Fix smck bug#2525
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In msp_smc_k_common_ancestor_event, gsl_ran_flat occasionally draws random_mass == 0 (probability ~1/2^32 per CA event). With random_mass of zero, fenwick_find returns the first non-zero hull and remaining_mass = cum_sum - 0 lands at exactly x_hull->count. The walk loop with predicate `remaining_mass >= 0` then over-iterates by one match, runs off the head of the AVL tree, and trips the tsk_bug_assert at line 7694. Clamp remaining_mass strictly below x_hull->count so the loop terminates after exactly `count` matches. The fix is local; it does not change the RNG draw count or pattern, so seeded simulations that did not previously trip the bug produce identical trajectories. Add a regression test (test_smc_k_bug_repro) that replays the user-reported failure (50 diploid samples, seq_length 2e7, recomb 1e-8, demography change at t=30, seed 3940783591). Pre-fix the test aborts after ~74821 events; post-fix it completes in about a second.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #2525 +/- ##
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Coverage 93.83% 93.83%
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Files 20 20
Lines 12104 12106 +2
Branches 2242 2243 +1
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+ Hits 11358 11360 +2
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Partials 179 179
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The prior test_smc_k_bug_repro replayed the user-reported failing
simulation (50 diploid samples, seq_length 2e7, ~75k events) to hit
the bug after about one second. Replace it with
test_smc_k_zero_random_mass, which uses a custom GSL rng_type whose
get_double callback returns successive doubles from a fixed array.
With the script {0.5, 0.0} and a 2-sample SMCk simulation, the first
common-ancestor event has gsl_ran_flat return 0 deterministically,
making remaining_mass == x_hull->count exactly — the same trigger the
clamp at lib/msprime.c handles. Pre-clamp the test aborts at line
7694; post-clamp it completes in about a millisecond.
The scripted RNG type is defined as static helpers in test_ancestry.c
next to the test that uses it.
Add chained-event SMCk clamp test
test_smc_k_zero_random_mass triggers the clamp at lib/msprime.c on
the very first CA event of a fresh 2-sample simulation, only walking
the loop once. Add a sibling test_smc_k_zero_random_mass_chained that
runs one CA event first (coalescing one pair of 4 lineages, freeing
and reusing hull slots, rearranging AVL trees) and then drives
gsl_ran_flat to 0 on the second CA event. Pre-fix the second event
aborts at line 7694; post-fix both complete in about a millisecond.
The test covers the clamp working from a non-trivial post-event
state. We initially hoped to also drive the second event to a hull
with count > 1 via the fenwick zero-skip path, but fenwick_find
always stops at the first non-zero slot and any non-zero predecessor
blocks the route to a higher-count hull. The honest scope (clamp in
chained events, count == 1) is documented in the test comment.
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The change here seems quite straightforward, so I think we can issue a bugfix release once this is merged. |
Member
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That's quite surprising -- if the proper distribution is uniform on [0, x), why is 0 a problem? |
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Closes #2523
This was a bit more subtle than the fix in #2524 implied (which would probably have led to biases). The issue is the rng producing a value of exactly zero.