go/oasis-node/cmd/storage: Add command that flattens consensus dbs

.changelog/6311.feature.md

@@ -0,0 +1,8 @@
+go/oasis-node: Add new command for compacting consensus databases
+
+A new experimental command `oasis-node storage compact-experimental`
+was added.
+
+The command triggers manual compactions for all the consensus databases.
+This way node operators can forcefuly release disk space if enabling late
+pruning.

docs/oasis-node/cli.md

@@ -331,3 +331,36 @@ response:
 ```
 oasis1qqncl383h8458mr9cytatygctzwsx02n4c5f8ed7
 ```
+
+## storage
+
+### compact-experimental
+
+Run
+
+```sh
+oasis-node storage compact-experimental --config /path/to/config/file
+```
+
+to trigger manual compaction of consensus database instances:
+
+```sh
+{"caller":"storage.go:310","level":"info","module":"cmd/storage", \
+"msg":"Starting database compactions. This may take a while...", \
+"ts":"2025-10-08T09:18:22.185451554Z"}
+```
+
+If pruning was not enabled from the start or was recently increased, then even
+after successful pruning, the disk usage may stay the same.
+
+This is due to the LSM-tree storage design that BadgerDB uses. Concretely,
+deleting a key only marks it as ready to be deleted (a tombstone entry). The
+actual removal of the stale data happens later during the compaction.
+
+During normal operation, compaction happens in the background. However, BadgerDB
+is intentionally lazy, trading write throughput for disk space among other
+things. Therefore it is expected that in case of late pruning, the disk space
+may stay constant or not be reclaimed for a very long time.
+
+This command gives operators manual control to release disk space during
+maintenance periods.

go/consensus/cometbft/db/badger/badger.go

@@ -63,13 +63,7 @@ func New(fn string, noSuffix bool) (dbm.DB, error) {
 
 	logger := baseLogger.With("path", fn)
 
-	opts := badger.DefaultOptions(fn) // This may benefit from LSMOnlyOptions.
-	opts = opts.WithLogger(cmnBadger.NewLogAdapter(logger))
-	opts = opts.WithSyncWrites(false)
-	opts = opts.WithCompression(options.Snappy)
-	opts = opts.WithBlockCacheSize(64 * 1024 * 1024)
-
-	db, err := badger.Open(opts)
+	db, err := OpenBadger(fn, logger)
 	if err != nil {
 		return nil, fmt.Errorf("cometbft/db/badger: failed to open database: %w", err)
 	}
@@ -86,6 +80,17 @@ func New(fn string, noSuffix bool) (dbm.DB, error) {
 	return impl, nil
 }
 
+// OpenBadger opens badgerDB instance used for constructing instance that implements
+// CometBFT DB interface.
+func OpenBadger(path string, logger *logging.Logger) (*badger.DB, error) {
+	opts := badger.DefaultOptions(path) // This may benefit from LSMOnlyOptions.
+	opts = opts.WithLogger(cmnBadger.NewLogAdapter(logger))
+	opts = opts.WithSyncWrites(false)
+	opts = opts.WithCompression(options.Snappy)
+	opts = opts.WithBlockCacheSize(64 * 1024 * 1024)
+	return badger.Open(opts)
+}
+
 func (d *badgerDBImpl) Get(key []byte) ([]byte, error) {
 	k := toDBKey(key)
 

go/oasis-node/cmd/storage/storage.go

@@ -5,16 +5,22 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io/fs"
 	"os"
 	"path/filepath"
+	"strings"
 	"time"
 
+	badgerDB "github.com/dgraph-io/badger/v4"
 	"github.com/spf13/cobra"
 
 	"github.com/oasisprotocol/oasis-core/go/common"
 	"github.com/oasisprotocol/oasis-core/go/common/crypto/hash"
 	"github.com/oasisprotocol/oasis-core/go/common/logging"
 	"github.com/oasisprotocol/oasis-core/go/config"
+	"github.com/oasisprotocol/oasis-core/go/consensus/cometbft/abci"
+	cmtCommon "github.com/oasisprotocol/oasis-core/go/consensus/cometbft/common"
+	cmtDBProvider "github.com/oasisprotocol/oasis-core/go/consensus/cometbft/db/badger"
 	cmdCommon "github.com/oasisprotocol/oasis-core/go/oasis-node/cmd/common"
 	roothash "github.com/oasisprotocol/oasis-core/go/roothash/api"
 	"github.com/oasisprotocol/oasis-core/go/runtime/bundle"
@@ -53,6 +59,17 @@ var (
 		RunE:  doRenameNs,
 	}
 
+	storageCompactCmd = &cobra.Command{
+		Use:   "compact-experimental",
+		Args:  cobra.NoArgs,
+		Short: "EXPERIMENTAL: trigger compaction for all consensus databases",
+		Long: `EXPERIMENTAL: Optimize the storage for all consensus databases by manually compacting the underlying storage engines.
+
+WARNING: Ensure you have at least as much of a free disk as your largest database.
+`,
+		RunE: doDBCompactions,
+	}
+
 	logger = logging.GetLogger("cmd/storage")
 
 	pretty = cmdCommon.Isatty(1)
@@ -283,12 +300,119 @@ func doRenameNs(_ *cobra.Command, args []string) error {
 	return nil
 }
 
+func doDBCompactions(_ *cobra.Command, args []string) error {
+	if err := cmdCommon.Init(); err != nil {
+		cmdCommon.EarlyLogAndExit(err)
+	}
+
+	dataDir := cmdCommon.DataDir()
+
+	logger.Info("Starting database compactions. This may take a while...")
+
+	// Compact CometBFT managed databases: block store, evidence and state (NOT application state).
+	if err := compactCometDBs(dataDir); err != nil {
+		return fmt.Errorf("failed to compact CometBFT managed databases: %w", err)
+	}
+
+	if err := compactConsensusNodeDB(dataDir); err != nil {
+		return fmt.Errorf("failed to compact consensus NodeDB: %w", err)
+	}
+
+	return nil
+}
+
+func compactCometDBs(dataDir string) error {
+	paths, err := findCometDBs(dataDir)
+	if err != nil {
+		return fmt.Errorf("failed to find database instances: %w", err)
+	}
+	for _, path := range paths {
+		if err := compactCometDB(path); err != nil {
+			return fmt.Errorf("failed to compact %s: %w", path, err)
+		}
+	}
+	return nil
+}
+
+func compactCometDB(path string) error {
+	logger := logger.With("path", path)
+	db, err := cmtDBProvider.OpenBadger(path, logger)
+	if err != nil {
+		return fmt.Errorf("failed to open BadgerDB: %w", err)
+	}
+
+	if err := flattenBadgerDB(db, logger); err != nil {
+		return fmt.Errorf("failed to compact %s: %w", path, err)
+	}
+
+	return nil
+}
+
+func findCometDBs(dataDir string) ([]string, error) {
+	dir := fmt.Sprintf("%s/consensus/data", dataDir)
+
+	var dbDirs []string
+	err := filepath.WalkDir(dir, func(path string, d fs.DirEntry, err error) error {
+		if err != nil {
+			return err
+		}
+		if d.IsDir() && strings.HasSuffix(d.Name(), ".db") {
+			dbDirs = append(dbDirs, path)
+		}
+		return nil
+	})
+	if err != nil {
+		return nil, fmt.Errorf("failed to walk dir %s: %w", dataDir, err)
+	}
+
+	if len(dbDirs) == 0 {
+		return nil, fmt.Errorf("zero database instances found")
+	}
+
+	return dbDirs, nil
+}
+
+func flattenBadgerDB(db *badgerDB.DB, logger *logging.Logger) error {
+	logger.Info("compacting")
+
+	if err := db.Flatten(1); err != nil {
+		return fmt.Errorf("failed to flatten db: %w", err)
+	}
+
+	logger.Info("compaction completed")
+
+	return nil
+}
+
+func compactConsensusNodeDB(dataDir string) error {
+	ldb, ndb, _, err := abci.InitStateStorage(
+		&abci.ApplicationConfig{
+			DataDir:             filepath.Join(dataDir, cmtCommon.StateDir),
+			StorageBackend:      config.GlobalConfig.Storage.Backend,
+			MemoryOnlyStorage:   false,
+			ReadOnlyStorage:     false,
+			DisableCheckpointer: true,
+		},
+	)
+	if err != nil {
+		return fmt.Errorf("failed to initialize ABCI storage backend: %w", err)
+	}
+
+	// Close the resources. Both Close and Cleanup only close NodeDB.
+	// Closing both here, to prevent resource leaks if things change in the future.
+	defer ndb.Close()
+	defer ldb.Cleanup()
+
+	return ndb.Compact()
+}
+
 // Register registers the client sub-command and all of its children.
 func Register(parentCmd *cobra.Command) {
 	storageMigrateCmd.Flags().AddFlagSet(bundle.Flags)
 	storageCheckCmd.Flags().AddFlagSet(bundle.Flags)
 	storageCmd.AddCommand(storageMigrateCmd)
 	storageCmd.AddCommand(storageCheckCmd)
 	storageCmd.AddCommand(storageRenameNsCmd)
+	storageCmd.AddCommand(storageCompactCmd)
 	parentCmd.AddCommand(storageCmd)
 }

go/storage/mkvs/db/api/api.go

@@ -184,6 +184,12 @@ type NodeDB interface {
 	// Only the earliest version can be pruned, passing any other version will result in an error.
 	Prune(version uint64) error
 
+	// Compact triggers compaction of the NodeDB underlying storage engine.
+	//
+	// Warning: Depending on the NodeDB implementation this may be only safe to call when no
+	// writes are happening.
+	Compact() error
+
 	// Size returns the size of the database in bytes.
 	Size() (int64, error)
 
@@ -294,6 +300,10 @@ func (d *nopNodeDB) Prune(uint64) error {
 	return nil
 }
 
+func (d *nopNodeDB) Compact() error {
+	return nil
+}
+
 func (d *nopNodeDB) Size() (int64, error) {
 	return 0, nil
 }

go/storage/mkvs/db/badger/badger.go

@@ -101,6 +101,17 @@ func New(cfg *api.Config) (api.NodeDB, error) {
 	db.gc = cmnBadger.NewGCWorker(db.logger, db.db)
 	db.gc.Start()
 
+	// Setting a discard timestamp of the BadgerDB is not persistent and is currently
+	// only done during the prune operation.
+	//
+	// Imagine a scenario where during the previous boot of the BadgerDB, data was successfully pruned,
+	// but not yet compacted. Then the NodeDB is restarted, only this time with pruning disabled.
+	// Unless setting discard timestamp to the earliest version manually, the data stored for the
+	// already pruned versions may never be compacted, resulting in redundant disk usage.
+	if discardTs := versionToTs(db.GetEarliestVersion()) - 1; discardTs > tsMetadata {
+		db.db.SetDiscardTs(discardTs)
+	}
+
 	return db, nil
 }
 
@@ -915,6 +926,18 @@ func (d *badgerNodeDB) NewBatch(oldRoot node.Root, version uint64, chunk bool) (
 	}, nil
 }
 
+func (d *badgerNodeDB) Compact() error {
+	d.logger.Info("compacting")
+
+	if err := d.db.Flatten(1); err != nil {
+		return fmt.Errorf("failed to flatten db: %w", err)
+	}
+
+	d.logger.Info("compaction completed")
+
+	return nil
+}
+
 func (d *badgerNodeDB) Size() (int64, error) {
 	lsm, vlog := d.db.Size()
 	return lsm + vlog, nil

go/storage/mkvs/db/pathbadger/pathbadger.go

@@ -58,6 +58,17 @@ func New(cfg *api.Config) (api.NodeDB, error) {
 	db.gc = cmnBadger.NewGCWorker(db.logger, db.db)
 	db.gc.Start()
 
+	// Setting a discard timestamp of the BadgerDB is not persistent and is currently
+	// only done during the prune operation.
+	//
+	// Imagine a scenario where during the previous boot of the BadgerDB, data was successfully pruned,
+	// but not yet compacted. Then the NodeDB is restarted, only this time with pruning disabled.
+	// Unless setting discard timestamp to the earliest version manually, the data stored for the
+	// already pruned versions may never be compacted, resulting in redundant disk usage.
+	if discardTs := versionToTs(db.GetEarliestVersion()) - 1; discardTs > tsMetadata {
+		db.db.SetDiscardTs(discardTs)
+	}
+
 	return db, nil
 }
 
@@ -726,6 +737,18 @@ func (d *badgerNodeDB) NewBatch(oldRoot node.Root, version uint64, chunk bool) (
 	}, nil
 }
 
+func (d *badgerNodeDB) Compact() error {
+	d.logger.Info("compacting")
+
+	if err := d.db.Flatten(1); err != nil {
+		return fmt.Errorf("failed to flatten db: %w", err)
+	}
+
+	d.logger.Info("compaction completed")
+
+	return nil
+}
+
 // Implements api.NodeDB.
 func (d *badgerNodeDB) Size() (int64, error) {
 	lsm, vlog := d.db.Size()