OCPBUGS-105508: Re-apply MC /etc files after OS update to fix ostree 3-way merge overwrites - #6409
OCPBUGS-105508: Re-apply MC /etc files after OS update to fix ostree 3-way merge overwrites#6409isabella-janssen wants to merge 2 commits into
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WalkthroughThe daemon now records a marker when an OS update affects managed ChangesPost-OS-update
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: 🟡 Moderate · up to The change can fail to restore managed /etc files after an OS update if reapplication errors or if a force-triggered run exits first, leaving nodes with incorrect configuration and potentially degraded status. The PR is not merge-ready until these marker-handling paths are corrected or explicitly accepted by the owner. Sequence Diagram(s)sequenceDiagram
participant updateOS as updateOS
participant marker as postOSUpdateEtcFilesMarkerPath
participant firstRun as checkStateOnFirstRun
participant writeFiles as writeFiles
updateOS->>marker: Create marker when managed /etc files exist
firstRun->>marker: Detect and remove marker after reboot
firstRun->>writeFiles: Reapply managed /etc files from current Ignition
Suggested reviewers: 🚥 Pre-merge checks | ✅ 14 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (14 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Inline comments:
In `@pkg/daemon/rpm-ostree.go`:
- Around line 113-118: Use the deployment checksum rather than the base checksum
when constructing OSTree paths: update deploymentRoot in
pkg/daemon/rpm-ostree.go lines 113-118 to use d.Checksum, and update
expectedRoot in test/e2e-1of2/mcd_test.go lines 924-925 to use booted.Checksum.
In `@pkg/daemon/update.go`:
- Around line 1312-1315: Update the staged-root handling in the osUpdate path
after applyOSChanges succeeds so GetStagedDeploymentRoot errors are returned
instead of logged and ignored, causing the OS update to fail before storing the
new current config. Skip staged-root resolution only when no staged deployment
is required.
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📒 Files selected for processing (7)
pkg/daemon/config_drift_monitor_test.gopkg/daemon/file_writers.gopkg/daemon/pinned_image_set.gopkg/daemon/rpm-ostree.gopkg/daemon/update.gopkg/daemon/update_test.gotest/e2e-1of2/mcd_test.go
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Inline comments:
In `@pkg/daemon/update.go`:
- Around line 1314-1325: Collect the managed /etc files before resolving the
staged deployment root, then guard both GetStagedDeploymentRoot and writeFiles
with osUpdate && len(etcFiles) > 0. Keep file-only MachineConfig updates on the
existing successful path without attempting staged-root lookup.
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pkg/daemon/rpm-ostree.gopkg/daemon/update.gotest/e2e-1of2/mcd_test.go
🚧 Files skipped from review as they are similar to previous changes (2)
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…rge overwrites Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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Inline comments:
In `@pkg/daemon/daemon.go`:
- Around line 2198-2211: Make marker handling in the post-OS-update
reapplication flow failure-safe: distinguish os.IsNotExist from other os.Stat
errors and return unexpected errors, perform config parsing and dn.writeFiles
before consuming postOSUpdateEtcFilesMarkerPath, then remove the marker only
after successful reapplication and return any non-ENOENT removal error instead
of merely logging it.
- Around line 2198-2204: The post-OS-update marker handling must run before the
force-file early return, so a force file cannot skip re-applying MC-managed /etc
files. Reorder the logic around postOSUpdateEtcFilesMarkerPath and the
force-file check while preserving the existing marker processing and force
behavior.
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pkg/daemon/daemon.gopkg/daemon/update.gotest/e2e-1of2/mcd_test.go
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@isabella-janssen: This pull request references Jira Issue OCPBUGS-105508, which is invalid:
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@isabella-janssen: This pull request references Jira Issue OCPBUGS-105508, which is valid. The bug has been moved to the POST state. 3 validation(s) were run on this bug
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Very interesting side-effect. I wonder if this is something we can fix on the ostree side as well, since I assume that's where the 3-way merge logic lives. I guess it probably has no way of knowing "the file is pinned and owned by something else, just looks the same as the default" vs "it's actually the default". Might be worth getting some ostree SME feedback on the approach.
Also, do you plan to add any testing around this?
| return fmt.Errorf("checking post-OS-update marker: %w", err) | ||
| } else if err == nil { | ||
| klog.Infof("Post-OS-update marker found; re-applying MC /etc files to correct 3-way merge overwrites") | ||
| if err := os.Remove(postOSUpdateEtcFilesMarkerPath); err != nil { |
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In case of an error with the re-write below, we removed this marker already and gets into a bad state. I guess if something fails we're probably in a bad state anyways, but probably better to move this marker deletion after the write? Unless you're explicitly wanting the MCD not to retry this?
Also, I think the function is runs in checkStateOnFirstRun runs every restart of the MCD. I guess it's conceivable that the MCD somehow restarts after writing the marker, we delete this here, and a reboot happens. In practice though I don't think we really should ever get into that state? (Also, this means we're potentially re-writing it more than once, but I guess not really a problem?)
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In case of an error with the re-write below, we removed this marker already and gets into a bad state. I guess if something fails we're probably in a bad state anyways, but probably better to move this marker deletion after the write? Unless you're explicitly wanting the MCD not to retry this?
Code rabbit pointed out this concern also; here is my response to the 🐰 #6409 (comment). In my mind, if we fail this then the customer gets a degrade from the content mismatch and can resolve it through known work arounds. I'm happy to retry if we want, but I kind of figured if it fails, we might want to give humans the notice and option to investigate and fix themselves.
Also, I think the function is runs in checkStateOnFirstRun runs every restart of the MCD. I guess it's conceivable that the MCD somehow restarts after writing the marker, we delete this here, and a reboot happens. In practice though I don't think we really should ever get into that state? (Also, this means we're potentially re-writing it more than once, but I guess not really a problem?)
I'm not sure about if or when we might get into this state, as I never considered it. However, if we re-write more than once, I don't see that as being a big issue since we would be writing the desired content.
In general, I could see this not being the best solution as we discussed in Slack. However, it seems like the cleanest and safest approach for now. Long term, I think an rpm-ostree fix is the best approach, but since the issue is surfacing through supported MCO operations, I think the customer may not love that answer. 🙂
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Thanks for the review, @yuqi-zhang! Here are some responses to your questions.
I wondered this as well, but I'm not sure what the appetite would be for this from that team and what the timing for a fix would look like. Since this is a customer case, I wanted to propose at least some working fix MCO-side to see if some progress can be made in the meantime.
In my opinion, the only good way to test this is through an upgrade job, so I was planning to discuss adding such a job with QE when this PR was ready for that review. (I don't want to waste anyone's time writing a complicated test if we end up abandoning this approach.) |
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Closes: OCPBUGS-105508
- What I did
During version upgrades, the ostree merge can overwrite user defined overrides of managed files when their content matches the old OS base. After reboot, when the MCD validates on-disk state against the rendered MachineConfig, it marks the node
Degradedif the content does not match what is defined in the MC.With this change, when an OS update includes MC-managed /etc files, write a persistent marker at /etc/machine-config-daemon/post-os-update-etc-files before rebooting. On the next first-run,
checkStateOnFirstRun()detects the marker, re-applies all MC /etc files to the live filesystem before validation, then removes the marker. This corrects any overwrites the 3-way merge performed at boot time.- How to verify it
/etc/ssh/sshd_configand wait for the worker MCP to return to updated.Note: I used Clusterbot to create the release payload:
build 4.22.0-0.nightly-2026-08-13-103840,openshift/machine-config-operator#6410/etc/ssh/sshd_configmatch what is expected.- Description for the changelog
OCPBUGS-105508: Re-apply MC /etc files after OS update to fix ostree 3-way merge overwrites
Summary by CodeRabbit
/etcconfiguration files are reapplied after an operating system update when needed./etcfiles are present.