HADOOP-18526. Leak of S3AInstrumentation instances via hadoop Metrics references (#5144)

This has triggered an OOM in a process which was churning through s3a fs
instances; the increased memory footprint of IOStatistics amplified what
must have been a long-standing issue with FS instances being created
and not closed()

*  Makes sure instrumentation is closed when the FS is closed.
*  Uses a weak reference from metrics to instrumentation, so even
   if the FS wasn't closed (see HADOOP-18478), this back reference
   would not cause the S3AInstrumentation reference to be retained.
*  If S3AFileSystem is configured to log at TRACE it will log the
   calling stack of initialize(), so help identify where the
   instance is being created. This should help track down
   the cause of instance leakage.

Contributed by Steve Loughran.

hadoop-common-project/hadoop-common/src/main/java/org/apache/hadoop/fs/impl/WeakRefMetricsSource.java

@@ -0,0 +1,97 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License 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.
+ */
+
+package org.apache.hadoop.fs.impl;
+
+import java.lang.ref.WeakReference;
+
+import org.apache.hadoop.classification.InterfaceAudience;
+import org.apache.hadoop.metrics2.MetricsCollector;
+import org.apache.hadoop.metrics2.MetricsSource;
+
+import static java.util.Objects.requireNonNull;
+
+/**
+ * A weak referenced metrics source which avoids hanging on to large objects
+ * if somehow they don't get fully closed/cleaned up.
+ * The JVM may clean up all objects which are only weakly referenced whenever
+ * it does a GC, <i>even if there is no memory pressure</i>.
+ * To avoid these refs being removed, always keep a strong reference around
+ * somewhere.
+ */
+@InterfaceAudience.Private
+public class WeakRefMetricsSource implements MetricsSource {
+
+  /**
+   * Name to know when unregistering.
+   */
+  private final String name;
+
+  /**
+   * Underlying metrics source.
+   */
+  private final WeakReference<MetricsSource> sourceWeakReference;
+
+  /**
+   * Constructor.
+   * @param name Name to know when unregistering.
+   * @param source metrics source
+   */
+  public WeakRefMetricsSource(final String name, final MetricsSource source) {
+    this.name = name;
+    this.sourceWeakReference = new WeakReference<>(requireNonNull(source));
+  }
+
+  /**
+   * If the weak reference is non null, update the metrics.
+   * @param collector to contain the resulting metrics snapshot
+   * @param all if true, return all metrics even if unchanged.
+   */
+  @Override
+  public void getMetrics(final MetricsCollector collector, final boolean all) {
+    MetricsSource metricsSource = sourceWeakReference.get();
+    if (metricsSource != null) {
+      metricsSource.getMetrics(collector, all);
+    }
+  }
+
+  /**
+   * Name to know when unregistering.
+   * @return the name passed in during construction.
+   */
+  public String getName() {
+    return name;
+  }
+
+  /**
+   * Get the source, will be null if the reference has been GC'd
+   * @return the source reference
+   */
+  public MetricsSource getSource() {
+    return sourceWeakReference.get();
+  }
+
+  @Override
+  public String toString() {
+    return "WeakRefMetricsSource{" +
+        "name='" + name + '\'' +
+        ", sourceWeakReference is " +
+        (sourceWeakReference.get() == null ? "unset" : "set") +
+        '}';
+  }
+}

hadoop-tools/hadoop-aws/src/main/java/org/apache/hadoop/fs/s3a/S3AFileSystem.java

@@ -136,7 +136,6 @@ import org.apache.hadoop.fs.s3a.tools.MarkerToolOperationsImpl;
 import org.apache.hadoop.fs.statistics.DurationTracker;
 import org.apache.hadoop.fs.statistics.DurationTrackerFactory;
 import org.apache.hadoop.fs.statistics.IOStatistics;
-import org.apache.hadoop.fs.statistics.IOStatisticsLogging;
 import org.apache.hadoop.fs.statistics.IOStatisticsSource;
 import org.apache.hadoop.fs.statistics.IOStatisticsContext;
 import org.apache.hadoop.fs.statistics.impl.IOStatisticsStore;
@@ -444,6 +443,13 @@ public class S3AFileSystem extends FileSystem implements StreamCapabilities,
     AuditSpan span = null;
     try {
       LOG.debug("Initializing S3AFileSystem for {}", bucket);
+      if (LOG.isTraceEnabled()) {
+        // log a full trace for deep diagnostics of where an object is created,
+        // for tracking down memory leak issues.
+        LOG.trace("Filesystem for {} created; fs.s3a.impl.disable.cache = {}",
+            name, originalConf.getBoolean("fs.s3a.impl.disable.cache", false),
+            new RuntimeException(super.toString()));
+      }
       // clone the configuration into one with propagated bucket options
       Configuration conf = propagateBucketOptions(originalConf, bucket);
       // HADOOP-17894. remove references to s3a stores in JCEKS credentials.
@@ -3944,22 +3950,18 @@ public class S3AFileSystem extends FileSystem implements StreamCapabilities,
     }
     isClosed = true;
     LOG.debug("Filesystem {} is closed", uri);
+    try {
+      super.close();
+    } finally {
+      stopAllServices();
+      // log IO statistics, including of any file deletion during
+      // superclass close
       if (getConf() != null) {
         String iostatisticsLoggingLevel =
             getConf().getTrimmed(IOSTATISTICS_LOGGING_LEVEL,
                 IOSTATISTICS_LOGGING_LEVEL_DEFAULT);
         logIOStatisticsAtLevel(LOG, iostatisticsLoggingLevel, getIOStatistics());
       }
-    try {
-      super.close();
-    } finally {
-      stopAllServices();
-    }
-    // Log IOStatistics at debug.
-    if (LOG.isDebugEnabled()) {
-      // robust extract and convert to string
-      LOG.debug("Statistics for {}: {}", uri,
-          IOStatisticsLogging.ioStatisticsToPrettyString(getIOStatistics()));
     }
   }
 

hadoop-tools/hadoop-aws/src/main/java/org/apache/hadoop/fs/s3a/S3AInstrumentation.java

@@ -27,6 +27,7 @@ import org.slf4j.LoggerFactory;
 import org.apache.hadoop.classification.InterfaceAudience;
 import org.apache.hadoop.classification.InterfaceStability;
 import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.impl.WeakRefMetricsSource;
 import org.apache.hadoop.fs.s3a.statistics.BlockOutputStreamStatistics;
 import org.apache.hadoop.fs.s3a.statistics.ChangeTrackerStatistics;
 import org.apache.hadoop.fs.s3a.statistics.CommitterStatistics;
@@ -160,7 +161,10 @@ public class S3AInstrumentation implements Closeable, MetricsSource,
 
   private final DurationTrackerFactory durationTrackerFactory;
 
-  private String metricsSourceName;
+  /**
+   * Weak reference so there's no back reference to the instrumentation.
+   */
+  private WeakRefMetricsSource metricsSourceReference;
 
   private final MetricsRegistry registry =
       new MetricsRegistry("s3aFileSystem").setContext(CONTEXT);
@@ -233,19 +237,33 @@ public class S3AInstrumentation implements Closeable, MetricsSource,
         new MetricDurationTrackerFactory());
   }
 
+  /**
+   * Get the current metrics system; demand creating.
+   * @return a metric system, creating if need be.
+   */
   @VisibleForTesting
-  public MetricsSystem getMetricsSystem() {
+  static MetricsSystem getMetricsSystem() {
     synchronized (METRICS_SYSTEM_LOCK) {
       if (metricsSystem == null) {
         metricsSystem = new MetricsSystemImpl();
         metricsSystem.init(METRICS_SYSTEM_NAME);
+        LOG.debug("Metrics system inited {}", metricsSystem);
       }
     }
     return metricsSystem;
   }
 
   /**
-   * Register this instance as a metrics source.
+   * Does the instrumentation have a metrics system?
+   * @return true if the metrics system is present.
+   */
+  @VisibleForTesting
+  static boolean hasMetricSystem() {
+    return metricsSystem != null;
+  }
+
+  /**
+   * Register this instance as a metrics source via a weak reference.
    * @param name s3a:// URI for the associated FileSystem instance
    */
   private void registerAsMetricsSource(URI name) {
@@ -257,8 +275,9 @@ public class S3AInstrumentation implements Closeable, MetricsSource,
       number = ++metricsSourceNameCounter;
     }
     String msName = METRICS_SOURCE_BASENAME + number;
-    metricsSourceName = msName + "-" + name.getHost();
-    metricsSystem.register(metricsSourceName, "", this);
+    String metricsSourceName = msName + "-" + name.getHost();
+    metricsSourceReference = new WeakRefMetricsSource(metricsSourceName, this);
+    metricsSystem.register(metricsSourceName, "", metricsSourceReference);
   }
 
   /**
@@ -680,12 +699,34 @@ public class S3AInstrumentation implements Closeable, MetricsSource,
     registry.snapshot(collector.addRecord(registry.info().name()), true);
   }
 
+  /**
+   * if registered with the metrics, return the
+   * name of the source.
+   * @return the name of the metrics, or null if this instance is not bonded.
+   */
+  public String getMetricSourceName() {
+    return metricsSourceReference != null
+        ? metricsSourceReference.getName()
+        : null;
+  }
+
   public void close() {
+    if (metricsSourceReference != null) {
+      // get the name
+      String name = metricsSourceReference.getName();
+      LOG.debug("Unregistering metrics for {}", name);
+      // then set to null so a second close() is a noop here.
+      metricsSourceReference = null;
       synchronized (METRICS_SYSTEM_LOCK) {
         // it is critical to close each quantile, as they start a scheduled
         // task in a shared thread pool.
+        if (metricsSystem == null) {
+          LOG.debug("there is no metric system to unregister {} from", name);
+          return;
+        }
         throttleRateQuantile.stop();
-      metricsSystem.unregisterSource(metricsSourceName);
+
+        metricsSystem.unregisterSource(name);
         metricsSourceActiveCounter--;
         int activeSources = metricsSourceActiveCounter;
         if (activeSources == 0) {
@@ -696,6 +737,7 @@ public class S3AInstrumentation implements Closeable, MetricsSource,
         }
       }
     }
+  }
 
   /**
    * A duration tracker which updates a mutable counter with a metric.

hadoop-tools/hadoop-aws/src/test/java/org/apache/hadoop/fs/s3a/ITestS3AClosedFS.java

@@ -103,4 +103,16 @@ public class ITestS3AClosedFS extends AbstractS3ATestBase {
         () ->  getFileSystem().open(path("to-open")));
   }
 
+  @Test
+  public void testClosedInstrumentation() throws Exception {
+    // no metrics
+    Assertions.assertThat(S3AInstrumentation.hasMetricSystem())
+        .describedAs("S3AInstrumentation.hasMetricSystem()")
+        .isFalse();
+
+    Assertions.assertThat(getFileSystem().getIOStatistics())
+        .describedAs("iostatistics of %s", getFileSystem())
+        .isNotNull();
+  }
+
 }

hadoop-tools/hadoop-aws/src/test/java/org/apache/hadoop/fs/s3a/TestInstrumentationLifecycle.java

@@ -0,0 +1,104 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License 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.
+ */
+
+package org.apache.hadoop.fs.s3a;
+
+import java.net.URI;
+
+import org.assertj.core.api.Assertions;
+import org.junit.Test;
+
+import org.apache.hadoop.fs.impl.WeakRefMetricsSource;
+import org.apache.hadoop.metrics2.MetricsSource;
+import org.apache.hadoop.metrics2.MetricsSystem;
+import org.apache.hadoop.test.AbstractHadoopTestBase;
+
+import static org.apache.hadoop.fs.s3a.S3AInstrumentation.getMetricsSystem;
+import static org.apache.hadoop.fs.s3a.Statistic.DIRECTORIES_CREATED;
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Test the {@link S3AInstrumentation} lifecycle,  in particular how
+ * it binds to hadoop metrics through a {@link WeakRefMetricsSource}
+ * and that it will deregister itself in {@link S3AInstrumentation#close()}.
+ */
+public class TestInstrumentationLifecycle extends AbstractHadoopTestBase {
+
+  @Test
+  public void testDoubleClose() throws Throwable {
+    S3AInstrumentation instrumentation = new S3AInstrumentation(new URI("s3a://example/"));
+
+    // the metric system is created in the constructor
+    assertThat(S3AInstrumentation.hasMetricSystem())
+        .describedAs("S3AInstrumentation.hasMetricSystem()")
+        .isTrue();
+    // ask for a metric
+    String metricName = DIRECTORIES_CREATED.getSymbol();
+    assertThat(instrumentation.lookupMetric(metricName))
+        .describedAs("lookupMetric(%s) while open", metricName)
+        .isNotNull();
+
+    MetricsSystem activeMetrics = getMetricsSystem();
+    final String metricSourceName = instrumentation.getMetricSourceName();
+    final MetricsSource source = activeMetrics.getSource(metricSourceName);
+    // verify the source is registered through a weak ref, and that the
+    // reference maps to the instance.
+    Assertions.assertThat(source)
+        .describedAs("metric source %s", metricSourceName)
+        .isNotNull()
+        .isInstanceOf(WeakRefMetricsSource.class)
+        .extracting(m -> ((WeakRefMetricsSource) m).getSource())
+        .isSameAs(instrumentation);
+
+    // this will close the metrics system
+    instrumentation.close();
+
+    // iostats is still valid
+    assertThat(instrumentation.getIOStatistics())
+        .describedAs("iostats of %s", instrumentation)
+        .isNotNull();
+
+    // no metrics
+    assertThat(S3AInstrumentation.hasMetricSystem())
+        .describedAs("S3AInstrumentation.hasMetricSystem()")
+        .isFalse();
+
+    // metric lookup still works, so any invocation of an s3a
+    // method which still updates a metric also works
+    assertThat(instrumentation.lookupMetric(metricName))
+        .describedAs("lookupMetric(%s) when closed", metricName)
+        .isNotNull();
+
+    // which we can implicitly verify by asking for it and
+    // verifying that we get given a different one back
+    // from the demand-created instance
+    MetricsSystem metrics2 = getMetricsSystem();
+    assertThat(metrics2)
+        .describedAs("metric system 2")
+        .isNotSameAs(activeMetrics);
+
+    // this is going to be a no-op
+    instrumentation.close();
+
+    // which we can verify because the metrics system doesn't
+    // get closed this time
+    assertThat(getMetricsSystem())
+        .describedAs("metric system 3")
+        .isSameAs(metrics2);
+  }
+}

hadoop-tools/hadoop-aws/src/test/resources/log4j.properties

@@ -53,6 +53,8 @@ log4j.logger.org.apache.hadoop.ipc.Server=WARN
 # for debugging low level S3a operations, uncomment these lines
 # Log all S3A classes
 log4j.logger.org.apache.hadoop.fs.s3a=DEBUG
+# when logging at trace, the stack of the initialize() call is logged
+#log4j.logger.org.apache.hadoop.fs.s3a.S3AFileSystem=TRACE
 #log4j.logger.org.apache.hadoop.fs.s3a.S3AUtils=INFO
 #log4j.logger.org.apache.hadoop.fs.s3a.Listing=INFO
 log4j.logger.org.apache.hadoop.fs.s3a.SDKV2Upgrade=WARN