ARM64: evolve() hangs when crossover_rate or mutation_rate set before set_allele_frequencies()

[corneliusroemer]

Description

haploid_highd.evolve() hangs indefinitely on ARM64 (Apple Silicon) when crossover_rate or mutation_rate are set before calling set_allele_frequencies(). This appears to be an ARM64-specific issue, as x86_64 CI tests pass successfully.

Environment

• Architecture: ARM64 (Apple M4 Max)
• OS: macOS 15.0.0 (Darwin 25.0.0)
• Python: 3.11
• Build: Fresh build with MACOSX_DEPLOYMENT_TARGET=14.0, C++11, GSL 2.8, Boost (Homebrew)

Root Cause

The hang occurs when:

1. Setting crossover_rate OR mutation_rate (or both)
2. Calling set_allele_frequencies()
3. Then calling evolve()

Reproduction

Script that HANGS on ARM64

import FFPopSim as h
import numpy as np

L = 10
N = 500

pop = h.haploid_highd(L)
pop.carrying_capacity = N
pop.outcrossing_rate = 1
pop.crossover_rate = 0.02 / L  # Setting this causes the hang
# OR
# pop.mutation_rate = 0.1 / N  # Setting this also causes the hang

initial_af = 0.5 * np.ones(L)
pop.set_allele_frequencies(initial_af, N)

# Hangs indefinitely on ARM64:
pop.evolve(10)

Result on ARM64: Hangs indefinitely in evolve(). No output, no error, just infinite loop or hang.

Script that WORKS on ARM64

import FFPopSim as h
import numpy as np

L = 10
N = 500

pop = h.haploid_highd(L)
pop.carrying_capacity = N
pop.outcrossing_rate = 1
# NO crossover_rate or mutation_rate set

initial_af = 0.5 * np.ones(L)
pop.set_allele_frequencies(initial_af, N)

# Works fine without mutation/crossover rates:
pop.evolve(10)
print("SUCCESS!")

Result on ARM64: Completes successfully.

Test Matrix

crossover_rate	mutation_rate	set_allele_frequencies	Result on ARM64
❌ Not set	❌ Not set	✅ Called	✅ Works
✅ Set	❌ Not set	✅ Called	❌ Hangs
❌ Not set	✅ Set	✅ Called	❌ Hangs
✅ Set	✅ Set	✅ Called	❌ Hangs
✅ Set	✅ Set	❌ Not called	✅ Works

Key Findings

1. Size-independent: The hang occurs even with tiny parameters (L=10, N=500)
2. set_allele_frequencies() is the trigger: Setting rates before set_allele_frequencies() causes the subsequent evolve() to hang
3. x86_64 appears unaffected: Ubuntu x86_64 CI passes all tests including genetic_drift.py
4. Either rate causes the issue: Both crossover_rate and mutation_rate independently trigger the hang

Affected Examples

The examples/genetic_drift.py example is affected by this issue on ARM64 as it sets both rates before calling set_allele_frequencies().

Impact

• ARM64 macOS users cannot use crossover_rate or mutation_rate with set_allele_frequencies()
• Affects macOS 15 ARM64 CI builds
• Does not appear to affect Intel/x86_64 builds
• Prevents running realistic population genetics simulations on Apple Silicon

Possible Causes

• ARM64-specific code generation issue in evolution loop with recombination/mutation
• Incorrect loop termination condition only triggered on ARM64
• Memory ordering or atomics issue with ARM64 architecture
• Interaction between set_allele_frequencies() internal state and mutation/recombination code paths

Workaround

For ARM64 users, avoid setting crossover_rate or mutation_rate when using set_allele_frequencies(). Use set_wildtype() instead if mutation/recombination are needed.