Merge branch 'master' into master

metrizable · web-flow · commit 461967187540 · 2020-12-16T08:39:13.000-08:00
diff --git a/tests/integ/test_workflow.py b/tests/integ/test_workflow.py
@@ -16,12 +16,18 @@
 import os
 import re
 import time
+import uuid
 
 import boto3
 import pytest
 
 from botocore.config import Config
 from botocore.exceptions import WaiterError
+from sagemaker.debugger import (
+    DebuggerHookConfig,
+    Rule,
+    rule_configs,
+)
 from sagemaker.inputs import CreateModelInput, TrainingInput
 from sagemaker.model import Model
 from sagemaker.processing import ProcessingInput, ProcessingOutput
@@ -433,3 +439,93 @@ def test_conditional_pytorch_training_model_registration(
             pipeline.delete()
         except Exception:
             pass
+
+
+def test_training_job_with_debugger(
+    sagemaker_session,
+    pipeline_name,
+    role,
+    pytorch_training_latest_version,
+    pytorch_training_latest_py_version,
+):
+    instance_count = ParameterInteger(name="InstanceCount", default_value=1)
+    instance_type = ParameterString(name="InstanceType", default_value="ml.m5.xlarge")
+
+    rules = [
+        Rule.sagemaker(rule_configs.vanishing_gradient()),
+        Rule.sagemaker(base_config=rule_configs.all_zero(), rule_parameters={"tensor_regex": ".*"}),
+        Rule.sagemaker(rule_configs.loss_not_decreasing()),
+    ]
+    debugger_hook_config = DebuggerHookConfig(
+        s3_output_path=f"s3://{sagemaker_session.default_bucket()}/{uuid.uuid4()}/tensors"
+    )
+
+    base_dir = os.path.join(DATA_DIR, "pytorch_mnist")
+    script_path = os.path.join(base_dir, "mnist.py")
+    input_path = sagemaker_session.upload_data(
+        path=os.path.join(base_dir, "training"),
+        key_prefix="integ-test-data/pytorch_mnist/training",
+    )
+    inputs = TrainingInput(s3_data=input_path)
+
+    pytorch_estimator = PyTorch(
+        entry_point=script_path,
+        role="SageMakerRole",
+        framework_version=pytorch_training_latest_version,
+        py_version=pytorch_training_latest_py_version,
+        instance_count=instance_count,
+        instance_type=instance_type,
+        sagemaker_session=sagemaker_session,
+        rules=rules,
+        debugger_hook_config=debugger_hook_config,
+    )
+
+    step_train = TrainingStep(
+        name="pytorch-train",
+        estimator=pytorch_estimator,
+        inputs=inputs,
+    )
+
+    pipeline = Pipeline(
+        name=pipeline_name,
+        parameters=[instance_count, instance_type],
+        steps=[step_train],
+        sagemaker_session=sagemaker_session,
+    )
+
+    try:
+        response = pipeline.create(role)
+        create_arn = response["PipelineArn"]
+
+        execution = pipeline.start()
+        response = execution.describe()
+        assert response["PipelineArn"] == create_arn
+
+        try:
+            execution.wait(delay=10, max_attempts=60)
+        except WaiterError:
+            pass
+        execution_steps = execution.list_steps()
+        training_job_arn = execution_steps[0]["Metadata"]["TrainingJob"]["Arn"]
+        job_description = sagemaker_session.sagemaker_client.describe_training_job(
+            TrainingJobName=training_job_arn.split("/")[1]
+        )
+
+        assert len(execution_steps) == 1
+        assert execution_steps[0]["StepName"] == "pytorch-train"
+        assert execution_steps[0]["StepStatus"] == "Succeeded"
+
+        for index, rule in enumerate(rules):
+            config = job_description["DebugRuleConfigurations"][index]
+            assert config["RuleConfigurationName"] == rule.name
+            assert config["RuleEvaluatorImage"] == rule.image_uri
+            assert config["VolumeSizeInGB"] == 0
+            assert (
+                config["RuleParameters"]["rule_to_invoke"] == rule.rule_parameters["rule_to_invoke"]
+            )
+        assert job_description["DebugHookConfig"] == debugger_hook_config._to_request_dict()
+    finally:
+        try:
+            pipeline.delete()
+        except Exception:
+            pass
diff --git a/tests/integ/test_workflow_with_clarify.py b/tests/integ/test_workflow_with_clarify.py
@@ -0,0 +1,285 @@
+# Copyright 2020 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License"). You
+# may not use this file except in compliance with the License. A copy of
+# the License is located at
+#
+#     http://aws.amazon.com/apache2.0/
+#
+# or in the "license" file accompanying this file. This file is
+# distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
+# ANY KIND, either express or implied. See the License for the specific
+# language governing permissions and limitations under the License.
+from __future__ import absolute_import
+
+import json
+import os
+import statistics
+import time
+import tempfile
+
+import pytest
+import numpy as np
+import pandas as pd
+from botocore.exceptions import WaiterError
+from sagemaker.amazon.linear_learner import LinearLearner, LinearLearnerPredictor
+from sagemaker.clarify import (
+    BiasConfig,
+    DataConfig,
+    ModelConfig,
+    ModelPredictedLabelConfig,
+    SageMakerClarifyProcessor,
+)
+from sagemaker.processing import ProcessingInput, ProcessingOutput
+from sagemaker.session import get_execution_role
+from sagemaker.workflow.conditions import ConditionLessThanOrEqualTo
+from sagemaker.workflow.condition_step import ConditionStep, JsonGet
+from sagemaker.workflow.parameters import (
+    ParameterInteger,
+    ParameterString,
+)
+from sagemaker.workflow.steps import ProcessingStep
+from sagemaker.workflow.properties import PropertyFile
+from sagemaker.workflow.pipeline import Pipeline
+
+from sagemaker import utils
+from tests import integ
+from tests.integ import timeout
+
+
+@pytest.fixture(scope="module")
+def role(sagemaker_session):
+    return get_execution_role(sagemaker_session)
+
+
+@pytest.fixture
+def pipeline_name():
+    return f"my-pipeline-clarify-{int(time.time() * 10**7)}"
+
+
+@pytest.fixture(scope="module")
+def training_set():
+    label = (np.random.rand(100, 1) > 0.5).astype(np.int32)
+    features = np.random.rand(100, 4)
+    return features, label
+
+
+@pytest.yield_fixture(scope="module")
+def data_path(training_set):
+    features, label = training_set
+    data = pd.concat([pd.DataFrame(label), pd.DataFrame(features)], axis=1, sort=False)
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        filename = os.path.join(tmpdirname, "train.csv")
+        data.to_csv(filename, index=False, header=False)
+        yield filename
+
+
+@pytest.fixture(scope="module")
+def headers():
+    return [
+        "Label",
+        "F1",
+        "F2",
+        "F3",
+        "F4",
+    ]
+
+
+@pytest.fixture(scope="module")
+def data_config(sagemaker_session, data_path, headers):
+    output_path = f"s3://{sagemaker_session.default_bucket()}/linear_learner_analysis_result"
+    return DataConfig(
+        s3_data_input_path=data_path,
+        s3_output_path=output_path,
+        label="Label",
+        headers=headers,
+        dataset_type="text/csv",
+    )
+
+
+@pytest.fixture(scope="module")
+def data_bias_config():
+    return BiasConfig(
+        label_values_or_threshold=[1],
+        facet_name="F1",
+        facet_values_or_threshold=[0.5],
+        group_name="F2",
+    )
+
+
+@pytest.yield_fixture(scope="module")
+def model_name(sagemaker_session, cpu_instance_type, training_set):
+    job_name = utils.unique_name_from_base("clarify-xgb")
+
+    with timeout.timeout(minutes=integ.TRAINING_DEFAULT_TIMEOUT_MINUTES):
+        ll = LinearLearner(
+            "SageMakerRole",
+            1,
+            cpu_instance_type,
+            predictor_type="binary_classifier",
+            sagemaker_session=sagemaker_session,
+            disable_profiler=True,
+        )
+        ll.binary_classifier_model_selection_criteria = "accuracy"
+        ll.early_stopping_tolerance = 0.0001
+        ll.early_stopping_patience = 3
+        ll.num_models = 1
+        ll.epochs = 1
+        ll.num_calibration_samples = 1
+
+        features, label = training_set
+        ll.fit(
+            ll.record_set(features.astype(np.float32), label.reshape(-1).astype(np.float32)),
+            job_name=job_name,
+        )
+
+    with timeout.timeout_and_delete_endpoint_by_name(job_name, sagemaker_session):
+        ll.deploy(1, cpu_instance_type, endpoint_name=job_name, model_name=job_name, wait=True)
+        yield job_name
+
+
+@pytest.fixture(scope="module")
+def model_config(model_name):
+    return ModelConfig(
+        model_name=model_name,
+        instance_type="ml.c5.xlarge",
+        instance_count=1,
+        accept_type="application/jsonlines",
+    )
+
+
+@pytest.fixture(scope="module")
+def model_predicted_label_config(sagemaker_session, model_name, training_set):
+    predictor = LinearLearnerPredictor(
+        model_name,
+        sagemaker_session=sagemaker_session,
+    )
+    result = predictor.predict(training_set[0].astype(np.float32))
+    predictions = [float(record.label["score"].float32_tensor.values[0]) for record in result]
+    probability_threshold = statistics.median(predictions)
+    return ModelPredictedLabelConfig(label="score", probability_threshold=probability_threshold)
+
+
+def test_workflow_with_clarify(
+    data_config,
+    data_bias_config,
+    model_config,
+    model_predicted_label_config,
+    pipeline_name,
+    role,
+    sagemaker_session,
+):
+
+    instance_type = ParameterString(name="InstanceType", default_value="ml.m5.xlarge")
+    instance_count = ParameterInteger(name="InstanceCount", default_value=1)
+
+    analysis_config = data_config.get_config()
+    analysis_config.update(data_bias_config.get_config())
+    (
+        probability_threshold,
+        predictor_config,
+    ) = model_predicted_label_config.get_predictor_config()
+    predictor_config.update(model_config.get_predictor_config())
+    analysis_config["methods"] = {"post_training_bias": {"methods": "all"}}
+    analysis_config["predictor"] = predictor_config
+    analysis_config["probability_threshold"] = probability_threshold
+    analysis_config["methods"]["report"] = {"name": "report", "title": "Analysis Report"}
+
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        analysis_config_file = os.path.join(tmpdirname, "analysis_config.json")
+        with open(analysis_config_file, "w") as f:
+            json.dump(analysis_config, f)
+        config_input = ProcessingInput(
+            input_name="analysis_config",
+            source=analysis_config_file,
+            destination="/opt/ml/processing/input/config",
+            s3_data_type="S3Prefix",
+            s3_input_mode="File",
+            s3_compression_type="None",
+        )
+
+        data_input = ProcessingInput(
+            input_name="dataset",
+            source=data_config.s3_data_input_path,
+            destination="/opt/ml/processing/input/data",
+            s3_data_type="S3Prefix",
+            s3_input_mode="File",
+            s3_data_distribution_type=data_config.s3_data_distribution_type,
+            s3_compression_type=data_config.s3_compression_type,
+        )
+
+        result_output = ProcessingOutput(
+            source="/opt/ml/processing/output",
+            destination=data_config.s3_output_path,
+            output_name="analysis_result",
+            s3_upload_mode="EndOfJob",
+        )
+
+        processor = SageMakerClarifyProcessor(
+            role="SageMakerRole",
+            instance_count=instance_count,
+            instance_type=instance_type,
+            sagemaker_session=sagemaker_session,
+        )
+
+        property_file = PropertyFile(
+            name="BiasOutput",
+            output_name="analysis_result",
+            path="analysis.json",
+        )
+
+        step_process = ProcessingStep(
+            name="my-process",
+            processor=processor,
+            inputs=[data_input, config_input],
+            outputs=[result_output],
+            property_files=[property_file],
+        )
+
+        cond_left = JsonGet(
+            step=step_process,
+            property_file="BiasOutput",
+            json_path="post_training_bias_metrics.facets.F1[0].metrics[0].value",
+        )
+
+        step_condition = ConditionStep(
+            name="bias-condition",
+            conditions=[ConditionLessThanOrEqualTo(left=cond_left, right=1)],
+            if_steps=[],
+            else_steps=[],
+        )
+
+        pipeline = Pipeline(
+            name=pipeline_name,
+            parameters=[instance_type, instance_count],
+            steps=[step_process, step_condition],
+            sagemaker_session=sagemaker_session,
+        )
+
+        try:
+            response = pipeline.create(role)
+            create_arn = response["PipelineArn"]
+
+            execution = pipeline.start(parameters={})
+
+            response = execution.describe()
+            assert response["PipelineArn"] == create_arn
+
+            try:
+                execution.wait(delay=30, max_attempts=60)
+            except WaiterError:
+                pass
+            execution_steps = execution.list_steps()
+
+            assert len(execution_steps) == 2
+            assert execution_steps[1]["StepName"] == "my-process"
+            assert execution_steps[1]["StepStatus"] == "Succeeded"
+            assert execution_steps[0]["StepName"] == "bias-condition"
+            assert execution_steps[0]["StepStatus"] == "Succeeded"
+            assert execution_steps[0]["Metadata"]["Condition"]["Outcome"] == "True"
+
+        finally:
+            try:
+                pipeline.delete()
+            except Exception:
+                pass
