
-   since it is possible to compile and run NEMO on a single processor.
-   However most realistic configurations will require the parallel capabilities of NEMO and
-   these use the MPI standard.
-
-.. note::
-
-   On older systems, that do not support MPI-3 features,
-   the ``key_mpi2`` preprocessor key should be used at compile time.
-   This will limit MPI features to those defined within the MPI-2 standard
-   (but will lose some performance benefits).
-
-.. |OpenMPI| replace:: *OpenMPI*
-.. _OpenMPI: https://www.open-mpi.org
-.. |MPICH|   replace:: *MPICH*
-.. _MPICH:   https://www.mpich.org
-.. |NetCDF|  replace:: *Network Common Data Form (NetCDF)*
-.. _NetCDF:  https://www.unidata.ucar.edu
-.. |HDF|     replace:: *Hierarchical Data Form (HDF)*
-.. _HDF:     https://www.hdfgroup.org
-
-Specifics for NetCDF and HDF
-----------------------------
-
-NetCDF and HDF versions from official repositories may have not been compiled with MPI support.
-However access to all the options available with the XIOS IO-server will require
-the parallelism of these libraries.
-
-| **To satisfy these requirements, it is common to have to compile from source
-  in this order HDF (C library) then NetCDF (C and Fortran libraries)**
-| It is also necessary to compile these libraries with the same version of the MPI implementation that
-  both NEMO and XIOS (see below) have been compiled and linked with.
-
-.. hint::
-
-   | It is difficult to define the options for the compilation as
-     they differ from one architecture to another according to
-     the hardware used and the software installed.
-   | The following is provided without any warranty
-
-   .. code-block:: console
-
-      $ ./configure [--{enable-fortran,disable-shared,enable-parallel}] ...
-
-   It is recommended to build the tests ``--enable-parallel-tests`` and run them with ``make check``
-
-Particular versions of these libraries may have their own restrictions.
-State the following requirements for netCDF-4 support:
-
-.. caution::
-
-   | When building NetCDF-C library versions older than 4.4.1, use only HDF5 1.8.x versions.
-   | Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files
-     that are not readable by lots of older software.
-
-Extract and install XIOS
-========================
-
-With the sole exception of running NEMO in mono-processor mode
-(in which case output options are limited to those supported by the ``IOIPSL`` library),
-diagnostic outputs from NEMO are handled by the third party ``XIOS`` library.
-It can be used in two different modes:
-
-:*attached*:  Every NEMO process also acts as a XIOS server
-:*detached*:  Every NEMO process runs as a XIOS client.
-  Output is collected and collated by external, stand-alone XIOS server processors.
-
-Instructions on how to install XIOS can be found on its :xios:`wiki<>`.
-
-.. hint::
-
-   It is recommended to use XIOS 2.5 release.
-   This version should be more stable (in terms of future code changes) than the XIOS trunk.
-   It is also the one used by the NEMO system team when testing all developments and new releases.
-
-   This particular version has its own branch and can be checked out with:
-
-   .. code:: console
-
-      $ svn co https://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
-
-Download and install the NEMO code
-==================================
-
-Checkout the NEMO sources
--------------------------
-
-.. code:: console
-
-   $ svn co https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk
-
-Description of 1\ :sup:`st` level tree structure
-------------------------------------------------
-
-+---------------+----------------------------------------+
-| :file:`arch`  | Compilation settings                   |
-+---------------+----------------------------------------+
-| :file:`cfgs`  | :doc:`Reference configurations <cfgs>` |
-+---------------+----------------------------------------+
-| :file:`doc`   | :doc:`Documentation <doc>`             |
-+---------------+----------------------------------------+
-| :file:`ext`   | Dependencies included                  |
-|               | (``AGRIF``, ``FCM`` & ``IOIPSL``)      |
-+---------------+----------------------------------------+
-| :file:`mk`    | Compilation scripts                    |
-+---------------+----------------------------------------+
-| :file:`src`   | :doc:`Modelling routines <src>`        |
-+---------------+----------------------------------------+
-| :file:`tests` | :doc:`Test cases <tests>`              |
-|               | (unsupported)                          |
-+---------------+----------------------------------------+
-| :file:`tools` | :doc:`Utilities <tools>`               |
-|               | to {pre,post}process data              |
-+---------------+----------------------------------------+
-
-Setup your architecture configuration file
-------------------------------------------
-
-All compiler options in NEMO are controlled using files in :file:`./arch/arch-'my_arch'.fcm` where
-``my_arch`` is the name of the computing architecture
-(generally following the pattern ``HPCC-compiler`` or ``OS-compiler``).
-It is recommended to copy and rename an configuration file from an architecture similar to your owns.
-You will need to set appropriate values for all of the variables in the file.
-In particular the FCM variables:
-``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to
-the installation directories used for XIOS installation
-
-.. code-block:: sh
-
-   %NCDF_HOME    /usr/local/path/to/netcdf
-   %HDF5_HOME    /usr/local/path/to/hdf5
-   %XIOS_HOME    /home/$( whoami )/path/to/xios-2.5
-   %OASIS_HOME   /home/$( whoami )/path/to/oasis
-
-Create and compile a new configuration
-======================================
-
-The main script to {re}compile and create executable is called :file:`makenemo` located at
-the root of the working copy.
-It is used to identify the routines you need from the source code, to build the makefile and run it.
-As an example, compile a :file:`MY_GYRE` configuration from GYRE with 'my_arch':
-
-.. code-block:: sh
-
-   ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE'
-
-Then at the end of the configuration compilation,
-:file:`MY_GYRE` directory will have the following structure.
-
-+------------+----------------------------------------------------------------------------+
-| Directory  | Purpose                                                                    |
-+============+============================================================================+
-| ``BLD``    | BuiLD folder: target executable, headers, libs, preprocessed routines, ... |
-+------------+----------------------------------------------------------------------------+
-| ``EXP00``  | Run   folder: link to executable, namelists, ``*.xml`` and IOs             |
-+------------+----------------------------------------------------------------------------+
-| ``EXPREF`` | Files under version control only for :doc:`official configurations <cfgs>` |
-+------------+----------------------------------------------------------------------------+
-| ``MY_SRC`` | New routines or modified copies of NEMO sources                            |
-+------------+----------------------------------------------------------------------------+
-| ``WORK``   | Links to all raw routines from :file:`./src` considered                    |
-+------------+----------------------------------------------------------------------------+
-
-After successful execution of :file:`makenemo` command,
-the executable called `nemo` is available in the :file:`EXP00` directory
-
-More :file:`makenemo` options
------------------------------
-
-``makenemo`` has several other options that can control which source files are selected and
-the operation of the build process itself.
-
-.. literalinclude:: ../../../makenemo
-   :language: text
-   :lines: 119-143
-   :caption: Output of ``makenemo -h``
-
-These options can be useful for maintaining several code versions with only minor differences but
-they should be used sparingly.
-Note however the ``-j`` option which should be used more routinely to speed up the build process.
-For example:
-
-.. code-block:: sh
-
-        ./makenemo –m 'my_arch' –r GYRE -n 'MY_GYRE' -j 8
-
-will compile up to 8 processes simultaneously.
-
-Default behaviour
------------------
-
-At the first use,
-you need the ``-m`` option to specify the architecture configuration file
-(compiler and its options, routines and libraries to include),
-then for next compilation, it is assumed you will be using the same compiler.
-If the ``-n`` option is not specified the last compiled configuration will be used.
-
-Tools used during the process
------------------------------
-
-* :file:`functions.sh`: bash functions used by ``makenemo``, for instance to create the WORK directory
-* :file:`cfg.txt`     : text list of configurations and source directories
-* :file:`bld.cfg`     : FCM rules for compilation
-
-Examples
---------
-
-.. literalinclude:: ../../../makenemo
-   :language: text
-   :lines: 146-153
-
-Running the model
-=================
-
-Once :file:`makenemo` has run successfully,
-the ``nemo`` executable is available in :file:`./cfgs/MY_CONFIG/EXP00`.
-For the reference configurations, the :file:`EXP00` folder also contains the initial input files
-(namelists, ``*.xml`` files for the IOs, ...).
-If the configuration needs other input files, they have to be placed here.
-
-.. code-block:: sh
-
-   cd 'MY_CONFIG'/EXP00
-   mpirun -n $NPROCS ./nemo   # $NPROCS is the number of processes
-                              # mpirun is your MPI wrapper
-
-Viewing and changing list of active CPP keys
-============================================
-
-For a given configuration (here called ``MY_CONFIG``),
-the list of active CPP keys can be found in :file:`./cfgs/'MYCONFIG'/cpp_MY_CONFIG.fcm`
-
-This text file can be edited by hand or with :file:`makenemo` to change the list of active CPP keys.
-Once changed, one needs to recompile ``nemo`` in order for this change to be taken in account.
-Note that most NEMO configurations will need to specify the following CPP keys:
-``key_xios`` for IOs. MPI parallelism is activated by default. Use ``key_mpi_off`` to compile without MPI.