Merge pull request #998 from benjeffery/batch-coverage

Improve batch-match coverage

Author: benjeffery

docs/large_scale.md

@@ -195,8 +195,7 @@ of ancestors. There are three API methods that work together to enable distribut
 3. {meth}`match_samples_batch_finalise`
 
 {meth}`match_samples_batch_init` should be called to set up the batch matching and to determine the
-groupings of samples. Similar to {meth}`match_ancestors_batch_init` is has a `min_work_per_job` and
-`max_num_partitions` arguments to control the level of parallelism. The method writes a file
+groupings of samples. Similar to {meth}`match_ancestors_batch_init` it has a `min_work_per_job`  argument to control the level of parallelism. The method writes a file
 `metadata.json` to the directory `work_dir` that contains a JSON encoded dictionary with
 configuration for later steps. This is also returned by the call. The `num_partitions` key in
 this dictionary is the number of times {meth}`match_samples_batch_partition` will need

tests/test_inference.py

@@ -35,8 +35,10 @@
 import msprime
 import numpy as np
 import pytest
+import sgkit
 import tskit
 import tsutil
+import xarray as xr
 from tskit import MetadataSchema
 
 import _tsinfer
@@ -1401,16 +1403,16 @@ def test_equivalance_many_at_once(self, tmp_path, tmpdir):
             tmpdir / "ancestors.zarr",
             1000,
         )
-        tsinfer.match_ancestors_batch_groups(
-            tmpdir / "work", 0, len(metadata["ancestor_grouping"]) // 2, 2
-        )
+        num_groupings = len(metadata["ancestor_grouping"])
+        tsinfer.match_ancestors_batch_groups(tmpdir / "work", 0, num_groupings // 2, 2)
         tsinfer.match_ancestors_batch_groups(
             tmpdir / "work",
-            len(metadata["ancestor_grouping"]) // 2,
-            len(metadata["ancestor_grouping"]),
+            num_groupings // 2,
+            num_groupings,
             2,
         )
-        # TODO Check which ones written to disk
+        assert (tmpdir / "work" / f"ancestors_{(num_groupings//2)-1}.trees").exists()
+        assert (tmpdir / "work" / f"ancestors_{num_groupings-1}.trees").exists()
         ts = tsinfer.match_ancestors_batch_finalise(tmpdir / "work")
         ts2 = tsinfer.match_ancestors(samples, ancestors)
         ts.tables.assert_equals(ts2.tables, ignore_provenance=True)
@@ -1438,6 +1440,11 @@ def test_equivalance_with_partitions(self, tmp_path, tmpdir):
                     tsinfer.match_ancestors_batch_group_partition(
                         tmpdir / "work", group_index, p_index
                     )
+                with pytest.raises(ValueError, match="out of range"):
+                    tsinfer.match_ancestors_batch_group_partition(
+                        tmpdir / "work", group_index, p_index + 1000
+                    )
+
                 ts = tsinfer.match_ancestors_batch_group_finalise(
                     tmpdir / "work", group_index
                 )
@@ -1523,6 +1530,34 @@ def test_errors(self, tmp_path, tmpdir):
         with pytest.raises(ValueError, match="sequence length is different"):
             tsinfer.match_ancestors_batch_groups(tmpdir / "work", 2, 3)
 
+    def test_low_min_work_per_job(self, tmp_path, tmpdir):
+        ts, zarr_path = tsutil.make_ts_and_zarr(tmp_path)
+        samples = tsinfer.VariantData(zarr_path, "variant_ancestral_allele")
+        _ = tsinfer.generate_ancestors(samples, path=str(tmpdir / "ancestors.zarr"))
+        metadata = tsinfer.match_ancestors_batch_init(
+            tmpdir / "work",
+            zarr_path,
+            "variant_ancestral_allele",
+            tmpdir / "ancestors.zarr",
+            min_work_per_job=1,
+            max_num_partitions=2,
+        )
+        for group in metadata["ancestor_grouping"]:
+            assert group["partitions"] is None or len(group["partitions"]) <= 2
+
+        metadata = tsinfer.match_ancestors_batch_init(
+            tmpdir / "work2",
+            zarr_path,
+            "variant_ancestral_allele",
+            tmpdir / "ancestors.zarr",
+            min_work_per_job=1,
+            max_num_partitions=20000,
+        )
+        for group in metadata["ancestor_grouping"]:
+            if group["partitions"] is not None:
+                for partition in group["partitions"]:
+                    assert len(partition) == 1
+
 
 @pytest.mark.skipif(sys.platform == "win32", reason="No cyvcf2 on windows")
 class TestBatchSampleMatching:
@@ -1543,8 +1578,8 @@ def test_match_samples_batch(self, tmp_path, tmpdir):
             ancestral_state="variant_ancestral_allele",
             ancestor_ts_path=tmpdir / "mat_anc.trees",
             min_work_per_job=1,
-            max_num_partitions=10,
         )
+        assert mat_wd.num_partitions == mat_sd.num_samples
         for i in range(mat_wd.num_partitions):
             tsinfer.match_samples_batch_partition(
                 work_dir=tmpdir / "working_mat",
@@ -1564,7 +1599,6 @@ def test_match_samples_batch(self, tmp_path, tmpdir):
             ancestral_state="variant_ancestral_allele",
             ancestor_ts_path=tmpdir / "mask_anc.trees",
             min_work_per_job=1,
-            max_num_partitions=10,
             site_mask="variant_mask_foobar",
             sample_mask="samples_mask_foobar",
         )
@@ -1588,6 +1622,82 @@ def test_match_samples_batch(self, tmp_path, tmpdir):
             mat_ts_batch.tables, ignore_timestamps=True, ignore_provenance=True
         )
 
+    def test_force_sample_times(self, tmp_path, tmpdir):
+        ts, zarr_path = tsutil.make_ts_and_zarr(tmp_path)
+        ds = sgkit.load_dataset(zarr_path)
+        array = [0.0001] * ts.num_individuals
+        ds.update(
+            {
+                "individuals_time": xr.DataArray(
+                    data=array, dims=["sample"], name="individuals_time"
+                )
+            }
+        )
+        sgkit.save_dataset(
+            ds.drop_vars(set(ds.data_vars) - {"individuals_time"}), zarr_path, mode="a"
+        )
+        samples = tsinfer.VariantData(zarr_path, "variant_ancestral_allele")
+        anc = tsinfer.generate_ancestors(samples, path=str(tmpdir / "ancestors.zarr"))
+        anc_ts = tsinfer.match_ancestors(samples, anc)
+        anc_ts.dump(tmpdir / "anc.trees")
+
+        wd = tsinfer.match_samples_batch_init(
+            work_dir=tmpdir / "working",
+            sample_data_path=samples.path,
+            ancestral_state="variant_ancestral_allele",
+            ancestor_ts_path=tmpdir / "anc.trees",
+            min_work_per_job=1e6,
+            force_sample_times=True,
+        )
+        for i in range(wd.num_partitions):
+            tsinfer.match_samples_batch_partition(
+                work_dir=tmpdir / "working",
+                partition_index=i,
+            )
+        ts_batch = tsinfer.match_samples_batch_finalise(tmpdir / "working")
+        ts = tsinfer.match_samples(samples, anc_ts, force_sample_times=True)
+        ts.tables.assert_equals(ts_batch.tables, ignore_provenance=True)
+
+    def test_array_args(self, tmp_path, tmpdir):
+        ts, zarr_path = tsutil.make_ts_and_zarr(tmp_path)
+        sample_mask = np.zeros(ts.num_individuals, dtype=bool)
+        sample_mask[42] = True
+        site_mask = np.zeros(ts.num_sites, dtype=bool)
+        site_mask[42] = True
+        rng = np.random.RandomState(42)
+        sites_time = rng.uniform(0, 1, ts.num_sites - 1)
+        samples = tsinfer.VariantData(
+            zarr_path,
+            "variant_ancestral_allele",
+            sample_mask=sample_mask,
+            site_mask=site_mask,
+            sites_time=sites_time,
+        )
+        anc = tsinfer.generate_ancestors(samples, path=str(tmpdir / "ancestors.zarr"))
+        anc_ts = tsinfer.match_ancestors(samples, anc)
+        anc_ts.dump(tmpdir / "anc.trees")
+
+        wd = tsinfer.match_samples_batch_init(
+            work_dir=tmpdir / "working",
+            sample_data_path=samples.path,
+            sample_mask=sample_mask,
+            site_mask=site_mask,
+            ancestral_state="variant_ancestral_allele",
+            ancestor_ts_path=tmpdir / "anc.trees",
+            min_work_per_job=1e6,
+        )
+        for i in range(wd.num_partitions):
+            tsinfer.match_samples_batch_partition(
+                work_dir=tmpdir / "working",
+                partition_index=i,
+            )
+        ts_batch = tsinfer.match_samples_batch_finalise(tmpdir / "working")
+        ts = tsinfer.match_samples(
+            samples,
+            anc_ts,
+        )
+        ts.tables.assert_equals(ts_batch.tables, ignore_provenance=True)
+
 
 class TestAncestorGeneratorsEquivalant:
     """

tsinfer/inference.py

@@ -28,6 +28,7 @@
 import json
 import logging
 import math
+import operator
 import os
 import pathlib
 import pickle
@@ -714,34 +715,35 @@ def match_ancestors_batch_init(
     for group_index, group_ancestors in matcher.group_by_linesweep().items():
         # Make ancestor_ids JSON serialisable
         group_ancestors = list(map(int, group_ancestors))
-        partitions = []
-        current_partition = []
-        current_partition_work = 0
-        # TODO: Can do better here by packing ancestors
-        # into as equal sized partitions as possible
+        # The first group is trivial so never partition
         if group_index == 0:
-            partitions.append(group_ancestors)
+            partitions = [group_ancestors]
         else:
             total_work = sum(ancestor_lengths[ancestor] for ancestor in group_ancestors)
-            min_work_per_job_group = min_work_per_job
-            if total_work / max_num_partitions > min_work_per_job:
-                min_work_per_job_group = total_work / max_num_partitions
-            for ancestor in group_ancestors:
-                if (
-                    current_partition_work + ancestor_lengths[ancestor]
-                    > min_work_per_job_group
-                ):
-                    partitions.append(current_partition)
-                    current_partition = [ancestor]
-                    current_partition_work = ancestor_lengths[ancestor]
-                else:
-                    current_partition.append(ancestor)
-                    current_partition_work += ancestor_lengths[ancestor]
-            partitions.append(current_partition)
+            partition_count = math.ceil(total_work / min_work_per_job)
+            if partition_count > max_num_partitions:
+                partition_count = max_num_partitions
+
+            # Partition into roughly equal sized bins (by work)
+            sorted_ancestors = sorted(
+                group_ancestors, key=lambda x: ancestor_lengths[x], reverse=True
+            )
+
+            # Use greedy bin packing - place each ancestor in the bin with
+            # lowest total length
+            heap = [(0, []) for _ in range(partition_count)]
+            for ancestor in sorted_ancestors:
+                sum_len, partition = heapq.heappop(heap)
+                partition.append(ancestor)
+                sum_len += ancestor_lengths[ancestor]
+                heapq.heappush(heap, (sum_len, partition))
+            partitions = [
+                sorted(partition) for sum_len, partition in heap if sum_len > 0
+            ]
         if len(partitions) > 1:
             group_dir = work_dir / f"group_{group_index}"
             group_dir.mkdir()
-        # TODO: Should be a dataclass
+
         group = {
             "ancestors": group_ancestors,
             "partitions": partitions if len(partitions) > 1 else None,
@@ -902,7 +904,7 @@ def match_ancestors_batch_group_partition(work_dir, group_index, partition_index
     )
     logger.info(f"Dumping to {partition_path}")
     with open(partition_path, "wb") as f:
-        pickle.dump((start_time, timing.metrics, results), f)
+        pickle.dump((start_time, timing.metrics, ancestors_to_match, results), f)
 
 
 def match_ancestors_batch_group_finalise(work_dir, group_index):
@@ -935,17 +937,18 @@ def match_ancestors_batch_group_finalise(work_dir, group_index):
         )
         start_times = []
         timings = []
-        results = []
+        results = {}
         for partition_index in range(len(group["partitions"])):
             partition_path = os.path.join(
                 work_dir, f"group_{group_index}", f"partition_{partition_index}.pkl"
             )
             with open(partition_path, "rb") as f:
-                start_time, part_timing, result = pickle.load(f)
+                start_time, part_timing, ancestors, result = pickle.load(f)
                 start_times.append(start_time)
-                results.extend(result)
+                for ancestor, r in zip(ancestors, result):
+                    results[ancestor] = r
                 timings.append(part_timing)
-
+        results = list(map(operator.itemgetter(1), sorted(results.items())))
         ts = matcher.finalise_group(group, results, group_index)
         path = os.path.join(work_dir, f"ancestors_{group_index}.trees")
         ts.dump(path)
@@ -1186,7 +1189,6 @@ def match_samples_batch_init(
     ancestor_ts_path,
     min_work_per_job,
     *,
-    max_num_partitions=None,
     sample_mask=None,
     site_mask=None,
     recombination_rate=None,
@@ -1206,7 +1208,7 @@ def match_samples_batch_init(
 ):
     """
     match_samples_batch_init(work_dir, sample_data_path, ancestral_state,
-    ancestor_ts_path, min_work_per_job, \\*, max_num_partitions=None,
+    ancestor_ts_path, min_work_per_job, \\*,
     sample_mask=None, site_mask=None, recombination_rate=None, mismatch_ratio=None,
     path_compression=True, indexes=None, post_process=None, force_sample_times=False)
 
@@ -1237,9 +1239,6 @@ def match_samples_batch_init(
         genotypes) to allocate to a single parallel job. If the amount of work in
         a group of samples exceeds this level it will be broken up into parallel
         partitions, subject to the constraint of `max_num_partitions`.
-    :param int max_num_partitions: The maximum number of partitions to split a
-        group of samples into. Useful for limiting the number of jobs in a
-        workflow to avoid job overhead. Defaults to 1000.
     :param Union(array, str) sample_mask: A numpy array of booleans specifying
         which samples to mask out (exclude) from the dataset. Alternatively, a
         string can be provided, giving the name of an array in the input dataset
@@ -1277,9 +1276,6 @@ def match_samples_batch_init(
     :return: A dictionary of the job metadata, as written to `metadata.json` in
         `work_dir`.
     """
-    if max_num_partitions is None:
-        max_num_partitions = 1000
-
     # Convert working_dir to pathlib.Path
     work_dir = pathlib.Path(work_dir)
 
@@ -1329,9 +1325,9 @@ def match_samples_batch_init(
     sample_times = sample_times.tolist()
     wd.sample_indexes = sample_indexes
     wd.sample_times = sample_times
-    num_samples_per_partition = int(min_work_per_job // variant_data.num_sites)
-    if num_samples_per_partition == 0:
-        num_samples_per_partition = 1
+    num_samples_per_partition = max(
+        1, math.ceil(min_work_per_job // variant_data.num_sites)
+    )
     wd.num_samples_per_partition = num_samples_per_partition
     wd.num_partitions = math.ceil(len(sample_indexes) / num_samples_per_partition)
     wd_path = work_dir / "metadata.json"