daniel1noble / BACE / 25297527702
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coverage: 42.923%. Remained the same
25297527702

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daniel1noble 
Add shell-level stdout heartbeat to keep GHA runner alive

Three of five matrix datasets in run 25294935456 (globtherm, leptraits,
pantheria) and two in run 25287097270 (globtherm, leptraits) hit the
exact same failure: "The runner has received a shutdown signal" /
"The operation was canceled" partway through bace_final_imp's
parallel final-imputation phase. Pattern is consistent regardless of
n_cores (4 -> 2 -> 1) -- so it isn't memory pressure.

Diagnosis: GHA's runner has a no-stdout-heartbeat watchdog that kills
the runner after ~10-15min of stdout silence. R's parallel/parallel
workers stream their output internally to the worker process, not
back to the parent, so during long-running MCMCglmm fits in workers
the parent looks idle from the outside. Datasets where each
worker-iteration finishes quickly (bien, all-continuous on real
phylogeny) ship before the watchdog fires; datasets with slower
per-iter fits (taxonomy-built trees, or trait mixes including
ordinal/threshold/categorical) get killed.

Fix: a shell while-loop spits "[heartbeat ...]" to stdout every 60s
in the background while Rscript runs in the foreground. The runner
sees a steady stream of output; the watchdog stays calm. trap on
EXIT cleans up the heartbeat process when Rscript finishes.

This is a workflow-level fix that benefits every matrix entry
without touching the per-dataset wrappers. Dataset-specific n_cores
overrides (globtherm/leptraits at n_cores=1) remain in place as
defense-in-depth -- minor cost given their reduced trait sets.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

1574 of 3667 relevant lines covered (42.92%)

39.49 hits per line

Jobs
ID Job ID Ran Files Coverage
1 25297527702.1 15
42.92
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Source Files on build 25297527702