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ci: stop losing CI rounds to full disks, EBI outages and the family-joint main comparison #2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| name: Free disk space | ||
| description: >- | ||
| Removes the preinstalled toolchains no OwnGenome job uses and the | ||
| preinstalled Docker images, and prints the free space before and after. | ||
| The free space on / varies with the runner image, and the e2e legs and the | ||
| Nextflow stub runs ran out of it on 2026-11-04. Java stays in the tool | ||
| cache for setup-java; the scripts run the system python3, not the tool | ||
| cache's. | ||
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| runs: | ||
| using: composite | ||
| steps: | ||
| - name: Free disk space | ||
| shell: bash | ||
| run: | | ||
| echo "Free space before:" | ||
| df -h / /mnt 2> /dev/null || df -h / | ||
| before=$(df --output=avail -k / | tail -1) | ||
| # The deletions run side by side: the Android SDK alone is about | ||
| # 100,000 files. A path that is not there is skipped. | ||
| for d in /usr/local/lib/android /usr/share/dotnet /opt/ghc /usr/local/.ghcup \ | ||
| /usr/local/share/boost /usr/share/swift /usr/local/share/powershell \ | ||
| /usr/local/share/chromium /opt/microsoft /opt/google /opt/az \ | ||
| /opt/hostedtoolcache/CodeQL /opt/hostedtoolcache/go /opt/hostedtoolcache/PyPy \ | ||
| /opt/hostedtoolcache/Python \ | ||
| /opt/hostedtoolcache/Ruby /opt/hostedtoolcache/node; do | ||
| [ -e "$d" ] && sudo rm -rf "$d" & | ||
| done | ||
| # The images the runner image ships (none of them is ours). | ||
| if command -v docker > /dev/null 2>&1; then | ||
| docker image prune -a -f > /dev/null 2>&1 & | ||
| fi | ||
| wait | ||
| after=$(df --output=avail -k / | tail -1) | ||
| echo "Free space after:" | ||
| df -h / /mnt 2> /dev/null || df -h / | ||
| msg="Free disk: $(( (after - before) / 1048576 )) GB freed on /, $(( after / 1048576 )) GB free now, in ${SECONDS} s" | ||
| echo "$msg" | ||
| echo "$msg" >> "$GITHUB_STEP_SUMMARY" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -437,20 +437,16 @@ jobs: | |
| echo "$cpu" | ||
| echo "Runner: ${cpu}" >> "$GITHUB_STEP_SUMMARY" | ||
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| # Before anything is pulled or restored: the legs ran out of disk on | ||
| # 2026-11-04 with only part of the preinstalled software removed. | ||
| - uses: ./.github/actions/free-disk | ||
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There was a problem hiding this comment. Add the disk action to the E2E scope. A PR that changes only
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| # Images go to /var/lib/docker on /; the work area goes to whichever of | ||
| # / and /mnt has more room, so the two do not compete for one disk. The | ||
| # base outputs unpack only under the work area they were packed in, so | ||
| # a shard leg takes the base leg's choice when its artifact arrives. | ||
| - name: Pick the work area | ||
| run: | | ||
| work="${RUNNER_TEMP}/e2e-work" | ||
| if [ "$(df --output=avail -k /mnt | tail -1)" -gt "$(df --output=avail -k / | tail -1)" ]; then | ||
| work=/mnt/e2e-work | ||
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@@ -600,6 +596,8 @@ jobs: | |
| grep -qx nextflow-hardening-2-nf "$list" && echo "parity_hardening=true" >> "$GITHUB_OUTPUT" | ||
| grep -qx mocha-1 "$list" && echo "data_mocha=true" >> "$GITHUB_OUTPUT" | ||
| grep -qx archaic-ancestry-1 "$list" && echo "data_archaic=true" >> "$GITHUB_OUTPUT" | ||
| grep -qx bash-step-08-hla "$list" && echo "data_hla=true" >> "$GITHUB_OUTPUT" | ||
| grep -qx prs-scores-and-run-options-1-strand-sex "$list" && echo "data_pgs=true" >> "$GITHUB_OUTPUT" | ||
| echo "list=${list}" >> "$GITHUB_OUTPUT" | ||
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| # Before the base outputs: the base leg pulled the same images. | ||
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@@ -651,12 +649,18 @@ jobs: | |
| # runs" there) and downloads what a miss leaves out. Saved like the | ||
| # images: on main, or a run by hand with save_images, on a miss. Only | ||
| # the leg whose cases include the case restores and saves its entry. | ||
| # Two small ones the same way, keyed by e2e-run.sh --data-key: hla.dat | ||
| # of two IPD-IMGT/HLA releases and GENCODE's genes and exons | ||
| # (bash-step-08-hla, which then runs with the network blocked), and the | ||
| # four real PGS Catalog score files of prs-scores-and-run-options-1. | ||
| - name: Data cache keys | ||
| id: data-keys | ||
| run: | | ||
| . versions.env | ||
| echo "mocha=e2e-data-mocha-${MOCHA_PANEL_MANIFEST_SHA256:0:16}-chr20" | tee -a "$GITHUB_OUTPUT" | ||
| echo "archaic=e2e-data-1kg-sites-${ARCHAIC_1KG_SITES_MD5}" | tee -a "$GITHUB_OUTPUT" | ||
| echo "hla=$(scripts/ci/e2e-run.sh --data-key hla)" | tee -a "$GITHUB_OUTPUT" | ||
| echo "pgs=$(scripts/ci/e2e-run.sh --data-key pgs)" | tee -a "$GITHUB_OUTPUT" | ||
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| - name: Restore cached data, MoChA panel | ||
| id: data-mocha | ||
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@@ -674,6 +678,49 @@ jobs: | |
| path: ${{ env.E2E_DATA_CACHE }}/archaic | ||
| key: ${{ steps.data-keys.outputs.archaic }} | ||
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| - name: Restore cached data, IPD-IMGT/HLA and GENCODE | ||
| id: data-hla | ||
| if: steps.cases-list.outputs.data_hla == 'true' | ||
| uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/hla | ||
| key: ${{ steps.data-keys.outputs.hla }} | ||
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| - name: Restore cached data, PGS Catalog scores | ||
| id: data-pgs | ||
| if: steps.cases-list.outputs.data_pgs == 'true' | ||
| uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/pgs | ||
| key: ${{ steps.data-keys.outputs.pgs }} | ||
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| # The PGS Catalog's synthetic HAPNEST panel (prs-2-ancestry and | ||
| # prs-scores-and-run-options-2, 268 MB), from EBI's FTP server, keyed | ||
| # on the sha256 tests/e2e/lib.sh pins. The cases take it from | ||
| # E2E_DATA_CACHE/hapnest, check it and then run setup.sh with EBI | ||
| # unreachable; on a miss the first one downloads it and puts it there | ||
| # (setup_ancestry_panel in lib.sh). Saved like the entries above: on | ||
| # main, or a run by hand with save_images, on a miss. | ||
| - name: Data cache, HAPNEST panel | ||
| id: hapnest | ||
| env: | ||
| LIST: ${{ steps.cases-list.outputs.list }} | ||
| SAVE: ${{ (github.ref == 'refs/heads/main' || inputs.save_images) && 'true' || 'false' }} | ||
| run: | | ||
| grep -qxE 'prs-2-ancestry|prs-scores-and-run-options-2-panel-chrx' "$LIST" || exit 0 | ||
| sha=$(sed -n 's/^HAPNEST_SHA256=//p' tests/e2e/lib.sh) | ||
| [ "${#sha}" -eq 64 ] || { echo "::error::No HAPNEST_SHA256= line in tests/e2e/lib.sh"; exit 1; } | ||
| { echo "run=true"; echo "key=e2e-data-hapnest-${sha:0:16}"; } | tee -a "$GITHUB_OUTPUT" | ||
| echo "E2E_HAPNEST_KEEP=${SAVE}" >> "$GITHUB_ENV" | ||
|
There was a problem hiding this comment. Keep the panel locally on cache misses. On a pull request,
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| - name: Restore cached data, HAPNEST panel | ||
| id: data-hapnest | ||
| if: steps.hapnest.outputs.run == 'true' | ||
| uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/hapnest | ||
| key: ${{ steps.hapnest.outputs.key }} | ||
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| - name: Run the e2e cases | ||
| id: cases | ||
| env: | ||
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@@ -686,14 +733,15 @@ jobs: | |
| E2E_BASE_OUT: ${{ matrix.job == 'base' && format('{0}/base.tar.zst', runner.temp) || '' }} | ||
| E2E_BASE_IN: ${{ matrix.job != 'base' && format('{0}/e2e-base/base.tar.zst', runner.temp) || '' }} | ||
| # Keep the downloads to the end of the job only when a save step uses them. | ||
| E2E_DATA_KEEP: ${{ (github.ref == 'refs/heads/main' || inputs.save_images) && ((steps.cases-list.outputs.data_mocha == 'true' && steps.data-mocha.outputs.cache-hit != 'true') || (steps.cases-list.outputs.data_archaic == 'true' && steps.data-archaic.outputs.cache-hit != 'true') || (steps.cases-list.outputs.data_hla == 'true' && steps.data-hla.outputs.cache-hit != 'true') || (steps.cases-list.outputs.data_pgs == 'true' && steps.data-pgs.outputs.cache-hit != 'true')) && 'true' || 'false' }} | ||
| HIT_MOCHA: ${{ steps.data-mocha.outputs.cache-hit || 'false' }} | ||
| HIT_ARCHAIC: ${{ steps.data-archaic.outputs.cache-hit || 'false' }} | ||
| HIT_HLA: ${{ steps.data-hla.outputs.cache-hit || 'false' }} | ||
| HIT_PGS: ${{ steps.data-pgs.outputs.cache-hit || 'false' }} | ||
| DATA_ANY: ${{ steps.cases-list.outputs.data_mocha || steps.cases-list.outputs.data_archaic || steps.cases-list.outputs.data_hla || steps.cases-list.outputs.data_pgs || 'false' }} | ||
| run: | | ||
| if [ "$DATA_ANY" = true ]; then | ||
| echo "Data cache (${JOB}): exact key hit, MoChA panel ${HIT_MOCHA}, 1000 Genomes sites ${HIT_ARCHAIC}, IPD-IMGT/HLA and GENCODE ${HIT_HLA}, PGS scores ${HIT_PGS}" | tee -a "$GITHUB_STEP_SUMMARY" | ||
| fi | ||
| scripts/ci/e2e-run.sh | ||
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@@ -707,6 +755,8 @@ jobs: | |
| env: | ||
| HIT_MOCHA: ${{ steps.data-mocha.outputs.cache-hit }} | ||
| HIT_ARCHAIC: ${{ steps.data-archaic.outputs.cache-hit }} | ||
| HIT_HLA: ${{ steps.data-hla.outputs.cache-hit }} | ||
| HIT_PGS: ${{ steps.data-pgs.outputs.cache-hit }} | ||
| run: | | ||
| d=$E2E_DATA_CACHE | ||
| if [ "$HIT_MOCHA" != true ] && [ -s "${d}/mocha/manifest.txt" ] \ | ||
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@@ -716,6 +766,13 @@ jobs: | |
| if [ "$HIT_ARCHAIC" != true ] && [ -s "${d}/archaic/1kg_sites.vcf.gz" ]; then | ||
| echo "archaic=true" >> "$GITHUB_OUTPUT" | ||
| fi | ||
| # Whole and checked (data_ok in e2e-run.sh), or not saved. | ||
| for n in hla pgs; do | ||
| hit=HIT_${n^^} | ||
| if [ "${!hit}" != true ] && [ -d "${d}/${n}" ] && scripts/ci/e2e-run.sh --data-check "$n"; then | ||
| echo "${n}=true" >> "$GITHUB_OUTPUT" | ||
| fi | ||
| done | ||
| du -sh "${d}"/* 2> /dev/null || echo "Data cache: nothing downloaded" | ||
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| - uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
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@@ -730,6 +787,36 @@ jobs: | |
| path: ${{ env.E2E_DATA_CACHE }}/archaic | ||
| key: ${{ steps.data-keys.outputs.archaic }} | ||
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| - uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| if: always() && steps.data-save.outputs.hla == 'true' | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/hla | ||
| key: ${{ steps.data-keys.outputs.hla }} | ||
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| - uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| if: always() && steps.data-save.outputs.pgs == 'true' | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/pgs | ||
| key: ${{ steps.data-keys.outputs.pgs }} | ||
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| # The case leaves the panel there only once its sha256 matched. | ||
| - name: Data cache, HAPNEST panel, what to save | ||
| id: hapnest-save | ||
| if: >- | ||
| always() && steps.hapnest.outputs.run == 'true' && env.E2E_HAPNEST_KEEP == 'true' && | ||
| steps.data-hapnest.outputs.cache-hit != 'true' | ||
| run: | | ||
| if [ -s "${E2E_DATA_CACHE}/hapnest/GRCh38_HAPNEST_reference.tar.zst" ]; then | ||
| echo "save=true" >> "$GITHUB_OUTPUT" | ||
| fi | ||
| du -sh "${E2E_DATA_CACHE}/hapnest" 2> /dev/null || echo "Data cache: no HAPNEST panel to save" | ||
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| - uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | ||
| if: always() && steps.hapnest-save.outputs.save == 'true' | ||
| with: | ||
| path: ${{ env.E2E_DATA_CACHE }}/hapnest | ||
| key: ${{ steps.hapnest.outputs.key }} | ||
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| - name: Upload the base outputs | ||
| if: matrix.job == 'base' | ||
| uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 | ||
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@@ -739,7 +826,8 @@ jobs: | |
| ${{ runner.temp }}/base.tar.zst | ||
| ${{ runner.temp }}/base.tar.zst.from | ||
| compression-level: 0 | ||
| # Three days, so "Re-run failed jobs" the next day still finds it. | ||
| retention-days: 3 | ||
| overwrite: true | ||
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| # The cases nextflow-from-fastq-1-bash and -2-nextflow ran the bash steps | ||
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@@ -803,8 +891,9 @@ jobs: | |
| # Each group keeps its smallest images up to GROUP_BUDGET_MB of zstd | ||
| # output; the rest are pulled on every run. Four groups of 1500 MB are | ||
| # 5.9 GB, and while main replaces one group the old and the new entry | ||
| # both count: 7.3 GB. With the five data entries above (about 2.3 GB: | ||
| # MoChA 0.64, 1000 Genomes sites 1.36, HAPNEST 0.27, hla and GENCODE | ||
| # 0.03, PGS a few KB) that is 9.6 GB, under the 10 GB limit. An image pinned by digest | ||
| # is never saved: docker load gives it back without its digest, so | ||
| # e2e-run.sh would pull it again anyway. | ||
| - name: Image sizes, and save images for the next run | ||
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Check each cleanup job’s exit status.
If a background removal or Docker prune fails,
waitstill returns success when called without process IDs. The action can report successful cleanup and leave a disk-limited job to fail later. Record each cleanup job’s PID and check its exit status before reporting success. (gnu.org)