[dask] Reduce the flakiness of tests. (#10678)

tests/test_distributed/test_gpu_with_dask/test_gpu_with_dask.py

@@ -221,16 +221,12 @@ class TestDistributedGPU:
         X_, y_ = load_breast_cancer(return_X_y=True)
         X = dd.from_array(X_, chunksize=100).to_backend("cudf")
         y = dd.from_array(y_, chunksize=100).to_backend("cudf")
-        divisions = copy(X.divisions)
+        run_boost_from_prediction(X, y, "hist", "cuda", local_cuda_client)
-        run_boost_from_prediction(X, y, "hist", "cuda", local_cuda_client, divisions)
 
         X_, y_ = load_iris(return_X_y=True)
         X = dd.from_array(X_, chunksize=50).to_backend("cudf")
         y = dd.from_array(y_, chunksize=50).to_backend("cudf")
-        divisions = copy(X.divisions)
+        run_boost_from_prediction_multi_class(X, y, "hist", "cuda", local_cuda_client)
-        run_boost_from_prediction_multi_class(
-            X, y, "hist", "cuda", local_cuda_client, divisions
-        )
 
     def test_init_estimation(self, local_cuda_client: Client) -> None:
         check_init_estimation("hist", "cuda", local_cuda_client)

tests/test_distributed/test_with_dask/test_with_dask.py

@@ -50,7 +50,7 @@ pytestmark = [tm.timeout(60), pytest.mark.skipif(**tm.no_dask())]
 import dask
 import dask.array as da
 import dask.dataframe as dd
-from distributed import Client, LocalCluster, Nanny, Worker
+from distributed import Client, LocalCluster, Nanny, Worker, wait
 from distributed.utils_test import async_poll_for, gen_cluster
 from toolz import sliding_window  # dependency of dask
 
@@ -146,28 +146,6 @@ def generate_array(
     return X, y, None
 
 
-Margin = TypeVar("Margin", dd.DataFrame, dd.Series, None)
-
-
-def deterministic_repartition(
-    client: Client,
-    X: dd.DataFrame,
-    y: dd.Series,
-    m: Margin,
-    divisions,
-) -> Tuple[dd.DataFrame, dd.Series, Margin]:
-    """Try to partition the dataframes according to divisions, this doesn't guarantee
-    the reproducibiliy.
-
-    """
-    X, y, margin = (
-        dd.repartition(X, divisions=divisions, force=True),
-        dd.repartition(y, divisions=divisions, force=True),
-        dd.repartition(m, divisions=divisions, force=True) if m is not None else None,
-    )
-    return X, y, margin
-
-
 @pytest.mark.parametrize("to_frame", [True, False])
 def test_xgbclassifier_classes_type_and_value(to_frame: bool, client: "Client"):
     X, y = make_classification(n_samples=1000, n_features=4, random_state=123)
@@ -429,7 +407,6 @@ def run_boost_from_prediction_multi_class(
     tree_method: str,
     device: str,
     client: "Client",
-    divisions: List[int],
 ) -> None:
     model_0 = xgb.dask.DaskXGBClassifier(
         learning_rate=0.3,
@@ -438,7 +415,6 @@ def run_boost_from_prediction_multi_class(
         max_bin=768,
         device=device,
     )
-    X, y, _ = deterministic_repartition(client, X, y, None, divisions)
     model_0.fit(X=X, y=y, eval_set=[(X, y)])
     margin = xgb.dask.inplace_predict(
         client, model_0.get_booster(), X, predict_type="margin"
@@ -452,7 +428,6 @@ def run_boost_from_prediction_multi_class(
         max_bin=768,
         device=device,
     )
-    X, y, margin = deterministic_repartition(client, X, y, margin, divisions)
     model_1.fit(
         X=X, y=y, base_margin=margin, eval_set=[(X, y)], base_margin_eval_set=[margin]
     )
@@ -470,7 +445,6 @@ def run_boost_from_prediction_multi_class(
         max_bin=768,
         device=device,
     )
-    X, y, _ = deterministic_repartition(client, X, y, None, divisions)
     model_2.fit(X=X, y=y, eval_set=[(X, y)])
     predictions_2 = xgb.dask.inplace_predict(
         client, model_2.get_booster(), X, predict_type="margin"
@@ -493,7 +467,6 @@ def run_boost_from_prediction(
     tree_method: str,
     device: str,
     client: "Client",
-    divisions: List[int],
 ) -> None:
     X, y = client.persist([X, y])
 
@@ -504,7 +477,6 @@ def run_boost_from_prediction(
         max_bin=512,
         device=device,
     )
-    X, y, _ = deterministic_repartition(client, X, y, None, divisions)
     model_0.fit(X=X, y=y, eval_set=[(X, y)])
     margin: dd.Series = model_0.predict(X, output_margin=True)
 
@@ -515,11 +487,9 @@ def run_boost_from_prediction(
         max_bin=512,
         device=device,
     )
-    X, y, margin = deterministic_repartition(client, X, y, margin, divisions)
     model_1.fit(
         X=X, y=y, base_margin=margin, eval_set=[(X, y)], base_margin_eval_set=[margin]
     )
-    X, y, margin = deterministic_repartition(client, X, y, margin, divisions)
     predictions_1: dd.Series = model_1.predict(X, base_margin=margin)
 
     model_2 = xgb.dask.DaskXGBClassifier(
@@ -529,7 +499,6 @@ def run_boost_from_prediction(
         max_bin=512,
         device=device,
     )
-    X, y, _ = deterministic_repartition(client, X, y, None, divisions)
     model_2.fit(X=X, y=y, eval_set=[(X, y)])
     predictions_2: dd.Series = model_2.predict(X)
 
@@ -541,13 +510,11 @@ def run_boost_from_prediction(
     np.testing.assert_allclose(logloss_concat, logloss_2, rtol=1e-4)
 
     margined = xgb.dask.DaskXGBClassifier(n_estimators=4)
-    X, y, margin = deterministic_repartition(client, X, y, margin, divisions)
     margined.fit(
         X=X, y=y, base_margin=margin, eval_set=[(X, y)], base_margin_eval_set=[margin]
     )
 
     unmargined = xgb.dask.DaskXGBClassifier(n_estimators=4)
-    X, y, margin = deterministic_repartition(client, X, y, margin, divisions)
     unmargined.fit(X=X, y=y, eval_set=[(X, y)], base_margin=margin)
 
     margined_res = margined.evals_result()["validation_0"]["logloss"]
@@ -560,18 +527,28 @@ def run_boost_from_prediction(
 
 
 @pytest.mark.parametrize("tree_method", ["hist", "approx"])
-def test_boost_from_prediction(tree_method: str, client: "Client") -> None:
+def test_boost_from_prediction(tree_method: str) -> None:
     from sklearn.datasets import load_breast_cancer, load_digits
 
-    X_, y_ = load_breast_cancer(return_X_y=True)
+    n_threads = os.cpu_count()
-    X, y = dd.from_array(X_, chunksize=200), dd.from_array(y_, chunksize=200)
+    assert n_threads is not None
-    divisions = copy(X.divisions)
+    # This test has strict reproducibility requirements. However, Dask is freed to move
-    run_boost_from_prediction(X, y, tree_method, "cpu", client, divisions)
+    # partitions between workers and modify the partitions' size during the test. Given
+    # the lack of control over the partitioning logic, here we use a single worker as a
+    # workaround.
+    n_workers = 1
 
-    X_, y_ = load_digits(return_X_y=True)
+    with LocalCluster(
-    X, y = dd.from_array(X_, chunksize=100), dd.from_array(y_, chunksize=100)
+        n_workers=n_workers, threads_per_worker=n_threads // n_workers
-    divisions = copy(X.divisions)
+    ) as cluster:
-    run_boost_from_prediction_multi_class(X, y, tree_method, "cpu", client, divisions)
+        with Client(cluster) as client:
+            X_, y_ = load_breast_cancer(return_X_y=True)
+            X, y = dd.from_array(X_, chunksize=200), dd.from_array(y_, chunksize=200)
+            run_boost_from_prediction(X, y, tree_method, "cpu", client)
+
+            X_, y_ = load_digits(return_X_y=True)
+            X, y = dd.from_array(X_, chunksize=100), dd.from_array(y_, chunksize=100)
+            run_boost_from_prediction_multi_class(X, y, tree_method, "cpu", client)
 
 
 def test_inplace_predict(client: "Client") -> None:
@@ -1574,7 +1551,6 @@ class TestWithDask:
     def test_empty_quantile_dmatrix(self, client: Client) -> None:
         X, y = make_categorical(client, 2, 30, 13)
         X_valid, y_valid = make_categorical(client, 10000, 30, 13)
-        divisions = copy(X_valid.divisions)
 
         Xy = xgb.dask.DaskQuantileDMatrix(client, X, y, enable_categorical=True)
         Xy_valid = xgb.dask.DaskQuantileDMatrix(