From 11b97f34a3541961f95b1ca1140f200dc0103df4 Mon Sep 17 00:00:00 2001 From: "minghang.li" Date: Wed, 10 Apr 2024 15:40:06 +1000 Subject: [PATCH] Update 01deg jra55 ryf bgc (#63) * Changed to access-om2 to 2024.03.0 * Update config.yaml * Adding .github from release-1deg_jra55_ryf * Added CC BY 4.0 License file * remove postscript and related comments in config.yaml * change ryf to repeat-year & remove blank lines in metadata.yaml * update manifests --------- Co-authored-by: minghangli --- .github/workflows/call-pr-1-ci.yml | 25 ++ .github/workflows/call-pr-3-bump-tag.yml | 19 ++ .github/workflows/pr-2-confirm.yml | 160 +++++++++ .github/workflows/validate-json.yml | 13 + LICENSE | 396 +++++++++++++++++++++++ config.yaml | 23 +- manifests/exe.yaml | 6 +- metadata.yaml | 26 +- 8 files changed, 646 insertions(+), 22 deletions(-) create mode 100644 .github/workflows/call-pr-1-ci.yml create mode 100644 .github/workflows/call-pr-3-bump-tag.yml create mode 100644 .github/workflows/pr-2-confirm.yml create mode 100644 .github/workflows/validate-json.yml create mode 100644 LICENSE diff --git a/.github/workflows/call-pr-1-ci.yml b/.github/workflows/call-pr-1-ci.yml new file mode 100644 index 00000000..57dbf1ba --- /dev/null +++ b/.github/workflows/call-pr-1-ci.yml @@ -0,0 +1,25 @@ +# This workflow is used to convert the `.version` in the `metadata.yaml` file into a valid `git tag` on push to `main`. +# We use the `.version` field in that file to denote the version of the config once a PR is merged. +name: pr-1-ci.yml +on: + pull_request: + branches: + - 'release-*' + - 'dev-*' + paths-ignore: + # These are ignored because they don't have anything to do with the model itself + - .github/** + - tools/** + - doc/** + - .* + - README.md +jobs: + call: + # We simply call the workflow on main so we don't have to propagate CI changes to + # multiple config branches all the time. + uses: access-nri/access-om2-configs/.github/workflows/pr-1-ci.yml@main + secrets: inherit + permissions: + contents: write + pull-requests: write + checks: write diff --git a/.github/workflows/call-pr-3-bump-tag.yml b/.github/workflows/call-pr-3-bump-tag.yml new file mode 100644 index 00000000..a9e2e37a --- /dev/null +++ b/.github/workflows/call-pr-3-bump-tag.yml @@ -0,0 +1,19 @@ +# This workflow is used to convert the `.version` in the `metadata.yaml` file +# into a valid `git tag` on push to `main`. +# We use the `.version` field in that file to denote the version of the config +# once a PR is merged. +name: Call pr-3-bump-tag.yml +on: + push: + branches: + - 'release-*' + paths: + - 'metadata.yaml' +jobs: + call: + # We simply call the workflow on main so we don't have to propagate CI changes to + # multiple config branches all the time. + uses: access-nri/access-om2-configs/.github/workflows/pr-3-bump-tag.yml@main + secrets: inherit + permissions: + contents: write diff --git a/.github/workflows/pr-2-confirm.yml b/.github/workflows/pr-2-confirm.yml new file mode 100644 index 00000000..adbcb472 --- /dev/null +++ b/.github/workflows/pr-2-confirm.yml @@ -0,0 +1,160 @@ +# This workflow is used to do a major/minor version bump to the `metadata.yaml` file, +# through a comment on the PR. It also commits and pushes the checksum file, +# as this is the last stage before merging. +# This is not done automatically because users may want to modify their config +# based on the result of the reproducibility check. +name: Confirm +on: + issue_comment: + types: + - created + - edited +env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} +jobs: + bump-version: + name: Bump metadata.yaml + # Bump the `metadata.yaml` file if the comment is made on a PR and starts with '!bump' + if: github.event.issue.pull_request && startsWith(github.event.comment.body, '!bump') + runs-on: ubuntu-latest + outputs: + # metadata.yaml version before being bumped + before: ${{ steps.bump.outputs.before }} + # metadata.yaml version after being bumped + after: ${{ steps.bump.outputs.after }} + # The type of bump - 'major' or 'minor' + type: ${{ steps.type.outputs.bump }} + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + token: ${{ secrets.GH_COMMIT_CHECK_TOKEN }} + + - name: Checkout Associated PR ${{ github.event.issue.number }} + # Since the trigger for this workflow was on.issue_comment, we need + # to do a bit more wrangling to checkout the pull request + id: pr + run: gh pr checkout ${{ github.event.issue.number }} + + - name: Get Type of Bump + id: type + run: | + if [[ "${{ contains(github.event.comment.body, 'minor') }}" == "true" ]]; then + echo "bump=minor" >> $GITHUB_OUTPUT + elif [[ ${{ contains(github.event.comment.body, 'major') }} == "true" ]]; then + echo "bump=major" >> $GITHUB_OUTPUT + else + echo "::error::Comment was not of the form: '!bump [major|minor]'" + exit 1 + fi + + - name: Bump + # Regarding the regex in the script: `([0-9]+)\.([0-9]+)` is broken down into: + # `([0-9]+)`: Major version (eg. `12`) + # `\.`: Version separator (eg. `.`) + # `([0-9]+)`: Minor version (eg. `1`) + # which would give `12.1` + id: bump + run: | + version=$(yq '.version' metadata.yaml) + regex="([0-9]+)\.([0-9]+)" + if [[ $version =~ $regex ]]; then + major_version="${BASH_REMATCH[1]}" + minor_version="${BASH_REMATCH[2]}" + else + echo "::error::Invalid version format in metadata.yaml file!" + exit 1 + fi + + if [[ "${{ steps.type.outputs.bump }}" == "minor" ]]; then + minor_version=$((minor_version + 1)) + elif [[ "${{ steps.type.outputs.bump }}" == "major" ]]; then + major_version=$((major_version + 1)) + minor_version=0 + fi + new_version="${major_version}.${minor_version}" + echo "before=$version" >> $GITHUB_OUTPUT + echo "after=$new_version" >> $GITHUB_OUTPUT + + commit: + name: Commit metadata.yaml and Checksum + needs: + - bump-version + runs-on: ubuntu-latest + permissions: + contents: write + pull-requests: write + env: + GH_TOKEN: ${{ secrets.GH_COMMIT_CHECK_TOKEN }} + ARTIFACT_LOCAL_LOCATION: /opt/artifact + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + token: ${{ secrets.GH_COMMIT_CHECK_TOKEN }} + + - name: Checkout Associated PR ${{ github.event.issue.number }} + # Since the trigger for this workflow was on.issue_comment, we need + # to do a bit more wrangling to checkout the pull request and get the branch name + id: pr + run: | + gh pr checkout ${{ github.event.issue.number }} + echo "branch=$(git rev-parse --abbrev-ref HEAD)" >> $GITHUB_OUTPUT + + - name: Download Newly Created Checksum + # Given the PR branch, we need to find the latest associated workflow run + # on this branch we can then download the associated artifact + run: | + associated_run=$(gh run list \ + --json='databaseId,headBranch,updatedAt,status' \ + --jq='[.[] | select(.headBranch == "${{ steps.pr.outputs.branch }}" and .status == "completed")] | sort_by(.updatedAt) | last | .databaseId') + gh run download $associated_run -D ${{ env.ARTIFACT_LOCAL_LOCATION }} + + - name: Update metadata.yaml and Checksum files + run: | + yq -i '.version = "${{ needs.bump-version.outputs.after }}"' metadata.yaml + cp --recursive --verbose ${{ env.ARTIFACT_LOCAL_LOCATION }}/*/* testing + + - name: Commit and Push Updates + run: | + git config user.name github-actions + git config user.email github-actions@github.com + + if [[ "${{ needs.bump-version.outputs.type }}" == "minor" ]]; then + git commit -am "Bumped version to ${{ needs.bump-version.outputs.after }} as part of ${{ env.RUN_URL }}" + elif [[ "${{ needs.bump-version.outputs.type }}" == "major" ]]; then + git commit -am "Updated checksums and bumped version to ${{ needs.bump-version.outputs.after }} as part of ${{ env.RUN_URL }}" + fi + git push + + - name: Comment Success + env: + BODY: | + :white_check_mark: Version bumped from `${{ needs.bump-version.outputs.before }}` to `${{ needs.bump-version.outputs.after }}` :white_check_mark: + run: gh pr comment --body '${{ env.BODY }}' + + failure-notifier: + name: Failure Notifier + if: failure() + needs: + - commit + runs-on: ubuntu-latest + permissions: + pull-requests: write + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_REPO: ${{ github.repository }} + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Checkout Associated PR ${{ github.event.issue.number }} + run: gh pr checkout ${{ github.event.issue.number }} + + - name: Comment Failure + env: + BODY: | + :x: Failed to bump VERSION or commit changes, see ${{ env.RUN_URL }} :x: + run: gh pr comment --body '${{ env.BODY }}' diff --git a/.github/workflows/validate-json.yml b/.github/workflows/validate-json.yml new file mode 100644 index 00000000..a23beac2 --- /dev/null +++ b/.github/workflows/validate-json.yml @@ -0,0 +1,13 @@ +name: Validate JSON files +on: + pull_request: + branches: + - main + paths: + - '**.json' +jobs: + validate: + name: Validate + uses: access-nri/actions/.github/workflows/validate-json.yml@main + with: + src: "config" diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..da6ab6cc --- /dev/null +++ b/LICENSE @@ -0,0 +1,396 @@ +Attribution 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. + diff --git a/config.yaml b/config.yaml index b65a97a1..3f8b0b18 100644 --- a/config.yaml +++ b/config.yaml @@ -12,6 +12,12 @@ queue: normal walltime: 5:00:00 jobname: 01deg_jra55_ryf_bgc +# Sync options for automatically copying data from ephemeral scratch space to +# longer term storage +sync: + enable: False # set path below and change to true + path: null # Set to location on /g/data or a remote server and path (rsync syntax) + # Model configuration name: common model: access-om2 @@ -22,7 +28,7 @@ input: submodels: - name: atmosphere model: yatm - exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ieiy3e7hidn4dzaqly3ly2yu45mecgq4/bin/yatm.exe + exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe input: - /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.01deg/2020.05.30/rmp_jrar_to_cict_CONSERV.nc - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data @@ -61,23 +67,23 @@ submodels: - /g/data/vk83/experiments/inputs/access-om2/ice/grids/global.01deg/2020.05.30/kmt.nc - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.01deg/2022.02.24/o2i.nc - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions_biogeochemistry/global.01deg/2022.02.24/i2o.nc - - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/monthly_sstsss.nc - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/u_star.nc + - /g/data/vk83/experiments/inputs/access-om2/ice/initial_conditions/global.01deg/2020.05.30/monthly_sstsss.nc ncpus: 722 # Collation collate: restart: true + mpi: true walltime: 1:00:00 mem: 16GB ncpus: 4 queue: normal - exe: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/mom5-git.2023.11.09=2023.11.09-ewcdbrfukblyjxpkhd3mfkj4yxfolal4/bin/mppnccombine.spack - + exe: /g/data/vk83/apps/mppnccombine-fast/0.2/bin/mppnccombine-fast # Misc runlog: true stacksize: unlimited -restart_freq: 1 # use tidy_restarts.py instead +restart_freq: '1YS' mpirun: --mca io ompio --mca io_ompio_num_aggregators 1 qsub_flags: -W umask=027 env: @@ -89,6 +95,7 @@ platform: userscripts: error: tools/resub.sh run: rm -f resubmit.count - -# DANGER! Do not uncomment this without checking the script is syncing to the correct location! -# postscript: sync_data.sh + sync: /g/data/vk83/apps/om2-scripts/concatenate_ice/concat_ice_daily.sh +manifest: + reproduce: + exe: true diff --git a/manifests/exe.yaml b/manifests/exe.yaml index c04ec40e..947728b5 100644 --- a/manifests/exe.yaml +++ b/manifests/exe.yaml @@ -2,10 +2,10 @@ format: yamanifest version: 1.0 --- work/atmosphere/yatm.exe: - fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ieiy3e7hidn4dzaqly3ly2yu45mecgq4/bin/yatm.exe + fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/libaccessom2-git.2023.10.26=2023.10.26-ltfg7jcn6t4cefotvj3kjnyu5nru26xo/bin/yatm.exe hashes: - binhash: 61890159678b68a1699cb989d2c2864e - md5: 7bbd1014eb48b16406877d1b93ae1a47 + binhash: 4e8b4ef76e971c4af3b26cfac632e160 + md5: 5baa1d417fe6708fc30cbeaa57d82f96 work/ice/cice_auscom_3600x2700_90x90_722p.exe: fullpath: /g/data/vk83/apps/spack/0.20/release/linux-rocky8-x86_64/intel-19.0.5.281/cice5-git.2023.10.19=2023.10.19-v3zncpqjj2gyseudbwiudolcjq3k3leo/bin/cice_auscom_3600x2700_90x90_722p.exe hashes: diff --git a/metadata.yaml b/metadata.yaml index 5dc404cc..5a9104c7 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -14,23 +14,27 @@ description: |- with all solid runoff converted to liquid runoff with no heat transfer. Spin up starts from a nominal year of 1 Jan 1900. notes: |- - Source code: https://github.com/COSIMA/access-om2 - License: Attribution-NonCommercial-NoDerivatives 4.0 International (http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode) - Conditions of use: - We request that users of this or other ACCESS-OM2 model code or output data: + COSIMA request that users of this or other ACCESS-OM2 model code or output data: (a) consider citing Kiss et al. (2020) [http://doi.org/10.5194/gmd-13-401-2020] (b) include an acknowledgement such as the following: "The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; http://www.cosima.org.au) for making the ACCESS-OM2 suite of models available at https://github.com/COSIMA/access-om2. Model runs were undertaken with the assistance of resources from the National Computational Infrastructure (NCI), which is supported by the Australian Government." - (c) let us know of any publications which use these models or data so we can add them to our list: + (c) let COSIMA know of any publications which use these models or data so they can add them to their list: https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ keywords: - - tenth - - cosima + - global + - JRA55 + - repeat-year - access-om2-01 - - jra55-do-v1.4.0 - - ryf - - bgc - \ No newline at end of file +version: null +realm: + - ocean + - seaIce + - ocnBgchem +nominal_resolution: 10 km +reference: https://doi.org/10.5194/gmd-13-401-2020 +license: CC-BY-4.0 +url: https://github.com/ACCESS-NRI/access-om2-configs/tree/release-01deg_jra55_ryf_bgc +model: access-om2-bgc