HDDS-13009. Background snapshot defrag service #9324

swamirishi · 2025-11-19T05:29:58Z

What changes were proposed in this pull request?

Implement SnapshotDefragService to defrag a snapshot rocksdb with the required locks

What is the link to the Apache JIRA

https://issues.apache.org/jira/browse/HDDS-13009

How was this patch tested?

Adding unit test WIP

Change-Id: I34536ff06efb7d5a4942853f0fd83942ab398b5f

…otLocalDataManager Change-Id: I34536ff06efb7d5a4942853f0fd83942ab398b5f

Change-Id: I32bcaf2a1fb290f1790c02872a0230cd65586636

Change-Id: I105a2e8178c0444d52de41b99801f4ceb6d57ffd # Conflicts: # hadoop-hdds/common/src/main/java/org/apache/hadoop/ozone/util/Checksum.java # hadoop-hdds/common/src/main/java/org/apache/hadoop/ozone/util/ObjectSerializer.java # hadoop-hdds/common/src/main/java/org/apache/hadoop/ozone/util/YamlSerializer.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/OmSnapshotLocalDataYaml.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/OmSnapshotLocalDataManager.java # hadoop-ozone/ozone-manager/src/test/java/org/apache/hadoop/ozone/om/TestOmSnapshotLocalDataYaml.java

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Change-Id: I26b66f266bb7677e4b1078f5fcd9f2ce3a651a70 # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/OmSnapshotLocalDataManager.java

Change-Id: I1d93dbc048a42cc55ff1f8ffa420e52f967527b8

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…calDataProvider Change-Id: I3a004b4b435075a4348960aeed642e8da71e7e72

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Change-Id: I31004e0c95dad64411c6fe848501a82f2f773cba

Change-Id: Id317c8b56e8b25c122b68eaf96599b9690d08f79

Change-Id: I3849387d064e093634e69cdaf870d27c1934cda5 # Conflicts: # hadoop-hdds/common/src/main/java/org/apache/hadoop/ozone/util/ObjectSerializer.java # hadoop-hdds/common/src/main/java/org/apache/hadoop/ozone/util/YamlSerializer.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/OmSnapshotLocalData.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/OmSnapshotLocalDataYaml.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/OmSnapshotManager.java # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/OmSnapshotLocalDataManager.java

Change-Id: Ie5e5f3dab4324103e8855dd15619d7755f0422e6

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Change-Id: Icb3092ca1234fc7acc77780613f0fc2ed9a0ac51 # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

Change-Id: Ieb28da9fbc06b2729c9b118a75436ba8a3f1a70f # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

Change-Id: If61213983561ed6f8c283d12bd07bd2097df710d

jojochuang · 2025-11-24T18:38:07Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+    // Binary search smallest existing version and delete the older versions starting from the smallest version.
+    // This is to ensure efficient crash recovery.
+    int smallestExistingVersion = 0;
+    int largestExistingVersion = previousVersion;
+    while (smallestExistingVersion <= largestExistingVersion) {
+      int midVersion = smallestExistingVersion + (largestExistingVersion - smallestExistingVersion) / 2;
+      Path path = OmSnapshotManager.getSnapshotPath(ozoneManager.getMetadataManager(), snapshotId, midVersion);
+      if (path.toFile().exists()) {
+        largestExistingVersion = midVersion - 1;
+      } else {
+        smallestExistingVersion = midVersion + 1;
+      }
+    }
+
+    // Acquire Snapshot DBHandle lock before removing the older version to ensure all readers are done with the
+    // snapshot db use.
+    try (UncheckedAutoCloseableSupplier<OMLockDetails> lock =
+             ozoneManager.getOmSnapshotManager().getSnapshotCache().lock(snapshotId)) {
+      if (!lock.get().isLockAcquired()) {
+        throw new IOException("Failed to acquire dbHandlelock on snapshot: " + snapshotId);
+      }
+      // Delete the older version directories. Always starting deletes from smallest version to largest version to
+      // ensure binary search works correctly on a later basis.
+      for (int version = smallestExistingVersion; version <= previousVersion; version++) {
+        Path path = OmSnapshotManager.getSnapshotPath(ozoneManager.getMetadataManager(), snapshotId, version);
+        deleteDirectory(path);
+      }
+    }


I would extract these lines into a method cleanupAndReleaseOlderVersions()

yeah working on it

jojochuang · 2025-11-24T18:41:16Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+        // Switch the snapshot DB location to the new version.
+        atomicSwitchSnapshotDB(snapshotId, checkpointLocation);
+      } finally {
+        snapshotContentLocks.releaseLock();


it may hold snapshot content lock for a long time if defrag service waits for the previous snapshot cache lock. What if we delay the clean-up of older versions after the release of snapshot content lock?

yeah makes sense

Consolidating both OMSNapshotPurgeResponse deleteCheckpoint and this logic in OmSnapshotManager

#9380 We should have done the delete subsequently under the same content lock to ensure we don't have some handles still hanging around in the snapshot cache which could have been used by a different thread after the defrag thread releases the snapshot cache lock

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

jojochuang · 2025-11-24T19:36:59Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+          Table checkpointTable = checkpointStore.getTable(table);
+          checkpointTable.loadFromFile(fileToBeIngested.toFile());


not sure the use of this. Does loadFromFile() have a side effect? Looks like it's no use. Or do we just want to make sure it does not corrupt and can load?

LoadFile if it fails would throw a ROcksDataBaseException the entire defrag would fail

jojochuang · 2025-11-24T19:37:13Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+          Table<byte[], byte[]> checkpointTable = checkpointDBStore.getTable(snapshotTableName, ByteArrayCodec.get(),
+              ByteArrayCodec.get());
+          checkpointTable.loadFromFile(tmpSstFile.toFile());


… content lock Change-Id: I07c9c2ecf969c9edc4f73e05abd5ce008e76ac9c

jojochuang

Ok the rest looks mostly good.
performIncrementalDefragmentation is too long and needs to simplify. But that can be split into a later task. I'd like to merge this one to unblock other PRs.

jojochuang · 2025-11-24T20:14:46Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+      String tableLowestValue = tableBounds.getLeft();
+      String tableHighestValue = tableBounds.getRight();
+
+      // If lowest value is not null and if the bucket prefix corresponding to the table is greater than lower then


The purpose is to filter out any keys not belong to the same bucket.

jojochuang · 2025-11-24T20:25:20Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+      for (Map.Entry<String, List<Pair<Path, SstFileInfo>>> entry : tableGroupedDeltaFiles.entrySet()) {
+        String table = entry.getKey();
+        List<Pair<Path, SstFileInfo>> deltaFiles = entry.getValue();
+        Path fileToBeIngested;
+        if (deltaFiles.size() == 1 && snapshotVersion > 0) {
+          // If there is only one delta file for the table and the snapshot version is also not 0 then the same delta
+          // file can reingested into the checkpointStore.
+          fileToBeIngested = deltaFiles.get(0).getKey();
+        } else {
+          Table<String, byte[]> snapshotTable = snapshot.get().getMetadataManager().getStore()
+              .getTable(table, StringCodec.get(), ByteArrayCodec.get());
+          Table<String, byte[]> previousSnapshotTable = previousSnapshot.get().getMetadataManager().getStore()
+              .getTable(table, StringCodec.get(), ByteArrayCodec.get());
+
+          String tableBucketPrefix = bucketPrefixInfo.getTablePrefix(table);
+          String sstFileReaderLowerBound = bucketPrefixInfo.getTablePrefix(entry.getKey());
+          String sstFileReaderUpperBound = null;
+          if (Strings.isNotEmpty(sstFileReaderLowerBound)) {
+            sstFileReaderUpperBound = getLexicographicallyHigherString(sstFileReaderLowerBound);
+          }
+          List<Path> deltaFilePaths = deltaFiles.stream().map(Pair::getKey).collect(Collectors.toList());
+          SstFileSetReader sstFileSetReader = new SstFileSetReader(deltaFilePaths);
+          fileToBeIngested = differTmpDir.resolve(table + "-" + UUID.randomUUID() + SST_FILE_EXTENSION);
+          // Delete all delta files after reingesting into the checkpointStore.
+          filesToBeDeleted.add(fileToBeIngested);
+          int deltaEntriesCount = 0;
+          try (ClosableIterator<String> keysToCheck =
+                   sstFileSetReader.getKeyStreamWithTombstone(sstFileReaderLowerBound, sstFileReaderUpperBound);
+               TableMergeIterator<String, byte[]> tableMergeIterator = new TableMergeIterator<>(keysToCheck,
+                  tableBucketPrefix, snapshotTable, previousSnapshotTable);
+               RDBSstFileWriter rdbSstFileWriter = new RDBSstFileWriter(fileToBeIngested.toFile())) {
+            while (tableMergeIterator.hasNext()) {
+              Table.KeyValue<String, List<byte[]>> kvs = tableMergeIterator.next();
+              // Check if the values are equal or if they are not equal then the value should be written to the
+              // delta sstFile.
+              if (!Arrays.equals(kvs.getValue().get(0), kvs.getValue().get(1))) {
+                try (CodecBuffer key = StringCodec.get().toHeapCodecBuffer(kvs.getKey())) {
+                  byte[] keyArray = key.asReadOnlyByteBuffer().array();
+                  byte[] val = kvs.getValue().get(0);
+                  // If the value is null then add a tombstone to the delta sstFile.
+                  if (val == null) {
+                    rdbSstFileWriter.delete(keyArray);
+                  } else {
+                    rdbSstFileWriter.put(keyArray, val);
+                  }
+                }
+                deltaEntriesCount++;
+              }
+            }
+          } catch (RocksDBException e) {
+            throw new RocksDatabaseException("Error while reading sst files.", e);
+          }
+          if (deltaEntriesCount == 0) {
+            // If there are no delta entries then delete the delta file. No need to ingest the file as a diff.
+            fileToBeIngested = null;
+          }
+        }
+        if (fileToBeIngested != null) {
+          if (!fileToBeIngested.toFile().exists()) {
+            throw new IOException("Delta file does not exist: " + fileToBeIngested);
+          }
+          Table checkpointTable = checkpointStore.getTable(table);
+          checkpointTable.loadFromFile(fileToBeIngested.toFile());
+        }
+      }


Too long. Please consider extracting this block into its own method.

Change-Id: If2f8107f66c1674f843ea445eeab7df8130b7a10

…ller functions Change-Id: I0c327fcec32670a00da3a06c1c1ac8320a531448

swamirishi · 2025-11-24T22:43:19Z

I am right now still working on the unit test cases(A few of them are already there). I will create a follow up jira for this just to unblock the next PRs.

Change-Id: Ib747352ff5b347a58717800ebb43824c50c1d645

Change-Id: Ic4f740d3b73399d9c14d95230bc09daafae20c0b

Change-Id: I50bdafa54faa54d5271299deb609f4a8b1cea66c

Change-Id: Ifaf410a79dbb96e9ae97e834b7150be88c27e0e1

Change-Id: I79d260ec71755e0894f335f46c91f51cdf886bf1

smengcl · 2025-11-25T07:52:31Z

...ager/src/test/java/org/apache/hadoop/ozone/om/snapshot/defrag/TestSnapshotDefragService.java

+    defragService.pause();
+    assertNotNull(defragService);
+
+    defragService.resume();
+    assertNotNull(defragService);


Should check running state inside

smengcl · 2025-11-25T07:52:46Z

...ager/src/test/java/org/apache/hadoop/ozone/om/snapshot/diff/delta/TestRDBDifferComputer.java

+
+

unused white lines

smengcl · 2025-11-25T07:56:05Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

  public SnapshotDefragService(long interval, TimeUnit unit, long serviceTimeout,
-      OzoneManager ozoneManager, OzoneConfiguration configuration) {
+      OzoneManager ozoneManager, OzoneConfiguration configuration) throws IOException {
    super("SnapshotDefragService", interval, unit, DEFRAG_CORE_POOL_SIZE,


Suggested change

super("SnapshotDefragService", interval, unit, DEFRAG_CORE_POOL_SIZE,

super(SnapshotDefragService.class.getSimpleName(), interval, unit, DEFRAG_CORE_POOL_SIZE,

smengcl · 2025-11-25T07:56:40Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

-    this.snapshotIdLocks = new MultiSnapshotLocks(omLock, SNAPSHOT_GC_LOCK, true, 1);
+    this.snapshotContentLocks = new MultiSnapshotLocks(omLock, SNAPSHOT_DB_CONTENT_LOCK, true, 1);
+    Path tmpDefragDirPath = ozoneManager.getMetadataManager().getSnapshotParentDir().toAbsolutePath()
+        .resolve("tmp_defrag");


nit: dir naming consistency

Suggested change

.resolve("tmp_defrag");

.resolve("defragTemp");

Also, extract this to a const in OzoneConsts instead.

Let me do it as part of the unit test PR

smengcl · 2025-11-25T07:57:37Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+    }
+    createDirectories(tmpDefragDirPath);
+    this.tmpDefragDir = tmpDefragDirPath.toString();
+    this.differTmpDir = tmpDefragDirPath.resolve("differSstFiles");


smengcl · 2025-11-25T08:00:48Z

...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

+   * @throws IOException if an I/O error occurs during processing
+   */
+  @VisibleForTesting
+  Pair<Path, Boolean> spillTableDiffIntoSstFile(List<Path> deltaFilePaths, Table<String, byte[]> snapshotTable,


We could move this and other helper methods to a separate static helper class to reduce length of SDS class

I might not want to do that specifically because this is very specific for SnapshotDefragService and doesn't have usecase outside of this scope. Would rather keep it here as a private method

swamirishi added 30 commits October 8, 2025 22:16

HDDS-13627. In memory Manager for Snapshot Local Data

252d338

Change-Id: I34536ff06efb7d5a4942853f0fd83942ab398b5f

HDDS-13767. Refactor SnapshotLocalDataYaml related code into OmSnapsh…

4099bc6

…otLocalDataManager Change-Id: I34536ff06efb7d5a4942853f0fd83942ab398b5f

HDDS-13767. Fix pmd

e02670c

Change-Id: I32bcaf2a1fb290f1790c02872a0230cd65586636

HDDS-13627. Fix checkstyle

79580e9

Change-Id: I985170e38fb8beeb784048e85a08a4c79e1aec97

Merge remote-tracking branch 'apache/master' into HEAD

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Change-Id: I33e6e6e825bf23c323ad7ed593d800a11720fa4f

Merge remote-tracking branch 'apache/master' into HEAD

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Change-Id: If30b2c766db82adde72145c8ecd3e590ef54cc2d

HDDS-13627. Add tests

afbc592

Change-Id: Id3f2c49050bc3476b9e0f5f51dacb6d9acc4c2f7

HDDS-13783. Implement locks for OmSnapshotLocalDataManager

70ac2c7

Change-Id: I432960725b4c6c55aa906b5780cc3027e41e10db

HDDS-13783. Implement locks for OmSnapshotLocalDataManager

b554cc7

Change-Id: I3c5514e5bbd251a2b5297d8f074cfde5c71fa543

HDDS-13783. Refactor inline variable

49eccfa

Change-Id: Ib5a9e6c91bdccba17820263c47eaf2c8400e930d

HDDS-13627. Refactor map data structure

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Change-Id: Ica36e0615c7bc6aa9b6a7f6fafafd0f830d4bafb

Merge remote-tracking branch 'origin/HDDS-13627' into HEAD

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Change-Id: I26b66f266bb7677e4b1078f5fcd9f2ce3a651a70 # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/OmSnapshotLocalDataManager.java

HDDS-13783. Add more condition to upsert

96689fa

Change-Id: I1d93dbc048a42cc55ff1f8ffa420e52f967527b8

HDDS-13783. Add java doc comment

0674299

Change-Id: I34202928a7a367dd0a1e57219317ff34de352b78

HDDS-13783. Add java doc comment

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Change-Id: Iad6f26cb71ec921c51ee2d138745df1a2663533f

HDDS-13783. Implement full lock

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Change-Id: Ic5f7e249cfb9cb3973cbcd4abd36b22a6ff8f5aa

HDDS-13783. Refactor and move modify method into WritableOmSnapshotLo…

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…calDataProvider Change-Id: I3a004b4b435075a4348960aeed642e8da71e7e72

HDDS-13783. Make full lock non static

686d0c7

Change-Id: I06990bc9ab8fc7e1eb7bec255646a650bd8c35fe

HDDS-13783. Fix remove

491a54b

Change-Id: I4c6c61c83aa9fadab8ecef854b99dcc0a89a2208

HDDS-13627. Fix findbugs

5e69ee9

Change-Id: I0e476322372a302572f1fe79cbf2e874bfeac2ed

HDDS-13785. Remove orphan versions from SnapshotLocalData Yaml file

d36622a

Change-Id: I31004e0c95dad64411c6fe848501a82f2f773cba

HDDS-13785. Fix findbugs

ee213d1

Change-Id: Id317c8b56e8b25c122b68eaf96599b9690d08f79

HDDS-13627. Fix tests

a95604e

Change-Id: Ie5e5f3dab4324103e8855dd15619d7755f0422e6

HDDS-13627. remove checksum interface

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Change-Id: I55bd5c3ef7fc32910a9111328638de2edffcd541

HDDS-13627. Fix test failures

20d7d6a

Change-Id: I880997d3eebdf378f14c203c61c2d63b2d17552e

HDDS-13785. Set defrag flag on previous snapshotId update

ae655cb

Change-Id: I13ba8e2fd012a3c964d657e83496c93a4f55a3be

Merge remote-tracking branch 'origin/HDDS-13627' into HEAD

25fa6ae

Change-Id: I20812cdf61886e55b4ead6003566e1d72db77f4a

HDDS-13783. Fix findbugs

d419283

Change-Id: I02de81771c9102f1212bf1962e65095910ab8207

swamirishi force-pushed the HDDS-13009 branch 2 times, most recently from bfbc38a to 6b856b7 Compare November 22, 2025 08:12

swamirishi added 5 commits November 22, 2025 03:14

Merge remote-tracking branch 'origin/HDDS-13978' into HEAD

6518866

Change-Id: I69cc5b8b37531aa51c7392c801eed4ff1ad42261

HDDS-13009. Move classes

1d399ae

Change-Id: I38eea689933bb979fefee9a8e44ec47d5fca1aff

HDDS-13993. Refactor and move SnapshotDefragService to snapshot package

843a1db

Change-Id: I510a85271278faeafe24c2f49d0afe2405211e40

Merge remote-tracking branch 'origin/HDDS-13993' into HEAD

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Change-Id: Icb3092ca1234fc7acc77780613f0fc2ed9a0ac51 # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

Merge remote-tracking branch 'apache/master' into HEAD

c731798

Change-Id: Ieb28da9fbc06b2729c9b118a75436ba8a3f1a70f # Conflicts: # hadoop-ozone/ozone-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java

smengcl mentioned this pull request Nov 24, 2025

HDDS-13009. Background snapshot defrag service #9227

Closed

HDDS-13009. Fix delete range bug

f4c4fcd

Change-Id: If61213983561ed6f8c283d12bd07bd2097df710d

jojochuang reviewed Nov 24, 2025

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smengcl reviewed Nov 24, 2025

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...-manager/src/main/java/org/apache/hadoop/ozone/om/snapshot/defrag/SnapshotDefragService.java Show resolved Hide resolved

jojochuang reviewed Nov 24, 2025

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HDDS-13009. Move deletion of snapshot directories outside of snapshot…

7d07377

… content lock Change-Id: I07c9c2ecf969c9edc4f73e05abd5ce008e76ac9c

jojochuang approved these changes Nov 24, 2025

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swamirishi added 2 commits November 24, 2025 17:11

HDDS-13009. Add unit test for needsDefrag method

cd2e529

Change-Id: If2f8107f66c1674f843ea445eeab7df8130b7a10

HDDS-13009. Split performIncrementalDefragmentation function into sma…

e8d1d8b

…ller functions Change-Id: I0c327fcec32670a00da3a06c1c1ac8320a531448

swamirishi added 2 commits November 24, 2025 17:56

HDDS-13009. Fix map grouping part in perform incremental Defragmentation

f7426fd

Change-Id: Ib747352ff5b347a58717800ebb43824c50c1d645

Merge remote-tracking branch 'apache/master' into HEAD

74c486a

Change-Id: Ic4f740d3b73399d9c14d95230bc09daafae20c0b

swamirishi marked this pull request as ready for review November 24, 2025 23:05

swamirishi added 3 commits November 24, 2025 18:59

HDDS-13009. Fix pmd findbugs

47682b4

Change-Id: I50bdafa54faa54d5271299deb609f4a8b1cea66c

HDDS-13009. Fix checkstyle

fc32f6f

Change-Id: Ifaf410a79dbb96e9ae97e834b7150be88c27e0e1

HDDS-13009. Fix snapshot cache lock

0572a12

Change-Id: I79d260ec71755e0894f335f46c91f51cdf886bf1

swamirishi merged commit 299b294 into apache:master Nov 25, 2025
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smengcl reviewed Nov 25, 2025

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		Table checkpointTable = checkpointStore.getTable(table);
		checkpointTable.loadFromFile(fileToBeIngested.toFile());

	super("SnapshotDefragService", interval, unit, DEFRAG_CORE_POOL_SIZE,
	super(SnapshotDefragService.class.getSimpleName(), interval, unit, DEFRAG_CORE_POOL_SIZE,

HDDS-13009. Background snapshot defrag service #9324

HDDS-13009. Background snapshot defrag service #9324

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swamirishi commented Nov 19, 2025

What changes were proposed in this pull request?

What is the link to the Apache JIRA

How was this patch tested?

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swamirishi Nov 26, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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jojochuang Nov 24, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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swamirishi commented Nov 24, 2025

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3 participants

swamirishi Nov 26, 2025 •

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jojochuang Nov 24, 2025 •

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