go/storage: Refactor checkpointing interface

Previously the way storage checkpoints were implemented had several
drawbacks, namely:

- Since the checkpoint only streamed key/value pairs this prevented
  correct tree reconstruction as tree nodes also include a Round field
  which specifies the round at which a given tree node was created.

- While old checkpoints were streamed in chunks and thus could be
  resumed or streamed in parallel from multiple nodes, there was no
  support for verifying the integrity of a single chunk.

This change introduces an explicit checkpointing mechanism with a simple
file-based backend reference implementation. The same mechanism could
also be used in the future with Tendermint's app state sync proposal.

.changelog/2659.internal.md

@@ -0,0 +1,16 @@
+go/storage: Refactor checkpointing interface
+
+Previously the way storage checkpoints were implemented had several
+drawbacks, namely:
+
+- Since the checkpoint only streamed key/value pairs this prevented
+  correct tree reconstruction as tree nodes also include a Round field
+  which specifies the round at which a given tree node was created.
+
+- While old checkpoints were streamed in chunks and thus could be
+  resumed or streamed in parallel from multiple nodes, there was no
+  support for verifying the integrity of a single chunk.
+
+This change introduces an explicit checkpointing mechanism with a simple
+file-based backend reference implementation. The same mechanism could
+also be used in the future with Tendermint's app state sync proposal.

go/common/cbor/cbor.go

@@ -5,13 +5,22 @@
 // to always have the same serialization.
 package cbor
 
-import "github.com/fxamacker/cbor"
+import (
+	"io"
+
+	"github.com/fxamacker/cbor"
+)
 
 // RawMessage is a raw encoded CBOR value. It implements Marshaler and
 // Unmarshaler interfaces and can be used to delay CBOR decoding or
 // precompute a CBOR encoding.
 type RawMessage = cbor.RawMessage
 
+var encOptions = cbor.EncOptions{
+	Canonical:   true,
+	TimeRFC3339: false, // Second granular unix timestamps
+}
+
 // FixSliceForSerde will convert `nil` to `[]byte` to work around serde
 // brain damage.
 func FixSliceForSerde(b []byte) []byte {
@@ -23,10 +32,7 @@ func FixSliceForSerde(b []byte) []byte {
 
 // Marshal serializes a given type into a CBOR byte vector.
 func Marshal(src interface{}) []byte {
-	b, err := cbor.Marshal(src, cbor.EncOptions{
-		Canonical:   true,
-		TimeRFC3339: false, // Second granular unix timestamps
-	})
+	b, err := cbor.Marshal(src, encOptions)
 	if err != nil {
 		panic("common/cbor: failed to marshal: " + err.Error())
 	}
@@ -49,3 +55,13 @@ func MustUnmarshal(data []byte, dst interface{}) {
 		panic(err)
 	}
 }
+
+// NewEncoder creates a new CBOR encoder.
+func NewEncoder(w io.Writer) *cbor.Encoder {
+	return cbor.NewEncoder(w, encOptions)
+}
+
+// NewDecoder creates a new CBOR decoder.
+func NewDecoder(r io.Reader) *cbor.Decoder {
+	return cbor.NewDecoder(r)
+}

go/common/crypto/hash/hash.go

@@ -8,6 +8,7 @@ import (
 	"encoding/base64"
 	"encoding/hex"
 	"errors"
+	"hash"
 
 	"github.com/oasislabs/oasis-core/go/common/cbor"
 )
@@ -107,3 +108,27 @@ func (h *Hash) IsEmpty() bool {
 func (h Hash) String() string {
 	return hex.EncodeToString(h[:])
 }
+
+// Builder is a hash builder that can be used to compute hashes iteratively.
+type Builder struct {
+	hasher hash.Hash
+}
+
+// Write adds more data to the running hash.
+// It never returns an error.
+func (b *Builder) Write(p []byte) (int, error) {
+	return b.hasher.Write(p)
+}
+
+// Build returns the current hash.
+// It does not change the underlying hash state.
+func (b *Builder) Build() (h Hash) {
+	sum := b.hasher.Sum([]byte{})
+	_ = h.UnmarshalBinary(sum[:])
+	return
+}
+
+// NewBuilder creates a new hash builder.
+func NewBuilder() *Builder {
+	return &Builder{hasher: sha512.New512_256()}
+}

go/go.mod

@@ -29,6 +29,7 @@ require (
 	github.com/glycerine/goconvey v0.0.0-20190410193231-58a59202ab31 // indirect
 	github.com/go-kit/kit v0.9.0
 	github.com/golang/protobuf v1.3.2
+	github.com/golang/snappy v0.0.1
 	github.com/google/gofuzz v1.0.0
 	github.com/gopherjs/gopherjs v0.0.0-20190430165422-3e4dfb77656c // indirect
 	github.com/grpc-ecosystem/go-grpc-middleware v1.0.0

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

@@ -4,6 +4,7 @@ import (
 	"context"
 	"crypto/tls"
 	"crypto/x509"
+	"io"
 
 	"github.com/pkg/errors"
 	"google.golang.org/grpc"
@@ -19,6 +20,7 @@ import (
 	"github.com/oasislabs/oasis-core/go/common/node"
 	scheduler "github.com/oasislabs/oasis-core/go/scheduler/api"
 	storage "github.com/oasislabs/oasis-core/go/storage/api"
+	"github.com/oasislabs/oasis-core/go/storage/mkvs/urkel/checkpoint"
 	"github.com/oasislabs/oasis-core/go/storage/mkvs/urkel/syncer"
 )
 
@@ -119,8 +121,12 @@ func (hns *honestNodeStorage) GetDiff(ctx context.Context, request *storage.GetD
 	return hns.client.GetDiff(ctx, request)
 }
 
-func (hns *honestNodeStorage) GetCheckpoint(ctx context.Context, request *storage.GetCheckpointRequest) (storage.WriteLogIterator, error) {
-	return hns.client.GetCheckpoint(ctx, request)
+func (hns *honestNodeStorage) GetCheckpoints(ctx context.Context, request *checkpoint.GetCheckpointsRequest) ([]*checkpoint.Metadata, error) {
+	return hns.client.GetCheckpoints(ctx, request)
+}
+
+func (hns *honestNodeStorage) GetCheckpointChunk(ctx context.Context, chunk *checkpoint.ChunkMetadata, w io.Writer) error {
+	return hns.client.GetCheckpointChunk(ctx, chunk, w)
 }
 
 func (hns *honestNodeStorage) Cleanup() {

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

@@ -22,6 +22,7 @@ import (
 	storageAPI "github.com/oasislabs/oasis-core/go/storage/api"
 	storageClient "github.com/oasislabs/oasis-core/go/storage/client"
 	storageDatabase "github.com/oasislabs/oasis-core/go/storage/database"
+	"github.com/oasislabs/oasis-core/go/storage/mkvs/urkel"
 )
 
 const cfgExportDir = "storage.export.dir"
@@ -98,26 +99,14 @@ func exportRuntime(dataDir, destDir string, id common.Namespace, rtg *registry.R
 	<-storageBackend.Initialized()
 	defer storageBackend.Cleanup()
 
-	// Get the checkpoint iterator.
 	root := storageAPI.Root{
 		Namespace: id,
 		Round:     rtg.Round,
 		Hash:      rtg.StateRoot,
 	}
-	it, err := storageBackend.GetCheckpoint(context.Background(),
-		&storageAPI.GetCheckpointRequest{
-			Root: root,
-		},
-	)
-	if err != nil {
-		logger.Error("failed getting checkpoint",
-			"err", err,
-			"namespace", root.Namespace,
-			"round", root.Round,
-			"root", root.Hash,
-		)
-		return err
-	}
+	tree := urkel.NewWithRoot(storageBackend, nil, root)
+	it := tree.NewIterator(context.Background(), urkel.IteratorPrefetch(10_000))
+	defer it.Close()
 
 	fn := fmt.Sprintf("storage-dump-%v-%d.json",
 		root.Namespace.String(),
@@ -127,7 +116,7 @@ func exportRuntime(dataDir, destDir string, id common.Namespace, rtg *registry.R
 	return exportIterator(fn, &root, it)
 }
 
-func exportIterator(fn string, root *storageAPI.Root, it storageAPI.WriteLogIterator) error {
+func exportIterator(fn string, root *storageAPI.Root, it urkel.Iterator) error {
 	// Create the dump file, and initialize a JSON stream encoder.
 	f, err := os.Create(fn)
 	if err != nil {
@@ -152,35 +141,18 @@ func exportIterator(fn string, root *storageAPI.Root, it storageAPI.WriteLogIter
 		return err
 	}
 
-	// Dump the write log.
-	for {
-		more, err := it.Next()
-		if err != nil {
-			logger.Error("failed to fetch next item from write log iterator",
-				"err", err,
-			)
-			return err
-		}
-
-		if !more {
-			return nil
-		}
-
-		val, err := it.Value()
-		if err != nil {
-			logger.Error("failed to get value from write log iterator",
-				"err", err,
-			)
-			return err
-		}
-
-		if err = enc.Encode([][]byte{val.Key, val.Value}); err != nil {
+	// Dump the tree.
+	for it.Rewind(); it.Valid(); it.Next() {
+		key, value := it.Key(), it.Value()
+		if err = enc.Encode([][]byte{key, value}); err != nil {
 			logger.Error("failed to encode write log entry",
 				"err", err,
 			)
 			return err
 		}
 	}
+
+	return nil
 }
 
 func newDirectStorageBackend(dataDir string, namespace common.Namespace) (storageAPI.Backend, error) {

go/oasis-node/cmd/registry/runtime/runtime.go

@@ -62,6 +62,9 @@ const (
 	CfgStorageMaxApplyOps             = "runtime.storage.max_apply_ops"
 	CfgStorageMaxMergeRoots           = "runtime.storage.max_merge_roots"
 	CfgStorageMaxMergeOps             = "runtime.storage.max_merge_ops"
+	CfgStorageCheckpointInterval      = "runtime.storage.checkpoint_interval"
+	CfgStorageCheckpointNumKept       = "runtime.storage.checkpoint_num_kept"
+	CfgStorageCheckpointChunkSize     = "runtime.storage.checkpoint_chunk_size"
 
 	// Transaction scheduler flags.
 	CfgTxnSchedulerGroupSize         = "runtime.txn_scheduler.group_size"
@@ -385,6 +388,9 @@ func runtimeFromFlags() (*registry.Runtime, signature.Signer, error) {
 			MaxApplyOps:             viper.GetUint64(CfgStorageMaxApplyOps),
 			MaxMergeRoots:           viper.GetUint64(CfgStorageMaxMergeRoots),
 			MaxMergeOps:             viper.GetUint64(CfgStorageMaxMergeOps),
+			CheckpointInterval:      viper.GetUint64(CfgStorageCheckpointInterval),
+			CheckpointNumKept:       viper.GetUint64(CfgStorageCheckpointNumKept),
+			CheckpointChunkSize:     viper.GetUint64(CfgStorageCheckpointChunkSize),
 		},
 	}
 	if teeHardware == node.TEEHardwareIntelSGX {
@@ -518,6 +524,9 @@ func init() {
 	runtimeFlags.Uint64(CfgStorageMaxApplyOps, 2, "Maximum number of apply operations in a batch")
 	runtimeFlags.Uint64(CfgStorageMaxMergeRoots, 8, "Maximum number of merge roots")
 	runtimeFlags.Uint64(CfgStorageMaxMergeOps, 2, "Maximum number of merge operations in a batch")
+	runtimeFlags.Uint64(CfgStorageCheckpointInterval, 0, "Storage checkpoint interval (in rounds)")
+	runtimeFlags.Uint64(CfgStorageCheckpointNumKept, 0, "Number of storage checkpoints to keep")
+	runtimeFlags.Uint64(CfgStorageCheckpointChunkSize, 0, "Storage checkpoint chunk size")
 
 	// Init Admission policy flags.
 	runtimeFlags.String(CfgAdmissionPolicy, "", "What type of node admission policy to have")

go/oasis-node/node_test.go

@@ -37,6 +37,7 @@ import (
 	staking "github.com/oasislabs/oasis-core/go/staking/api"
 	stakingTests "github.com/oasislabs/oasis-core/go/staking/tests"
 	"github.com/oasislabs/oasis-core/go/storage"
+	storageAPI "github.com/oasislabs/oasis-core/go/storage/api"
 	storageClient "github.com/oasislabs/oasis-core/go/storage/client"
 	storageClientTests "github.com/oasislabs/oasis-core/go/storage/client/tests"
 	storageTests "github.com/oasislabs/oasis-core/go/storage/tests"
@@ -388,11 +389,13 @@ func testStorage(t *testing.T, node *testNode) {
 	require.NoError(t, err, "TempDir")
 	defer os.RemoveAll(dataDir)
 
-	storage, err := storage.New(context.Background(), dataDir, testRuntimeID, node.Identity, node.Scheduler, node.Registry)
+	backend, err := storage.New(context.Background(), dataDir, testRuntimeID, node.Identity, node.Scheduler, node.Registry)
 	require.NoError(t, err, "storage.New")
-	defer storage.Cleanup()
+	defer backend.Cleanup()
+	// We are always testing a local storage backend here.
+	localBackend := backend.(storageAPI.LocalBackend)
 
-	storageTests.StorageImplementationTests(t, storage, testRuntimeID, 0)
+	storageTests.StorageImplementationTests(t, localBackend, backend, testRuntimeID, 0)
 }
 
 func testRegistry(t *testing.T, node *testNode) {
@@ -462,6 +465,11 @@ func testClient(t *testing.T, node *testNode) {
 func testStorageClientWithNode(t *testing.T, node *testNode) {
 	ctx := context.Background()
 
+	// Get the local storage backend (the one that the client is connecting to).
+	rt, err := node.RuntimeRegistry.GetRuntime(testRuntimeID)
+	require.NoError(t, err, "GetRuntime")
+	localBackend := rt.Storage().(storageAPI.LocalBackend)
+
 	client, err := storageClient.NewStatic(ctx, testRuntimeID, node.Identity, node.Registry, node.Identity.NodeSigner.Public())
 	require.NoError(t, err, "NewStatic")
 
@@ -470,7 +478,7 @@ func testStorageClientWithNode(t *testing.T, node *testNode) {
 	blk, err := node.RootHash.GetLatestBlock(ctx, testRuntimeID, consensusAPI.HeightLatest)
 	require.NoError(t, err, "GetLatestBlock")
 
-	storageTests.StorageImplementationTests(t, client, testRuntimeID, blk.Header.Round+1)
+	storageTests.StorageImplementationTests(t, localBackend, client, testRuntimeID, blk.Header.Round+1)
 }
 
 func testStorageClientWithoutNode(t *testing.T, node *testNode) {

go/oasis-test-runner/oasis/args.go

@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"path/filepath"
 	"strconv"
+	"time"
 
 	"github.com/oasislabs/oasis-core/go/common"
 	commonGrpc "github.com/oasislabs/oasis-core/go/common/grpc"
@@ -320,6 +321,13 @@ func (args *argBuilder) workerStorageDebugIgnoreApplies(ignore bool) *argBuilder
 	return args
 }
 
+func (args *argBuilder) workerStorageCheckpointCheckInterval(interval time.Duration) *argBuilder {
+	if interval > 0 {
+		args.vec = append(args.vec, "--"+workerStorage.CfgWorkerCheckpointCheckInterval, interval.String())
+	}
+	return args
+}
+
 func (args *argBuilder) workerTxnschedulerCheckTxEnabled() *argBuilder {
 	args.vec = append(args.vec, "--"+txnscheduler.CfgCheckTxEnabled)
 	return args

go/oasis-test-runner/oasis/cli/registry.go

@@ -77,6 +77,9 @@ func (r *RegistryHelpers) GenerateRegisterRuntimeTx(
 			"--"+cmdRegRt.CfgStorageMaxApplyOps, strconv.FormatUint(runtime.Storage.MaxApplyOps, 10),
 			"--"+cmdRegRt.CfgStorageMaxMergeRoots, strconv.FormatUint(runtime.Storage.MaxMergeRoots, 10),
 			"--"+cmdRegRt.CfgStorageMaxMergeOps, strconv.FormatUint(runtime.Storage.MaxMergeOps, 10),
+			"--"+cmdRegRt.CfgStorageCheckpointInterval, strconv.FormatUint(runtime.Storage.CheckpointInterval, 10),
+			"--"+cmdRegRt.CfgStorageCheckpointNumKept, strconv.FormatUint(runtime.Storage.CheckpointNumKept, 10),
+			"--"+cmdRegRt.CfgStorageCheckpointChunkSize, strconv.FormatUint(runtime.Storage.CheckpointChunkSize, 10),
 			"--"+cmdRegRt.CfgTxnSchedulerGroupSize, strconv.FormatUint(runtime.TxnScheduler.GroupSize, 10),
 			"--"+cmdRegRt.CfgTxnSchedulerAlgorithm, runtime.TxnScheduler.Algorithm,
 			"--"+cmdRegRt.CfgTxnSchedulerBatchFlushTimeout, runtime.TxnScheduler.BatchFlushTimeout.String(),

go/oasis-test-runner/oasis/controller.go

@@ -9,6 +9,7 @@ import (
 	registry "github.com/oasislabs/oasis-core/go/registry/api"
 	runtimeClient "github.com/oasislabs/oasis-core/go/runtime/client/api"
 	staking "github.com/oasislabs/oasis-core/go/staking/api"
+	storage "github.com/oasislabs/oasis-core/go/storage/api"
 )
 
 // Controller is a network controller that connects to one of the
@@ -21,6 +22,7 @@ type Controller struct {
 	Staking       staking.Backend
 	Registry      registry.Backend
 	RuntimeClient runtimeClient.RuntimeClient
+	Storage       storage.Backend
 
 	conn *grpc.ClientConn
 }
@@ -49,6 +51,7 @@ func NewController(socketPath string) (*Controller, error) {
 		Staking:         staking.NewStakingClient(conn),
 		Registry:        registry.NewRegistryClient(conn),
 		RuntimeClient:   runtimeClient.NewRuntimeClient(conn),
+		Storage:         storage.NewStorageClient(conn),
 
 		conn: conn,
 	}, nil

go/oasis-test-runner/oasis/fixture.go

@@ -2,6 +2,7 @@ package oasis
 
 import (
 	"fmt"
+	"time"
 
 	"github.com/oasislabs/oasis-core/go/common"
 	"github.com/oasislabs/oasis-core/go/common/node"
@@ -264,7 +265,8 @@ type StorageWorkerFixture struct { // nolint: maligned
 
 	Sentries []int `json:"sentries,omitempty"`
 
-	IgnoreApplies bool `json:"ignore_applies,omitempty"`
+	CheckpointCheckInterval time.Duration `json:"checkpoint_check_interval,omitempty"`
+	IgnoreApplies           bool          `json:"ignore_applies,omitempty"`
 }
 
 // Create instantiates the storage worker described by the fixture.
@@ -280,10 +282,11 @@ func (f *StorageWorkerFixture) Create(net *Network) (*Storage, error) {
 			LogWatcherHandlerFactories: f.LogWatcherHandlerFactories,
 			SubmissionGasPrice:         f.SubmissionGasPrice,
 		},
-		Backend:       f.Backend,
-		Entity:        entity,
-		SentryIndices: f.Sentries,
-		IgnoreApplies: f.IgnoreApplies,
+		Backend:                 f.Backend,
+		Entity:                  entity,
+		SentryIndices:           f.Sentries,
+		CheckpointCheckInterval: f.CheckpointCheckInterval,
+		IgnoreApplies:           f.IgnoreApplies,
 	})
 }