X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6bf9e1a4b5640f3cdd057810f0c9b8a945bb88bd..607033c33f2001c194fe8c68d0dc17e4bde849da:/sdk/go/arvados/fs_collection.go diff --git a/sdk/go/arvados/fs_collection.go b/sdk/go/arvados/fs_collection.go index 1de558a1bd..26012e2406 100644 --- a/sdk/go/arvados/fs_collection.go +++ b/sdk/go/arvados/fs_collection.go @@ -5,6 +5,7 @@ package arvados import ( + "bytes" "context" "encoding/json" "fmt" @@ -38,14 +39,25 @@ type CollectionFileSystem interface { // Total data bytes in all files. Size() int64 - - // Memory consumed by buffered file data. - memorySize() int64 } type collectionFileSystem struct { fileSystem - uuid string + uuid string + savedPDH atomic.Value + replicas int + storageClasses []string + // guessSignatureTTL tracks a lower bound for the server's + // configured BlobSigningTTL. The guess is initially zero, and + // increases when we come across a signature with an expiry + // time further in the future than the previous guess. + // + // When the guessed TTL is much smaller than the real TTL, + // preemptive signature refresh is delayed or missed entirely, + // which is OK. + guessSignatureTTL time.Duration + holdCheckChanges time.Time + lockCheckChanges sync.Mutex } // FileSystem returns a CollectionFileSystem for the collection. @@ -55,12 +67,17 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile modTime = time.Now() } fs := &collectionFileSystem{ - uuid: c.UUID, + uuid: c.UUID, + storageClasses: c.StorageClassesDesired, fileSystem: fileSystem{ fsBackend: keepBackend{apiClient: client, keepClient: kc}, thr: newThrottle(concurrentWriters), }, } + fs.savedPDH.Store(c.PortableDataHash) + if r := c.ReplicationDesired; r != nil { + fs.replicas = *r + } root := &dirnode{ fs: fs, treenode: treenode{ @@ -68,6 +85,7 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile name: ".", mode: os.ModeDir | 0755, modTime: modTime, + sys: func() interface{} { return c }, }, inodes: make(map[string]inode), }, @@ -81,18 +99,114 @@ func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFile return fs, nil } -func backdateTree(n inode, modTime time.Time) { +// caller must have lock (or guarantee no concurrent accesses somehow) +func eachNode(n inode, ffunc func(*filenode), dfunc func(*dirnode)) { switch n := n.(type) { case *filenode: - n.fileinfo.modTime = modTime + if ffunc != nil { + ffunc(n) + } case *dirnode: - n.fileinfo.modTime = modTime + if dfunc != nil { + dfunc(n) + } for _, n := range n.inodes { - backdateTree(n, modTime) + eachNode(n, ffunc, dfunc) } } } +// caller must have lock (or guarantee no concurrent accesses somehow) +func backdateTree(n inode, modTime time.Time) { + eachNode(n, func(fn *filenode) { + fn.fileinfo.modTime = modTime + }, func(dn *dirnode) { + dn.fileinfo.modTime = modTime + }) +} + +// Approximate portion of signature TTL remaining, usually between 0 +// and 1, or negative if some signatures have expired. +func (fs *collectionFileSystem) signatureTimeLeft() (float64, time.Duration) { + var ( + now = time.Now() + earliest = now.Add(time.Hour * 24 * 7 * 365) + latest time.Time + ) + fs.fileSystem.root.RLock() + eachNode(fs.root, func(fn *filenode) { + fn.Lock() + defer fn.Unlock() + for _, seg := range fn.segments { + seg, ok := seg.(storedSegment) + if !ok { + continue + } + expiryTime, err := signatureExpiryTime(seg.locator) + if err != nil { + continue + } + if expiryTime.Before(earliest) { + earliest = expiryTime + } + if expiryTime.After(latest) { + latest = expiryTime + } + } + }, nil) + fs.fileSystem.root.RUnlock() + + if latest.IsZero() { + // No signatures == 100% of TTL remaining. + return 1, 1 + } + + ttl := latest.Sub(now) + fs.fileSystem.root.Lock() + { + if ttl > fs.guessSignatureTTL { + // ttl is closer to the real TTL than + // guessSignatureTTL. + fs.guessSignatureTTL = ttl + } else { + // Use the previous best guess to compute the + // portion remaining (below, after unlocking + // mutex). + ttl = fs.guessSignatureTTL + } + } + fs.fileSystem.root.Unlock() + + return earliest.Sub(now).Seconds() / ttl.Seconds(), ttl +} + +func (fs *collectionFileSystem) updateSignatures(newmanifest string) { + newLoc := map[string]string{} + for _, tok := range regexp.MustCompile(`\S+`).FindAllString(newmanifest, -1) { + if mBlkRe.MatchString(tok) { + newLoc[stripAllHints(tok)] = tok + } + } + fs.fileSystem.root.Lock() + defer fs.fileSystem.root.Unlock() + eachNode(fs.root, func(fn *filenode) { + fn.Lock() + defer fn.Unlock() + for idx, seg := range fn.segments { + seg, ok := seg.(storedSegment) + if !ok { + continue + } + loc, ok := newLoc[stripAllHints(seg.locator)] + if !ok { + continue + } + seg.locator = loc + fn.segments[idx] = seg + } + }, nil) +} + func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime time.Time) (node inode, err error) { if name == "" || name == "." || name == ".." { return nil, ErrInvalidArgument @@ -176,7 +290,88 @@ func (fs *collectionFileSystem) Truncate(int64) error { return ErrInvalidOperation } +// Check for and incorporate upstream changes -- unless that has +// already been done recently, in which case this func is a no-op. +func (fs *collectionFileSystem) checkChangesOnServer() error { + if fs.uuid == "" && fs.savedPDH.Load() == "" { + return nil + } + + // First try UUID if any, then last known PDH. Stop if all + // signatures are new enough. + checkingAll := false + for _, id := range []string{fs.uuid, fs.savedPDH.Load().(string)} { + if id == "" { + continue + } + + fs.lockCheckChanges.Lock() + if !checkingAll && fs.holdCheckChanges.After(time.Now()) { + fs.lockCheckChanges.Unlock() + return nil + } + remain, ttl := fs.signatureTimeLeft() + if remain > 0.01 && !checkingAll { + fs.holdCheckChanges = time.Now().Add(ttl / 100) + } + fs.lockCheckChanges.Unlock() + + if remain >= 0.5 { + break + } + checkingAll = true + var coll Collection + err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+id, nil, map[string]interface{}{"select": []string{"portable_data_hash", "manifest_text"}}) + if err != nil { + continue + } + fs.updateSignatures(coll.ManifestText) + } + return nil +} + +// Refresh signature on a single locator, if necessary. Assume caller +// has lock. If an update is needed, and there are any storedSegments +// whose signatures can be updated, start a background task to update +// them asynchronously when the caller releases locks. +func (fs *collectionFileSystem) refreshSignature(locator string) string { + exp, err := signatureExpiryTime(locator) + if err != nil || exp.Sub(time.Now()) > time.Minute { + // Synchronous update is not needed. Start an + // asynchronous update if needed. + go fs.checkChangesOnServer() + return locator + } + var manifests string + for _, id := range []string{fs.uuid, fs.savedPDH.Load().(string)} { + if id == "" { + continue + } + var coll Collection + err := fs.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+id, nil, map[string]interface{}{"select": []string{"portable_data_hash", "manifest_text"}}) + if err != nil { + continue + } + manifests += coll.ManifestText + } + hash := stripAllHints(locator) + for _, tok := range regexp.MustCompile(`\S+`).FindAllString(manifests, -1) { + if mBlkRe.MatchString(tok) { + if stripAllHints(tok) == hash { + locator = tok + break + } + } + } + go fs.updateSignatures(manifests) + return locator +} + func (fs *collectionFileSystem) Sync() error { + err := fs.checkChangesOnServer() + if err != nil { + return err + } if fs.uuid == "" { return nil } @@ -184,19 +379,34 @@ func (fs *collectionFileSystem) Sync() error { if err != nil { return fmt.Errorf("sync failed: %s", err) } - coll := &Collection{ + if PortableDataHash(txt) == fs.savedPDH.Load() { + // No local changes since last save or initial load. + return nil + } + coll := Collection{ UUID: fs.uuid, ManifestText: txt, } - err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, nil, map[string]interface{}{ + + selectFields := []string{"uuid", "portable_data_hash"} + fs.lockCheckChanges.Lock() + remain, _ := fs.signatureTimeLeft() + fs.lockCheckChanges.Unlock() + if remain < 0.5 { + selectFields = append(selectFields, "manifest_text") + } + + err = fs.RequestAndDecode(&coll, "PUT", "arvados/v1/collections/"+fs.uuid, nil, map[string]interface{}{ "collection": map[string]string{ "manifest_text": coll.ManifestText, }, - "select": []string{"uuid"}, + "select": selectFields, }) if err != nil { return fmt.Errorf("sync failed: update %s: %s", fs.uuid, err) } + fs.updateSignatures(coll.ManifestText) + fs.savedPDH.Store(coll.PortableDataHash) return nil } @@ -232,10 +442,10 @@ func (fs *collectionFileSystem) Flush(path string, shortBlocks bool) error { return dn.flush(context.TODO(), names, flushOpts{sync: false, shortBlocks: shortBlocks}) } -func (fs *collectionFileSystem) memorySize() int64 { +func (fs *collectionFileSystem) MemorySize() int64 { fs.fileSystem.root.Lock() defer fs.fileSystem.root.Unlock() - return fs.fileSystem.root.(*dirnode).memorySize() + return fs.fileSystem.root.(*dirnode).MemorySize() } func (fs *collectionFileSystem) MarshalManifest(prefix string) (string, error) { @@ -248,6 +458,14 @@ func (fs *collectionFileSystem) Size() int64 { return fs.fileSystem.root.(*dirnode).TreeSize() } +func (fs *collectionFileSystem) Snapshot() (inode, error) { + return fs.fileSystem.root.Snapshot() +} + +func (fs *collectionFileSystem) Splice(r inode) error { + return fs.fileSystem.root.Splice(r) +} + // filenodePtr is an offset into a file that is (usually) efficient to // seek to. Specifically, if filenode.repacked==filenodePtr.repacked // then @@ -324,7 +542,7 @@ func (fn *filenode) seek(startPtr filenodePtr) (ptr filenodePtr) { // filenode implements inode. type filenode struct { parent inode - fs FileSystem + fs *collectionFileSystem fileinfo fileinfo segments []segment // number of times `segments` has changed in a @@ -371,6 +589,10 @@ func (fn *filenode) Read(p []byte, startPtr filenodePtr) (n int, ptr filenodePtr err = io.EOF return } + if ss, ok := fn.segments[ptr.segmentIdx].(storedSegment); ok { + ss.locator = fn.fs.refreshSignature(ss.locator) + fn.segments[ptr.segmentIdx] = ss + } n, err = fn.segments[ptr.segmentIdx].ReadAt(p, int64(ptr.segmentOff)) if n > 0 { ptr.off += int64(n) @@ -613,7 +835,11 @@ func (fn *filenode) pruneMemSegments() { fn.fs.throttle().Acquire() go func() { defer close(done) - locator, _, err := fn.FS().PutB(buf) + resp, err := fn.FS().BlockWrite(context.Background(), BlockWriteOptions{ + Data: buf, + Replicas: fn.fs.replicas, + StorageClasses: fn.fs.storageClasses, + }) fn.fs.throttle().Release() fn.Lock() defer fn.Unlock() @@ -634,7 +860,7 @@ func (fn *filenode) pruneMemSegments() { fn.memsize -= int64(len(buf)) fn.segments[idx] = storedSegment{ kc: fn.FS(), - locator: locator, + locator: resp.Locator, size: len(buf), offset: 0, length: len(buf), @@ -659,6 +885,47 @@ func (fn *filenode) waitPrune() { } } +func (fn *filenode) Snapshot() (inode, error) { + fn.RLock() + defer fn.RUnlock() + segments := make([]segment, 0, len(fn.segments)) + for _, seg := range fn.segments { + segments = append(segments, seg.Slice(0, seg.Len())) + } + return &filenode{ + fileinfo: fn.fileinfo, + segments: segments, + }, nil +} + +func (fn *filenode) Splice(repl inode) error { + repl, err := repl.Snapshot() + if err != nil { + return err + } + fn.parent.Lock() + defer fn.parent.Unlock() + fn.Lock() + defer fn.Unlock() + _, err = fn.parent.Child(fn.fileinfo.name, func(inode) (inode, error) { return repl, nil }) + if err != nil { + return err + } + switch repl := repl.(type) { + case *dirnode: + repl.parent = fn.parent + repl.fileinfo.name = fn.fileinfo.name + repl.setTreeFS(fn.fs) + case *filenode: + repl.parent = fn.parent + repl.fileinfo.name = fn.fileinfo.name + repl.fs = fn.fs + default: + return fmt.Errorf("cannot splice snapshot containing %T: %w", repl, ErrInvalidArgument) + } + return nil +} + type dirnode struct { fs *collectionFileSystem treenode @@ -677,6 +944,7 @@ func (dn *dirnode) Child(name string, replace func(inode) (inode, error)) (inode if err != nil { return nil, err } + coll.UUID = dn.fs.uuid data, err := json.Marshal(&coll) if err == nil { data = append(data, '\n') @@ -750,7 +1018,11 @@ func (dn *dirnode) commitBlock(ctx context.Context, refs []fnSegmentRef, bufsize go func() { defer close(done) defer close(errs) - locator, _, err := dn.fs.PutB(block) + resp, err := dn.fs.BlockWrite(context.Background(), BlockWriteOptions{ + Data: block, + Replicas: dn.fs.replicas, + StorageClasses: dn.fs.storageClasses, + }) dn.fs.throttle().Release() if err != nil { errs <- err @@ -782,7 +1054,7 @@ func (dn *dirnode) commitBlock(ctx context.Context, refs []fnSegmentRef, bufsize data := ref.fn.segments[ref.idx].(*memSegment).buf ref.fn.segments[ref.idx] = storedSegment{ kc: dn.fs, - locator: locator, + locator: resp.Locator, size: blocksize, offset: offsets[idx], length: len(data), @@ -879,24 +1151,26 @@ func (dn *dirnode) flush(ctx context.Context, names []string, opts flushOpts) er } // caller must have write lock. -func (dn *dirnode) memorySize() (size int64) { +func (dn *dirnode) MemorySize() (size int64) { for _, name := range dn.sortedNames() { node := dn.inodes[name] node.Lock() defer node.Unlock() switch node := node.(type) { case *dirnode: - size += node.memorySize() + size += node.MemorySize() case *filenode: + size += 64 for _, seg := range node.segments { switch seg := seg.(type) { case *memSegment: size += int64(seg.Len()) } + size += 64 } } } - return + return 64 + size } // caller must have write lock. @@ -1028,38 +1302,64 @@ func (dn *dirnode) marshalManifest(ctx context.Context, prefix string) (string, } func (dn *dirnode) loadManifest(txt string) error { - var dirname string - streams := strings.Split(txt, "\n") - if streams[len(streams)-1] != "" { + streams := bytes.Split([]byte(txt), []byte{'\n'}) + if len(streams[len(streams)-1]) != 0 { return fmt.Errorf("line %d: no trailing newline", len(streams)) } streams = streams[:len(streams)-1] segments := []storedSegment{} + // To reduce allocs, we reuse a single "pathparts" slice + // (pre-split on "/" separators) for the duration of this + // func. + var pathparts []string + // To reduce allocs, we reuse a single "toks" slice of 3 byte + // slices. + var toks = make([][]byte, 3) + // Similar to bytes.SplitN(token, []byte{c}, 3), but splits + // into the toks slice rather than allocating a new one, and + // returns the number of toks (1, 2, or 3). + splitToToks := func(src []byte, c rune) int { + c1 := bytes.IndexRune(src, c) + if c1 < 0 { + toks[0] = src + return 1 + } + toks[0], src = src[:c1], src[c1+1:] + c2 := bytes.IndexRune(src, c) + if c2 < 0 { + toks[1] = src + return 2 + } + toks[1], toks[2] = src[:c2], src[c2+1:] + return 3 + } for i, stream := range streams { lineno := i + 1 var anyFileTokens bool var pos int64 var segIdx int segments = segments[:0] - for i, token := range strings.Split(stream, " ") { + pathparts = nil + streamparts := 0 + for i, token := range bytes.Split(stream, []byte{' '}) { if i == 0 { - dirname = manifestUnescape(token) + pathparts = strings.Split(manifestUnescape(string(token)), "/") + streamparts = len(pathparts) continue } - if !strings.Contains(token, ":") { + if !bytes.ContainsRune(token, ':') { if anyFileTokens { return fmt.Errorf("line %d: bad file segment %q", lineno, token) } - toks := strings.SplitN(token, "+", 3) - if len(toks) < 2 { + if splitToToks(token, '+') < 2 { return fmt.Errorf("line %d: bad locator %q", lineno, token) } - length, err := strconv.ParseInt(toks[1], 10, 32) + length, err := strconv.ParseInt(string(toks[1]), 10, 32) if err != nil || length < 0 { return fmt.Errorf("line %d: bad locator %q", lineno, token) } segments = append(segments, storedSegment{ - locator: token, + locator: string(token), size: int(length), offset: 0, length: int(length), @@ -1068,23 +1368,26 @@ func (dn *dirnode) loadManifest(txt string) error { } else if len(segments) == 0 { return fmt.Errorf("line %d: bad locator %q", lineno, token) } - - toks := strings.SplitN(token, ":", 3) - if len(toks) != 3 { + if splitToToks(token, ':') != 3 { return fmt.Errorf("line %d: bad file segment %q", lineno, token) } anyFileTokens = true - offset, err := strconv.ParseInt(toks[0], 10, 64) + offset, err := strconv.ParseInt(string(toks[0]), 10, 64) if err != nil || offset < 0 { return fmt.Errorf("line %d: bad file segment %q", lineno, token) } - length, err := strconv.ParseInt(toks[1], 10, 64) + length, err := strconv.ParseInt(string(toks[1]), 10, 64) if err != nil || length < 0 { return fmt.Errorf("line %d: bad file segment %q", lineno, token) } - name := dirname + "/" + manifestUnescape(toks[2]) - fnode, err := dn.createFileAndParents(name) + if !bytes.ContainsAny(toks[2], `\/`) { + // optimization for a common case + pathparts = append(pathparts[:streamparts], string(toks[2])) + } else { + pathparts = append(pathparts[:streamparts], strings.Split(manifestUnescape(string(toks[2])), "/")...) + } + fnode, err := dn.createFileAndParents(pathparts) if fnode == nil && err == nil && length == 0 { // Special case: an empty file used as // a marker to preserve an otherwise @@ -1092,7 +1395,7 @@ func (dn *dirnode) loadManifest(txt string) error { continue } if err != nil || (fnode == nil && length != 0) { - return fmt.Errorf("line %d: cannot use path %q with length %d: %s", lineno, name, length, err) + return fmt.Errorf("line %d: cannot use name %q with length %d: %s", lineno, toks[2], length, err) } // Map the stream offset/range coordinates to // block/offset/range coordinates and add @@ -1143,7 +1446,7 @@ func (dn *dirnode) loadManifest(txt string) error { return fmt.Errorf("line %d: no file segments", lineno) } else if len(segments) == 0 { return fmt.Errorf("line %d: no locators", lineno) - } else if dirname == "" { + } else if streamparts == 0 { return fmt.Errorf("line %d: no stream name", lineno) } } @@ -1154,9 +1457,11 @@ func (dn *dirnode) loadManifest(txt string) error { // // If path is a "parent directory exists" marker (the last path // component is "."), the returned values are both nil. -func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) { +// +// Newly added nodes have modtime==0. Caller is responsible for fixing +// them with backdateTree. +func (dn *dirnode) createFileAndParents(names []string) (fn *filenode, err error) { var node inode = dn - names := strings.Split(path, "/") basename := names[len(names)-1] for _, name := range names[:len(names)-1] { switch name { @@ -1170,9 +1475,12 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) { node = node.Parent() continue } + node.Lock() + unlock := node.Unlock node, err = node.Child(name, func(child inode) (inode, error) { if child == nil { - child, err := node.FS().newNode(name, 0755|os.ModeDir, node.Parent().FileInfo().ModTime()) + // note modtime will be fixed later in backdateTree() + child, err := node.FS().newNode(name, 0755|os.ModeDir, time.Time{}) if err != nil { return nil, err } @@ -1184,6 +1492,7 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) { return child, nil } }) + unlock() if err != nil { return } @@ -1191,13 +1500,15 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) { if basename == "." { return } else if !permittedName(basename) { - err = fmt.Errorf("invalid file part %q in path %q", basename, path) + err = fmt.Errorf("invalid file part %q in path %q", basename, names) return } + node.Lock() + defer node.Unlock() _, err = node.Child(basename, func(child inode) (inode, error) { switch child := child.(type) { case nil: - child, err = node.FS().newNode(basename, 0755, node.FileInfo().ModTime()) + child, err = node.FS().newNode(basename, 0755, time.Time{}) if err != nil { return nil, err } @@ -1230,6 +1541,86 @@ func (dn *dirnode) TreeSize() (bytes int64) { return } +func (dn *dirnode) Snapshot() (inode, error) { + return dn.snapshot() +} + +func (dn *dirnode) snapshot() (*dirnode, error) { + dn.RLock() + defer dn.RUnlock() + snap := &dirnode{ + treenode: treenode{ + inodes: make(map[string]inode, len(dn.inodes)), + fileinfo: dn.fileinfo, + }, + } + for name, child := range dn.inodes { + dupchild, err := child.Snapshot() + if err != nil { + return nil, err + } + snap.inodes[name] = dupchild + dupchild.SetParent(snap, name) + } + return snap, nil +} + +func (dn *dirnode) Splice(repl inode) error { + repl, err := repl.Snapshot() + if err != nil { + return fmt.Errorf("cannot copy snapshot: %w", err) + } + switch repl := repl.(type) { + default: + return fmt.Errorf("cannot splice snapshot containing %T: %w", repl, ErrInvalidArgument) + case *dirnode: + dn.Lock() + defer dn.Unlock() + dn.inodes = repl.inodes + dn.setTreeFS(dn.fs) + case *filenode: + dn.parent.Lock() + defer dn.parent.Unlock() + removing, err := dn.parent.Child(dn.fileinfo.name, nil) + if err != nil { + return fmt.Errorf("cannot use Splice to replace a top-level directory with a file: %w", ErrInvalidOperation) + } else if removing != dn { + // If ../thisdirname is not this dirnode, it + // must be an inode that wraps a dirnode, like + // a collectionFileSystem or deferrednode. + if deferred, ok := removing.(*deferrednode); ok { + // More useful to report the type of + // the wrapped node rather than just + // *deferrednode. (We know the real + // inode is already loaded because dn + // is inside it.) + removing = deferred.realinode() + } + return fmt.Errorf("cannot use Splice to attach a file at top level of %T: %w", removing, ErrInvalidOperation) + } + dn.Lock() + defer dn.Unlock() + _, err = dn.parent.Child(dn.fileinfo.name, func(inode) (inode, error) { return repl, nil }) + if err != nil { + return fmt.Errorf("error replacing filenode: dn.parent.Child(): %w", err) + } + repl.fs = dn.fs + } + return nil +} + +func (dn *dirnode) setTreeFS(fs *collectionFileSystem) { + dn.fs = fs + for _, child := range dn.inodes { + switch child := child.(type) { + case *dirnode: + child.setTreeFS(fs) + case *filenode: + child.fs = fs + } + } +} + type segment interface { io.ReaderAt Len() int