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Fix Numba workqueue abort in feature streams - #184

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parashardhapola merged 1 commit into
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workqueue_fix
Sep 2, 2026
Merged

Fix Numba workqueue abort in feature streams#184
parashardhapola merged 1 commit into
masterfrom
workqueue_fix

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Summary

  • prevent concurrent entry into Numba workqueue parallel regions
  • run always-pooled kernels as serial GIL-free computations
  • serialize marker adapters that retain Numba inner parallelism
  • add a forced-workqueue subprocess regression

Impact

Public signatures and persisted artifacts are unchanged. RNA feature summaries and rank marker searches complete safely with multiple Scarf workers under the workqueue backend.

Performance concern

Default matrix layouts can yield only one outer stream task. In that case, the newly serial kernels cannot use the full worker budget. This should be resolved before merge if preserving OpenMP performance is required.

Run pooled Numba kernels as serial GIL-free code and order marker callbacks that retain inner parallelism. Add forced-workqueue coverage for RNA feature statistics and marker ranking.
@parashardhapola parashardhapola linked an issue Sep 2, 2026 that may be closed by this pull request
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✅ All modified and coverable lines are covered by tests.

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@parashardhapola
parashardhapola merged commit 9d34d03 into master Sep 2, 2026
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@parashardhapola
parashardhapola deleted the workqueue_fix branch September 2, 2026 16:02
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Kernel crashes with SIGABRT in Numba ( nthreads > 1 )

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