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Use spawn start method for multiprocessing inside the test to avoid deadlock/timeout #5213

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Merged
orbeckst merged 5 commits into develop from timeout_not_again
Mar 13, 2026
Merged

Use spawn start method for multiprocessing inside the test to avoid deadlock/timeout #5213

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2 changes: 1 addition & 1 deletion azure-pipelines.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ jobs:
displayName: 'Check installed packages'
- powershell: |
cd testsuite
pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis
pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis --durations=50
displayName: 'Run MDAnalysis Test Suite'
- script: |
curl -s https://codecov.io/bash | bash
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29 changes: 20 additions & 9 deletions testsuite/MDAnalysisTests/parallelism/test_multiprocessing.p y
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Expand Up @@ -129,12 +129,19 @@ def cog(u, ag, frame_id):

def test_multiprocess_COG(u):
ag = u.atoms[2:5]

ref = np.array([cog(u, ag, i) for i in range(3)])

p = multiprocessing.Pool(2)
res = np.array([p.apply(cog, args=(u, ag, i)) for i in range(3)])
p.close()
# Explicitly use `spawn` for multiprocessing tests
# As `fork` can lead to deadlock in pytest because each xdist worker creates a multiprocessing.Pool.
# related issue: #5191; PR #5213
ctx = multiprocessing.get_context("spawn")
# The commented code can lead to timeout that is not marked as a failure due.
# p = multiprocessing.Pool(2)
# res = np.array([p.apply(cog, args=(u, ag, i)) for i in range(3)])
# p.close()
with ctx.Pool(2) as p:
res = np.array(p.starmap(cog, [(u, ag, i) for i in range(3)]))

assert_equal(ref, res)


Expand All @@ -147,10 +154,11 @@ def test_universe_unpickle_in_new_process():
u = mda.Universe(GRO, XTC)
ref = [getnames(u, i) for i in range(3)]

p = multiprocessing.Pool(2)
res = [p.apply(getnames, args=(u, i)) for i in range(3)]
p.close()

# related issue: #5191; PR #5213
ctx = multiprocessing.get_context("spawn")
with ctx.Pool(2) as p:
res = [p.apply_async(getnames, args=(u, i)) for i in range(3)]
res = [r.get() for r in res]
assert_equal(ref, res)


Expand All @@ -162,7 +170,10 @@ def test_creating_multiple_universe_without_offset(temp_xtc, ncopies=3):
# a problem (see PR #3375 and issues #3230, #1988)

args = (GRO, str(temp_xtc))
with multiprocessing.Pool(2) as p:

# related issue: #5191; PR #5213
ctx = multiprocessing.get_context("spawn")
with ctx.Pool(2) as p:
universes = [p.apply_async(mda.Universe, args) for i in range(ncopies)]
universes = [universe.get() for universe in universes]

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