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Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
File size: 4,556 Bytes
ee5b44c | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 | from __future__ import annotations
import pytest
from simulator.slurm import (
SlurmEnvironmentError,
allocated_cpu_count,
distributed_context,
slurm_array_context,
slurm_cpu_count,
)
from simulator.utils import resolve_workers
def test_slurm_cpu_allocation_and_explicit_override() -> None:
env = {"SLURM_CPUS_PER_TASK": "16"}
assert slurm_cpu_count(env) == 16
assert allocated_cpu_count(env) == 16
assert allocated_cpu_count(env, override=7) == 7
assert resolve_workers(-1, environ=env) == 15
assert resolve_workers(-1, environ=env, cpu_count=5) == 4
assert resolve_workers(3, environ=env) == 3
@pytest.mark.parametrize("value", ["0", "-1", "many", "1.5"])
def test_invalid_slurm_cpu_allocation_is_rejected(value: str) -> None:
with pytest.raises(SlurmEnvironmentError, match="SLURM_CPUS_PER_TASK"):
slurm_cpu_count({"SLURM_CPUS_PER_TASK": value})
@pytest.mark.parametrize("value", [0, -1, True, 1.5])
def test_invalid_cpu_override_is_rejected(value) -> None:
with pytest.raises(ValueError, match="CPU-count override"):
allocated_cpu_count({}, override=value)
def test_regular_slurm_array_context() -> None:
context = slurm_array_context(
{
"SLURM_ARRAY_TASK_ID": "8",
"SLURM_ARRAY_TASK_MIN": "2",
"SLURM_ARRAY_TASK_MAX": "20",
"SLURM_ARRAY_TASK_STEP": "2",
"SLURM_ARRAY_TASK_COUNT": "10",
}
)
assert context is not None
assert context.task_id == 8
assert context.rank == 3
assert context.count == 10
assert context.minimum == 2
assert context.maximum == 20
assert context.step == 2
def test_incomplete_or_sparse_slurm_array_is_rejected() -> None:
with pytest.raises(SlurmEnvironmentError, match="require"):
slurm_array_context({"SLURM_ARRAY_TASK_ID": "1"})
with pytest.raises(SlurmEnvironmentError, match="regular range"):
slurm_array_context(
{
"SLURM_ARRAY_TASK_ID": "7",
"SLURM_ARRAY_TASK_MIN": "1",
"SLURM_ARRAY_TASK_MAX": "7",
"SLURM_ARRAY_TASK_STEP": "1",
"SLURM_ARRAY_TASK_COUNT": "3",
}
)
def test_distributed_context_combines_array_and_process_ranks() -> None:
context = distributed_context(
{
"SLURM_PROCID": "2",
"SLURM_NTASKS": "4",
"SLURM_ARRAY_TASK_ID": "3",
"SLURM_ARRAY_TASK_MIN": "0",
"SLURM_ARRAY_TASK_MAX": "7",
"SLURM_ARRAY_TASK_STEP": "1",
"SLURM_ARRAY_TASK_COUNT": "8",
}
)
assert context.rank == 14
assert context.world_size == 32
assert context.task_rank == 2
assert context.task_count == 4
assert context.array is not None
assert context.array.rank == 3
assert context.source == "slurm_array"
assert context.distributed
def test_array_only_context_and_single_process_default() -> None:
array_context = distributed_context(
{
"SLURM_ARRAY_TASK_ID": "4",
"SLURM_ARRAY_TASK_MIN": "0",
"SLURM_ARRAY_TASK_MAX": "9",
"SLURM_ARRAY_TASK_COUNT": "10",
}
)
assert (array_context.rank, array_context.world_size) == (4, 10)
single = distributed_context({})
assert (single.rank, single.world_size) == (0, 1)
assert not single.distributed
assert single.source == "single"
def test_explicit_distributed_override_takes_precedence() -> None:
context = distributed_context(
{"SLURM_PROCID": "invalid", "SLURM_NTASKS": "invalid"},
rank=3,
world_size=5,
)
assert (context.rank, context.world_size) == (3, 5)
assert context.source == "explicit"
@pytest.mark.parametrize(
("env", "message"),
[
({"SLURM_PROCID": "1"}, "without SLURM_NTASKS"),
({"SLURM_NTASKS": "2"}, "SLURM_PROCID is unavailable"),
({"SLURM_PROCID": "2", "SLURM_NTASKS": "2"}, "must be smaller"),
],
)
def test_inconsistent_slurm_process_topology_is_rejected(
env: dict[str, str],
message: str,
) -> None:
with pytest.raises(SlurmEnvironmentError, match=message):
distributed_context(env)
@pytest.mark.parametrize(
("rank", "world_size"),
[(None, 2), (1, None), (-1, 2), (2, 2), (0, 0), (True, 2)],
)
def test_invalid_explicit_distributed_override_is_rejected(
rank,
world_size,
) -> None:
with pytest.raises(ValueError):
distributed_context({}, rank=rank, world_size=world_size)
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