From 53a966dd0093631eaba93d34952fc49711584415 Mon Sep 17 00:00:00 2001 From: Jago Strong-Wright Date: Tue, 14 Nov 2023 19:18:30 +0000 Subject: [PATCH 1/9] Forgot fields don't take their meta data with them on GPU --- src/Light/2band.jl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/Light/2band.jl b/src/Light/2band.jl index 40ddc3929..36426d575 100644 --- a/src/Light/2band.jl +++ b/src/Light/2band.jl @@ -1,11 +1,9 @@ @kernel function update_TwoBandPhotosyntheticallyActiveRadiation!(PAR, grid, P, surface_PAR, t, PAR_model) i, j = @index(Global, NTuple) - LX, LY, _ = location(P) - k, k′ = domain_boundary_indices(RightBoundary(), grid.Nz) - X = z_boundary_node(i, j, k′, grid, LX(), LY()) + X = z_boundary_node(i, j, k′, grid, Center(), Center()) PAR⁰ = surface_PAR(X..., t) From cdb4ad89a4dd7c0f4cd33e69e3192540046b6f73 Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 20:36:44 +0000 Subject: [PATCH 2/9] add buildkite badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index c9fc9c8dc..35f7de6ba 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,7 @@ [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac) [![Testing](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml) +[![GPU testing status](https://badge.buildkite.com/3d79ccbf2cba42de1d4e54a2f31cc6f99d377198bf63334d0d.svg)](https://buildkite.com/oceanbiome-dot-jl/gpu-tests) [![codecov](https://codecov.io/gh/OceanBioME/OceanBioME.jl/branch/main/graph/badge.svg?token=3DIW4R7N3R)](https://codecov.io/gh/OceanBioME/OceanBioME.jl) [![Documentation](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml) # *Ocean* *Bio*geochemical *M*odelling *E*nvironment From ae6cc7cec705c816b493eaf98641583c9ffd80d3 Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 22:04:55 +0000 Subject: [PATCH 3/9] Remove old workflows --- .github/workflows/documentation.yml | 33 ------------------- .github/workflows/tests.yml | 51 ----------------------------- 2 files changed, 84 deletions(-) delete mode 100644 .github/workflows/documentation.yml delete mode 100644 .github/workflows/tests.yml diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml deleted file mode 100644 index 0ada82b0b..000000000 --- a/.github/workflows/documentation.yml +++ /dev/null @@ -1,33 +0,0 @@ -name: Documentation - -on: - push: - branches: - - main - tags: '*' - pull_request: - -env: - DATADEPS_ALWAYS_ACCEPT: true - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} - -jobs: - build: - permissions: - contents: write - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: julia-actions/setup-julia@latest - with: - version: '1.9' - - name: Install dependencies - run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - - name: Build and deploy - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token - DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key - run: JULIA_DEBUG=Documenter julia --color=yes --project=docs/ docs/make.jl diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml deleted file mode 100644 index 47f1dcc6e..000000000 --- a/.github/workflows/tests.yml +++ /dev/null @@ -1,51 +0,0 @@ -name: Tests -on: - push: - branches: - - main - pull_request: - branches: - - main - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} - -env: - DATADEPS_ALWAYS_ACCEPT: true - -jobs: - test: - name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - version: - - '1.9' - os: - - ubuntu-latest - arch: - - x64 - steps: - - uses: actions/checkout@v3 - - uses: julia-actions/setup-julia@v1 - with: - version: ${{ matrix.version }} - arch: ${{ matrix.arch }} - - uses: actions/cache@v1 - env: - cache-name: cache-artifacts - with: - path: ~/.julia/artifacts - key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }} - restore-keys: | - ${{ runner.os }}-test-${{ env.cache-name }}- - ${{ runner.os }}-test- - ${{ runner.os }}- - - uses: julia-actions/julia-buildpkg@v1 - - uses: julia-actions/julia-runtest@v1 - - uses: julia-actions/julia-processcoverage@v1 - - uses: codecov/codecov-action@v2 - with: - file: lcov.info From 0385314f318dea8b37c697ca62f69b0ee093d4d3 Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 22:34:13 +0000 Subject: [PATCH 4/9] updated badges --- README.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 35f7de6ba..736fb0dfe 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,13 @@ ![](OceanBioME_headerbar.jpg?raw=true) -[![Documentation](https://img.shields.io/badge/documentation-stable%20release-blue?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/stable/) -[![Documentation](https://img.shields.io/badge/documentation-dev%20release-orange?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/dev/) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05669/status.svg)](https://doi.org/10.21105/joss.05669) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10038575.svg)](https://doi.org/10.5281/zenodo.10038575) [![MIT license](https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square)](https://mit-license.org) [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac) -[![Testing](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/tests.yml) -[![GPU testing status](https://badge.buildkite.com/3d79ccbf2cba42de1d4e54a2f31cc6f99d377198bf63334d0d.svg)](https://buildkite.com/oceanbiome-dot-jl/gpu-tests) +[![Documentation](https://img.shields.io/badge/documentation-stable%20release-blue?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/stable/) +[![Documentation](https://img.shields.io/badge/documentation-dev%20release-orange?style=flat-square)](https://oceanbiome.github.io/OceanBioME.jl/dev/) +[![Testing build status](https://badge.buildkite.com/3d79ccbf2cba42de1d4e54a2f31cc6f99d377198bf63334d0d.svg)](https://buildkite.com/oceanbiome-dot-jl/gpu-tests) [![codecov](https://codecov.io/gh/OceanBioME/OceanBioME.jl/branch/main/graph/badge.svg?token=3DIW4R7N3R)](https://codecov.io/gh/OceanBioME/OceanBioME.jl) -[![Documentation](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml/badge.svg)](https://github.com/OceanBioME/OceanBioME.jl/actions/workflows/documentation.yml) # *Ocean* *Bio*geochemical *M*odelling *E*nvironment ## Description From 76712688fb0930619014ef969f12f2795953295f Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 22:55:04 +0000 Subject: [PATCH 5/9] added pipeline --- .buildkite/pipeline.yml | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 .buildkite/pipeline.yml diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml new file mode 100644 index 000000000..8cffccea8 --- /dev/null +++ b/.buildkite/pipeline.yml @@ -0,0 +1,44 @@ +env: + JULIA_VERSION: "1.9.3" + JULIA_MINOR_VERSION: "1.9" + JULIA_PATH: /var/lib/buildkite-agent/julia + DATADEPS_ALWAYS_ACCEPT: true + +steps: + - label: ":building_construction: initialize environment" + key: "init" + commands: + - "wget -N -P $JULIA_PATH https://julialang-s3.julialang.org/bin/linux/x64/$JULIA_MINOR_VERSION/julia-$JULIA_VERSION-linux-x86_64.tar.gz" + - "tar xf $JULIA_PATH/julia-$JULIA_VERSION-linux-x86_64.tar.gz -C $JULIA_PATH" + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.instantiate(; verbose=true)'" + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.build()'" + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.precompile()'" + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.status()'" + + - label: ":speedboat: GPU unit tests" + commands: + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'" + depends_on: "init" + + - label: ":rowboat: CPU unit tests" + env: + CUDA_VISIBLE_DEVICES: "-1" + commands: + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'" + depends_on: "init" + + - label: ":docusaurus: Documentation" + env: + CUDA_VISIBLE_DEVICES: "-1" + JULIA_DEBUG: "Documenter" + TMPDIR: "/var/lib/buildkite-agent/tmp" + commands: + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'" + - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ docs/make.jl" + depends_on: "init" + + - wait: ~ + continue_on_failure: true + + - label: ":skeleton-dance: clean up environment" + command: "rm -rf $JULIA_PATH" From 09c49ae63296368e8c807a60f334bdab7ad66d1e Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 22:58:28 +0000 Subject: [PATCH 6/9] attempt to fix status labels --- .buildkite/pipeline.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 8cffccea8..892b357ce 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -14,11 +14,17 @@ steps: - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.build()'" - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.precompile()'" - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.status()'" + notify: + - github_commit_status: + context: "Initialise enviroment" - label: ":speedboat: GPU unit tests" commands: - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'" depends_on: "init" + notify: + - github_commit_status: + context: "GPU tests" - label: ":rowboat: CPU unit tests" env: @@ -26,6 +32,9 @@ steps: commands: - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia -O0 --color=yes --project -e 'using Pkg; Pkg.test()'" depends_on: "init" + notify: + - github_commit_status: + context: "CPU tests" - label: ":docusaurus: Documentation" env: @@ -36,9 +45,15 @@ steps: - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'" - "$JULIA_PATH/julia-$JULIA_VERSION/bin/julia --color=yes --project=docs/ docs/make.jl" depends_on: "init" + notify: + - github_commit_status: + context: "Documentation" - wait: ~ continue_on_failure: true - label: ":skeleton-dance: clean up environment" command: "rm -rf $JULIA_PATH" + notify: + - github_commit_status: + context: "Clean up" From 0ff2d503837395542af8e4f25816ba4d6e6c56bb Mon Sep 17 00:00:00 2001 From: Jago Strong-Wright Date: Tue, 14 Nov 2023 23:00:28 +0000 Subject: [PATCH 7/9] Update .buildkite/pipeline.yml Co-authored-by: Navid C. Constantinou --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 892b357ce..4eaeec08f 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,5 +1,5 @@ env: - JULIA_VERSION: "1.9.3" + JULIA_VERSION: "1.9.4" JULIA_MINOR_VERSION: "1.9" JULIA_PATH: /var/lib/buildkite-agent/julia DATADEPS_ALWAYS_ACCEPT: true From cceacf6c95afee84fc8dce3fbae955c51a62533e Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 23:06:15 +0000 Subject: [PATCH 8/9] trigger new commit --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 4eaeec08f..1e3a9488b 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -56,4 +56,4 @@ steps: command: "rm -rf $JULIA_PATH" notify: - github_commit_status: - context: "Clean up" + context: "Clean up" \ No newline at end of file From 8960eecef8191d0320b8c516d2950e28376ccecf Mon Sep 17 00:00:00 2001 From: Jago Stong-Wright Date: Tue, 14 Nov 2023 23:12:58 +0000 Subject: [PATCH 9/9] bump patch number for bug fix --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d6fd60aa3..a36fa33b5 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "OceanBioME" uuid = "a49af516-9db8-4be4-be45-1dad61c5a376" authors = ["Jago Strong-Wright and contributors"] -version = "0.9.0" +version = "0.9.1" [deps] Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"