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Initial setup of Payu environment #1
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689a615
Initial setup: Change hard-coded paths and project for testing and ad…
jo-basevi 8b44eaf
Replace third-party ssh and rsync actions with access-nri/setup-ssh a…
jo-basevi d857c4b
Update paths in general configuration script to /g/data/vk83/
jo-basevi 21418db
Update payu test config: Uncommented settings required for tests to pass
jo-basevi ac82c8b
Update payu build script to patch python shebang on payu command to u…
jo-basevi 4d13e1f
Payu config.sh: remove ssh from the build arrays- so git signing works
jo-basevi 21de95c
Add payu-dev environment
jo-basevi b87e756
Install official latest micromamba when there's no pre-existing conda…
jo-basevi 4f1cc04
Add back pbs_tmrsh override to environment build options
jo-basevi 6db87a3
Comment out test checking for cdo - cdo is not currently installed in…
jo-basevi 5580a84
Use Github Variables for base installation paths and project specific…
jo-basevi d13f592
Environment's build_inner.sh: Add comments to the sed commands
jo-basevi 7caf352
payu environment: Remove payu-unstable alias from modulefiles
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,17 +9,34 @@ jobs: | |
| build: | ||
| name: Build environment | ||
| runs-on: ubuntu-latest | ||
| environment: Gadi | ||
| steps: | ||
| - name: Build environment | ||
| uses: appleboy/[email protected] | ||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| host: gadi.nci.org.au | ||
| username: ${{secrets.GADI_USER}} | ||
| key: ${{secrets.DEPLOY_KEY}} | ||
| command_timeout: 120m | ||
| script: | | ||
| export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts | ||
| eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh ) | ||
| eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh ) | ||
| cd $JOB_LOG_DIR | ||
| qsub -N build_${{ inputs.environment }} -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P kr06 -q copyq -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/build.sh | ||
| hosts: ${{ secrets.HOST }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Build environment | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| set -e | ||
| export SCRIPT_DIR="${{ secrets.REPO_PATH }}/scripts" | ||
| export CONDA_ENVIRONMENT="${{ inputs.environment }}" | ||
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | ||
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | ||
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | ||
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | ||
| PROJECT=${{ vars.PROJECT }} | ||
| STORAGE=${{ vars.STORAGE }} | ||
|
|
||
| source "${SCRIPT_DIR}"/install_config.sh | ||
| cd "${JOB_LOG_DIR}" | ||
|
|
||
| qsub -N build_"${CONDA_ENVIRONMENT}" -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage="${STORAGE}" \ | ||
| -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \ | ||
| -P "${PROJECT}" -q copyq -Wblock=true -Wumask=037 \ | ||
| "${SCRIPT_DIR}"/build.sh | ||
|
|
||
| EOT | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,16 +9,28 @@ jobs: | |
| deploy: | ||
| name: Deploy environment | ||
| runs-on: ubuntu-latest | ||
| environment: Gadi | ||
| steps: | ||
| - name: Deploy environment | ||
| uses: appleboy/[email protected] | ||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| host: gadi.nci.org.au | ||
| username: ${{secrets.GADI_USER}} | ||
| key: ${{secrets.DEPLOY_KEY}} | ||
| script: | | ||
| export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts | ||
| export CONDA_ENVIRONMENT=${{ inputs.environment }} | ||
| eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh ) | ||
| eval $( grep BUILD_STAGE_DIR $SCRIPT_DIR/install_config.sh ) | ||
| "${SCRIPT_DIR}"/deploy.sh | ||
| hosts: ${{ secrets.HOST }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Deploy environment | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| set -e | ||
| export SCRIPT_DIR="${{ secrets.REPO_PATH }}/scripts" | ||
| export CONDA_ENVIRONMENT="${{ inputs.environment }}" | ||
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | ||
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | ||
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | ||
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | ||
|
|
||
| source "${SCRIPT_DIR}"/install_config.sh | ||
|
|
||
| "${SCRIPT_DIR}"/deploy.sh | ||
|
|
||
| EOT | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -10,27 +10,42 @@ on: | |
| jobs: | ||
| setup: | ||
| runs-on: ubuntu-latest | ||
| environment: Gadi | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| hosts: | | ||
| ${{ secrets.HOST }} | ||
| ${{ secrets.HOST_DATA }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Sync repository to Gadi | ||
| uses: up9cloud/[email protected] | ||
| env: | ||
| HOST: gadi.nci.org.au | ||
| TARGET: ${{secrets.GADI_REPO_PATH}} | ||
| KEY: ${{secrets.DEPLOY_KEY}} | ||
| USER: ${{secrets.GADI_USER}} | ||
| run: | | ||
| rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \ | ||
| -avz --delete --exclude=/.git/ --exclude=/.github/ \ | ||
| ./ \ | ||
| ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }} | ||
|
|
||
| - name: Create Admin dirs on Gadi | ||
| uses: appleboy/[email protected] | ||
| with: | ||
| host: gadi.nci.org.au | ||
| username: ${{secrets.GADI_USER}} | ||
| key: ${{secrets.DEPLOY_KEY}} | ||
| script: | | ||
| source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh | ||
| source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh | ||
| mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | ||
| set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| set -e | ||
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | ||
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | ||
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | ||
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | ||
|
|
||
| source "${{ secrets.REPO_PATH }}/scripts/install_config.sh" | ||
| source "${{ secrets.REPO_PATH }}/scripts/functions.sh" | ||
| mkdir -p "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | ||
| set_admin_perms "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | ||
|
|
||
| EOT | ||
|
|
||
| build: | ||
| needs: setup | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,135 @@ | ||
| name: Build and test conda env | ||
|
|
||
| on: pull_request | ||
|
|
||
| jobs: | ||
| generate_matrix: | ||
| uses: ./.github/workflows/get_changed_env.yml | ||
| setup: | ||
|
|
||
| build_base_image: | ||
| runs-on: ubuntu-latest | ||
| needs: generate_matrix | ||
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | ||
| container: | ||
| image: quay.io/singularity/singularity:v3.11.4 | ||
| options: --privileged | ||
| outputs: | ||
| built-container: ${{ steps.changed-container-def.outputs.containerdef_any_changed }} | ||
| steps: | ||
| - name: Checkout repository | ||
| ### Latest at time of writing | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Check if container definition has changed | ||
| id: changed-container-def | ||
| uses: tj-actions/changed-files@v41 | ||
| uses: tj-actions/changed-files@48d8f15b2aaa3d255ca5af3eba4870f807ce6b3c # v43.0.2 | ||
| with: | ||
| files_yaml: | | ||
| containerdef: | ||
| - container/container.def | ||
|
|
||
| - name: Build container if definition has changed | ||
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | ||
| run: | | ||
| echo ${{ needs.generate_matrix.outputs.matrix }} | ||
| sudo -E singularity build container/base.sif container/container.def | ||
|
|
||
| - name: Upload base container | ||
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: base-container | ||
| path: container/base.sif | ||
|
|
||
| setup: | ||
| runs-on: ubuntu-latest | ||
| needs: [ generate_matrix, build_base_image ] | ||
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | ||
| environment: Gadi | ||
| steps: | ||
| - name: Check Gadi Github Environment configuration | ||
| run: | | ||
| vars_unset=false | ||
| if [ -z "${{ vars.ADMIN_DIR }}" ]; then | ||
| echo "::error::vars.ADMIN_DIR is unset. ADMIN_DIR is the base directory which will contain the staging and logs sub-directories" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ vars.CONDA_BASE }}" ]; then | ||
| echo "::error::vars.CONDA_BASE is unset. CONDA_BASE is the base deployment directory which will contain apps and module sub-directories" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ vars.PROJECT }}" ]; then | ||
| echo "::error::vars.PROJECT is unset. PROJECT is the project code passed to build+test qsub calls" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ vars.STORAGE }}" ]; then | ||
| echo "::error::vars.STORAGE is unset. STORAGE is the storage flags passed to build+test qsub calls" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ vars.APPS_USERS_GROUP }}" ]; then | ||
| echo "::error::vars.APPS_USERS_GROUP is unset. APPS_USERS_GROUP is used for setting file permissions" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ vars.APPS_OWNERS_GROUP }}" ]; then | ||
| echo "::error::APPS_OWNERS_GROUP is unset. APPS_OWNERS_GROUP is used for setting file permissions" | ||
| vars_unset=true | ||
| fi | ||
| if [ -z "${{ secrets.REPO_PATH }}" ]; then | ||
| echo "::error::secrets.REPO_PATH is unset. REPO_PATH is the path where this repository is synced to" | ||
| vars_unset=true | ||
| fi | ||
|
|
||
| if [ "$vars_unset" == "true" ]; then | ||
| echo "::error::Required vars in Gadi Github Environment are unset." | ||
| exit 1 | ||
| fi | ||
|
|
||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Download base container | ||
| if: needs.build_base_image.outputs.built-container == 'true' | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: base-container | ||
| path: container | ||
|
|
||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| hosts: | | ||
| ${{ secrets.HOST }} | ||
| ${{ secrets.HOST_DATA }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Create parent repository directories | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| mkdir -p ${{ secrets.REPO_PATH }} | ||
| EOT | ||
|
|
||
| - name: Sync repository to Gadi | ||
| ### Latest at time of writing | ||
| uses: up9cloud/[email protected] | ||
| env: | ||
| HOST: gadi.nci.org.au | ||
| TARGET: ${{secrets.GADI_REPO_PATH}} | ||
| KEY: ${{secrets.DEPLOY_KEY}} | ||
| USER: ${{secrets.GADI_USER}} | ||
| run: | | ||
| rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \ | ||
| -avz --delete --exclude=/.git/ --exclude=/.github/ \ | ||
| ./ \ | ||
| ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }} | ||
|
|
||
| - name: Create Admin dirs on Gadi | ||
| uses: appleboy/[email protected] | ||
| with: | ||
| host: gadi.nci.org.au | ||
| username: ${{secrets.GADI_USER}} | ||
| key: ${{secrets.DEPLOY_KEY}} | ||
| script: | | ||
| source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh | ||
| source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh | ||
| mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | ||
| set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| set -e | ||
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | ||
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | ||
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | ||
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | ||
|
|
||
| source "${{ secrets.REPO_PATH }}/scripts/install_config.sh" | ||
| source "${{ secrets.REPO_PATH }}/scripts/functions.sh" | ||
| mkdir -p "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | ||
| set_admin_perms "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | ||
| EOT | ||
|
|
||
| build: | ||
| needs: [ generate_matrix, setup ] | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -8,19 +8,26 @@ jobs: | |
|
|
||
| setup: | ||
| runs-on: ubuntu-latest | ||
| environment: Gadi | ||
| steps: | ||
| - name: Checkout repository | ||
| ### Latest at time of writing | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| hosts: ${{ secrets.HOST_DATA }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Sync repository to Gadi | ||
| ### Latest at time of writing | ||
| uses: up9cloud/[email protected] | ||
| env: | ||
| HOST: gadi.nci.org.au | ||
| TARGET: ${{secrets.GADI_REPO_PATH}} | ||
| KEY: ${{secrets.DEPLOY_KEY}} | ||
| USER: ${{secrets.GADI_USER}} | ||
|
|
||
| run: | | ||
| rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \ | ||
| -avz --delete --exclude=/.git/ --exclude=/.github/ \ | ||
| ./ \ | ||
| ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }} | ||
|
|
||
| deploy: | ||
| needs: [ generate_matrix, setup ] | ||
| uses: ./.github/workflows/deploy.yml | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -9,16 +9,34 @@ jobs: | |
| test: | ||
| name: Test environment | ||
| runs-on: ubuntu-latest | ||
| environment: Gadi | ||
| steps: | ||
| - name: Test environment | ||
| uses: appleboy/[email protected] | ||
| - name: Setup SSH | ||
| uses: access-nri/actions/.github/actions/setup-ssh@main | ||
| id: ssh | ||
| with: | ||
| host: gadi.nci.org.au | ||
| username: ${{secrets.GADI_USER}} | ||
| key: ${{secrets.DEPLOY_KEY}} | ||
| script: | | ||
| export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts | ||
| eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh ) | ||
| eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh ) | ||
| cd $JOB_LOG_DIR | ||
| qsub -N test_${{ inputs.environment }} -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage=gdata/v45+scratch/v45+gdata/hh5+scratch/hh5 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P kr06 -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/test.sh | ||
| hosts: ${{ secrets.HOST }} | ||
| private-key: ${{ secrets.SSH_KEY }} | ||
|
|
||
| - name: Test environment | ||
| run: | | ||
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | ||
| set -e | ||
| export SCRIPT_DIR="${{secrets.REPO_PATH}}/scripts" | ||
| export CONDA_ENVIRONMENT="${{ inputs.environment }}" | ||
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | ||
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | ||
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | ||
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | ||
| PROJECT=${{ vars.PROJECT }} | ||
| STORAGE=${{ vars.STORAGE }} | ||
|
|
||
| source "${SCRIPT_DIR}"/install_config.sh | ||
| cd "${JOB_LOG_DIR}" | ||
|
|
||
| qsub -N test_"${CONDA_ENVIRONMENT}" -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage="${STORAGE}" \ | ||
| -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \ | ||
| -P "${PROJECT}" -Wblock=true -Wumask=037 \ | ||
| "${SCRIPT_DIR}"/test.sh | ||
|
|
||
| EOT | ||
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One of the things that I'm not too sure about when using the relative
uses: ./.github/workflows/thingo.ymlas opposed to the version-specificuses: access-nri/model-release-condaenv/.github/workflows/thingo.yml@mainis that in the case where it ison.pull_request- the checkout that you do here means that the version of the deploy workflow that you use here would be the pull request version, rather than the@mainversion, for example.There was a problem hiding this comment.
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I think the relative paths were useful to the use the test the changes in this PR. But maybe if the
buildandtestworkflows work, the workflow changes should be separated into a different PR and merged first, with the versioned values@main?There was a problem hiding this comment.
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Yeah that will work :)