pat-s
a4b274f281
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## Problem
The arm64 `build-all` pipeline fills the macmini (gaia) host disk despite an 8h prune.
Root cause is not images or job volumes: it is the persistent dep-cache volume, specifically `pkgcache/R/pkgcache/_metadata`, which grew to ~165 GB.
`{pkgcache}` mints a new content hash for the "patched" binaries repo on every PACKAGES change, so each per-package build writes a fresh ~70 MB `pkgs-<hash>.rds` (+ `patched-<hash>/`) that is never evicted (2407 snapshots observed).
When the disk hits 100% OrbStack stops and the on-host prune can no longer connect to the daemon, so it never self-heals.
## Change (Workstream A of the disk-fill fix)
- Add `trim_pkgcache_metadata()` to `local/r-minor-helpers.R`: keeps the newest `keep` (default 20) `patched-*`/`pkgs-*.rds` entries under `_metadata`, deleting only entries older than `min_age_secs` (default 600s) so it never races the up-to-4 concurrent split-jobs sharing the volume.
Preserves `pkg/` downloads and the stable CRAN/BioC/INLA repo dirs.
No-op when `R_PKG_CACHE_DIR` is empty (amd64) or `_metadata` is absent (first run).
- Call it every 25 packages inside the build loop in `local/build-all.R`.
- Add a defensive start-of-run cleanup of `_metadata/patched-*` + `pkgs-*.rds` to the two workflows that mount the persistent volume (`build-all-versions.yaml`, `build-all-versions-install-deps.yaml`).
Only these paths are touched; `process-updates.yaml`/`weekly-rebuild-missing.yaml` (no persistent volume) are unchanged.
Follow-ups (separate workstreams): on-host self-healing prune watcher + OrbStack disk cap (ansible), and Prometheus/Grafana alerting (k8s-talos).
Upstream: bincraft patched-repo hash churn is the true source fix.
New unit tests (6) for the helper; full suite 24/24 green.
Reviewed-on: #110
92 lines
3.2 KiB
YAML
92 lines
3.2 KiB
YAML
# Consolidated install-deps for build-all (both arches in one file).
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# Triggered together with build-all-versions; `target_arch` routes the matrix.
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# Variables are declared so the manual-run form exposes them (crow #1165);
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# they are merged with build-all-versions' identical declarations.
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variables:
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target_arch:
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description: 'Architecture to build.'
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options:
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- amd64
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- arm64
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default: amd64
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OS:
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description: "Base OS image name."
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options:
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- alpine
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- redhat
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- ubuntu
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default: alpine
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OS_VERSION:
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description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
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options:
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- "3.24"
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- "8"
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- "9"
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- "10"
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- "jammy"
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- "noble"
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default: "3.24"
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R_VERSION:
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description: 'Primary R version under /opt/R.'
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options:
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- 4.5.3
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- 4.4.3
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default: 4.5.3
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when:
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- event: manual
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evaluate: 'target_arch == "${ARCH}"'
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skip_clone: true
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labels:
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platform: linux/${ARCH}
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group: rpkgs-${ARCH}
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matrix:
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include:
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- ARCH: amd64
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- ARCH: arm64
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steps:
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- name: 'Install deps and bincraft'
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image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}'
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pull: true
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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REPO_RO_TOKEN:
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from_secret: REPO_RO_TOKEN
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GITHUB_PAT:
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from_secret: GITHUB_PAT
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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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from_secret: B2_S3_SECRET_KEY
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PGPASS:
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from_secret: PGPASS
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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volumes:
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- ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
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commands:
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# one-time full wipe to fix corrupted .so files from previous failed builds
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# - rm -rf /mnt/cache/R-pkgs
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# Clear churny pkgcache metadata left by a prior crashed run (the "patched"
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# repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
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# Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs.
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- rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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# Pin the same bincraft version the build steps use, so the precomputed
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# snapshot and the per-agent library stay consistent across the pipeline.
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- /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); source("local/install-bincraft.R"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
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- /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))"
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backend_options:
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docker:
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resources:
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requests:
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memory: 5Gi
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cpu: 1000m
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