ci: upgrade gfortran 13.2 -> 14.x via toolchain PPA (SIGABRT hypothesis)#138
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Hypothesis test for the SIGABRT class tracked in docker/ci-repro/ and in the --deselect list in the release CI: on the developer host (gfortran 13.3.0) the tests pass; in CI (gfortran 13.2.0, the Ubuntu 24.04 default) a subset SIGABRTs inside the Fortran finalize path. 14.x is the closest widely-available bump and, if the problem is a 13.2-specific codegen / runtime bug, should make it disappear. Pulls gfortran-14 from `ppa:ubuntu-toolchain-r/test`, points /usr/bin/gfortran via update-alternatives so every module Makefile picks it up without per-file patches. If this turns CI green with the --deselect list relaxed, the SIGABRT was a 13.2 regression. If not, the Docker repro path (#137) + debug workflow (#136) remain the way forward. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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PR #138 added gfortran-14 from ubuntu-toolchain-r PPA on the hypothesis that the CI SIGABRT class was a 13.2 codegen bug. That hypothesis was disproven by valgrind in #139: the actual root cause was a BPSD species_kid OOB write (fixed by the patch applied in the next step of this workflow). Side effect of the gfortran-14 upgrade: FP equivalence baselines (generated by Phase-0 with gfortran 13.x) now drift from CI output by ~1e-9, breaking 37 fplib + 2 wrxlib equivalence tests at the 1e-10 tolerance. Fix: drop the PPA install, use Ubuntu 24.04's stock gfortran 13.2 which is close enough to the baseline-generation toolchain (both 13.x). Drops the sudo + add-apt-repository step too. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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* fix(bpsd): apply species-kid OOB patch + restore Layer-1 CI tests ROOT CAUSE LOCATED. The CI SIGABRT class that forced 22+ tests into --deselect was traced via valgrind in PR #139 to a write- past-end in upstream BPSD's bpsd_setup_species_kdata loop: do nd=0,speciesx%ndmax-1,3 speciesx%kid(nd+1)='species%pa' speciesx%kid(nd+2)='species%pz' speciesx%kid(nd+3)='species%npa' ! kid(21) when ndmax=20 → OOB ... With nsmax=4 the loop's last iteration (nd=18) writes kid(21) but the array is only size 20. Each kid slot is CHARACTER(LEN=32) so the OOB clobbers 32 bytes of the next malloc chunk's header. glibc later detects the smashed metadata when freeing the chunk ("corrupted size vs. prev_size") and SIGABRTs the process. This bug does not always reproduce locally — heap canary placement is layout-sensitive — but reliably fires in CI's glibc 2.39 heap layout. Changes: 1. docs/external-patches/bpsd/bpsd-species-kid-oob-fix.patch (new): patches the loop bound from `ndmax-1` to `ndmax-3` so the loop only writes complete triplets within bounds. 2. .github/workflows/python-tests.yml: apply the patch right after the BPSD clone (was a TODO comment until now). 3. .github/workflows/python-tests.yml: REMOVE the entire --deselect block. Per MEMORY.md feedback_never_skip_tests and feedback_equivalence_must_pass, SKIPping Layer-1 tests does not count as verification — fix the bug instead. property_boundary / property_fanout stay ignored: those crash on a separate, deferred bug class (tr NRMAX registry gap, fp/ti NSMAX range-guard, wr MDLWRI=2 unsupported) tracked in PR #125 body. Followup: - Submit equivalent fix upstream to ats-fukuyama/bpsd; drop this in-CI patch once merged. - Address property_boundary/fanout punch list in separate PRs. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(totlib): skipTest cleanly when KNAMEQ eqdata file is missing CI run after BPSD patch surfaced a different failure mode in totlib's equivalence tests: when test_run/test_output/<case>/ does not contain the eqdata-* file referenced by the fixture's KNAMEQ string, eq_load() fails with ierr=7 and the libtotapi caller path STOPs the worker process. pytest-forked then can't extract a clean test result and the whole pytest session crashes with INTERNALERROR. Mirror the trlib/tests/test_equivalence.py pattern: check for the KNAMEQ file before invoking the fixture, and call self.skipTest with an actionable message pointing at the run_tests.sh recipe that generates it. This is the *correct* kind of skip per MEMORY.md feedback_equivalence_must_pass: we're not masking a bug, we're saying "the input data needed to verify equivalence isn't present in this CI environment". The test would still run locally where the user has executed run_tests.sh. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * ci: revert to default gfortran 13.2 (no PPA upgrade) PR #138 added gfortran-14 from ubuntu-toolchain-r PPA on the hypothesis that the CI SIGABRT class was a 13.2 codegen bug. That hypothesis was disproven by valgrind in #139: the actual root cause was a BPSD species_kid OOB write (fixed by the patch applied in the next step of this workflow). Side effect of the gfortran-14 upgrade: FP equivalence baselines (generated by Phase-0 with gfortran 13.x) now drift from CI output by ~1e-9, breaking 37 fplib + 2 wrxlib equivalence tests at the 1e-10 tolerance. Fix: drop the PPA install, use Ubuntu 24.04's stock gfortran 13.2 which is close enough to the baseline-generation toolchain (both 13.x). Drops the sudo + add-apt-repository step too. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Upgrades CI gfortran from Ubuntu 24.04's default (13.2.0) to 14.x via the
ppa:ubuntu-toolchain-r/testPPA. Point of the experiment: on a developer host with gfortran 13.3.0 the Layer-1 tests PASS; in CI with 13.2.0 several SIGABRT inside the Fortran finalize path. 14.x is the closest widely-available bump. If the crash is a 13.2-specific codegen / runtime regression, this PR makes it disappear.Relation to other work
-finit-real=snan + fcheck=alldiagnostic tierApproaches 3 (this PR), 4 (#136), 2+1 (#137) are being pursued in parallel. The one that surfaces the fastest evidence wins.
What to look for post-merge
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Test plan
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Note
Low Risk
Low risk: CI-only change that affects the compiler/toolchain used to build test artifacts; main risk is CI instability or behavior differences from pulling a PPA toolchain.
Overview
Updates the
python-testsGitHub Actions workflow to installgfortran-14fromppa:ubuntu-toolchain-r/test(instead of Ubuntu 24.04’s defaultgfortran) and sets it as the default viaupdate-alternatives.This is intended to avoid CI
SIGABRTfailures seen withgfortran 13.2.0, and the job now logs the selectedgfortranversion during setup.Reviewed by Cursor Bugbot for commit 9fd27ae. Bugbot is set up for automated code reviews on this repo. Configure here.