X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/04b9d6e93ca8bd18dca697e56689820516c8c572..a7631a1ccb6e2a6925d00a06562e171c4ce4ea2f:/sdk/go/arvados/fs_collection.go diff --git a/sdk/go/arvados/fs_collection.go b/sdk/go/arvados/fs_collection.go index f6afadba5b..060b57b493 100644 --- a/sdk/go/arvados/fs_collection.go +++ b/sdk/go/arvados/fs_collection.go @@ -5,10 +5,10 @@ package arvados import ( + "context" "encoding/json" "fmt" "io" - "log" "os" "path" "regexp" @@ -16,10 +16,14 @@ import ( "strconv" "strings" "sync" + "sync/atomic" "time" ) -var maxBlockSize = 1 << 26 +var ( + maxBlockSize = 1 << 26 + concurrentWriters = 4 // max goroutines writing to Keep in background and during flush() +) // A CollectionFileSystem is a FileSystem that can be serialized as a // manifest and stored as a collection. @@ -34,6 +38,9 @@ type CollectionFileSystem interface { // Total data bytes in all files. Size() int64 + + // Memory consumed by buffered file data. + memorySize() int64 } type collectionFileSystem struct { @@ -43,16 +50,15 @@ type collectionFileSystem struct { // FileSystem returns a CollectionFileSystem for the collection. func (c *Collection) FileSystem(client apiClient, kc keepClient) (CollectionFileSystem, error) { - var modTime time.Time - if c.ModifiedAt == nil { + modTime := c.ModifiedAt + if modTime.IsZero() { modTime = time.Now() - } else { - modTime = *c.ModifiedAt } fs := &collectionFileSystem{ uuid: c.UUID, fileSystem: fileSystem{ fsBackend: keepBackend{apiClient: client, keepClient: kc}, + thr: newThrottle(concurrentWriters), }, } root := &dirnode{ @@ -115,31 +121,128 @@ func (fs *collectionFileSystem) newNode(name string, perm os.FileMode, modTime t } } +func (fs *collectionFileSystem) Child(name string, replace func(inode) (inode, error)) (inode, error) { + return fs.rootnode().Child(name, replace) +} + +func (fs *collectionFileSystem) FS() FileSystem { + return fs +} + +func (fs *collectionFileSystem) FileInfo() os.FileInfo { + return fs.rootnode().FileInfo() +} + +func (fs *collectionFileSystem) IsDir() bool { + return true +} + +func (fs *collectionFileSystem) Lock() { + fs.rootnode().Lock() +} + +func (fs *collectionFileSystem) Unlock() { + fs.rootnode().Unlock() +} + +func (fs *collectionFileSystem) RLock() { + fs.rootnode().RLock() +} + +func (fs *collectionFileSystem) RUnlock() { + fs.rootnode().RUnlock() +} + +func (fs *collectionFileSystem) Parent() inode { + return fs.rootnode().Parent() +} + +func (fs *collectionFileSystem) Read(_ []byte, ptr filenodePtr) (int, filenodePtr, error) { + return 0, ptr, ErrInvalidOperation +} + +func (fs *collectionFileSystem) Write(_ []byte, ptr filenodePtr) (int, filenodePtr, error) { + return 0, ptr, ErrInvalidOperation +} + +func (fs *collectionFileSystem) Readdir() ([]os.FileInfo, error) { + return fs.rootnode().Readdir() +} + +func (fs *collectionFileSystem) SetParent(parent inode, name string) { + fs.rootnode().SetParent(parent, name) +} + +func (fs *collectionFileSystem) Truncate(int64) error { + return ErrInvalidOperation +} + func (fs *collectionFileSystem) Sync() error { - log.Printf("cfs.Sync()") if fs.uuid == "" { return nil } txt, err := fs.MarshalManifest(".") if err != nil { - log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err) - return err + return fmt.Errorf("sync failed: %s", err) } coll := &Collection{ UUID: fs.uuid, ManifestText: txt, } - err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, fs.UpdateBody(coll), map[string]interface{}{"select": []string{"uuid"}}) + err = fs.RequestAndDecode(nil, "PUT", "arvados/v1/collections/"+fs.uuid, nil, map[string]interface{}{ + "collection": map[string]string{ + "manifest_text": coll.ManifestText, + }, + "select": []string{"uuid"}, + }) if err != nil { - log.Printf("WARNING: (collectionFileSystem)Sync() failed: %s", err) + return fmt.Errorf("sync failed: update %s: %s", fs.uuid, err) + } + return nil +} + +func (fs *collectionFileSystem) Flush(path string, shortBlocks bool) error { + node, err := rlookup(fs.fileSystem.root, path) + if err != nil { + return err + } + dn, ok := node.(*dirnode) + if !ok { + return ErrNotADirectory + } + dn.Lock() + defer dn.Unlock() + names := dn.sortedNames() + if path != "" { + // Caller only wants to flush the specified dir, + // non-recursively. Drop subdirs from the list of + // names. + var filenames []string + for _, name := range names { + if _, ok := dn.inodes[name].(*filenode); ok { + filenames = append(filenames, name) + } + } + names = filenames + } + for _, name := range names { + child := dn.inodes[name] + child.Lock() + defer child.Unlock() } - return err + return dn.flush(context.TODO(), names, flushOpts{sync: false, shortBlocks: shortBlocks}) +} + +func (fs *collectionFileSystem) memorySize() int64 { + fs.fileSystem.root.Lock() + defer fs.fileSystem.root.Unlock() + return fs.fileSystem.root.(*dirnode).memorySize() } func (fs *collectionFileSystem) MarshalManifest(prefix string) (string, error) { fs.fileSystem.root.Lock() defer fs.fileSystem.root.Unlock() - return fs.fileSystem.root.(*dirnode).marshalManifest(prefix) + return fs.fileSystem.root.(*dirnode).marshalManifest(context.TODO(), prefix) } func (fs *collectionFileSystem) Size() int64 { @@ -465,8 +568,6 @@ func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePt seg.Truncate(len(cando)) fn.memsize += int64(len(cando)) fn.segments[cur] = seg - cur++ - prev++ } } @@ -493,30 +594,70 @@ func (fn *filenode) Write(p []byte, startPtr filenodePtr) (n int, ptr filenodePt // Write some data out to disk to reduce memory use. Caller must have // write lock. func (fn *filenode) pruneMemSegments() { - // TODO: async (don't hold Lock() while waiting for Keep) - // TODO: share code with (*dirnode)sync() + // TODO: share code with (*dirnode)flush() // TODO: pack/flush small blocks too, when fragmented for idx, seg := range fn.segments { seg, ok := seg.(*memSegment) - if !ok || seg.Len() < maxBlockSize { - continue - } - locator, _, err := fn.FS().PutB(seg.buf) - if err != nil { - // TODO: stall (or return errors from) - // subsequent writes until flushing - // starts to succeed + if !ok || seg.Len() < maxBlockSize || seg.flushing != nil { continue } - fn.memsize -= int64(seg.Len()) - fn.segments[idx] = storedSegment{ - kc: fn.FS(), - locator: locator, - size: seg.Len(), - offset: 0, - length: seg.Len(), + // Setting seg.flushing guarantees seg.buf will not be + // modified in place: WriteAt and Truncate will + // allocate a new buf instead, if necessary. + idx, buf := idx, seg.buf + done := make(chan struct{}) + seg.flushing = done + // If lots of background writes are already in + // progress, block here until one finishes, rather + // than pile up an unlimited number of buffered writes + // and network flush operations. + fn.fs.throttle().Acquire() + go func() { + defer close(done) + locator, _, err := fn.FS().PutB(buf) + fn.fs.throttle().Release() + fn.Lock() + defer fn.Unlock() + if seg.flushing != done { + // A new seg.buf has been allocated. + return + } + if err != nil { + // TODO: stall (or return errors from) + // subsequent writes until flushing + // starts to succeed. + return + } + if len(fn.segments) <= idx || fn.segments[idx] != seg || len(seg.buf) != len(buf) { + // Segment has been dropped/moved/resized. + return + } + fn.memsize -= int64(len(buf)) + fn.segments[idx] = storedSegment{ + kc: fn.FS(), + locator: locator, + size: len(buf), + offset: 0, + length: len(buf), + } + }() + } +} + +// Block until all pending pruneMemSegments/flush work is +// finished. Caller must NOT have lock. +func (fn *filenode) waitPrune() { + var pending []<-chan struct{} + fn.Lock() + for _, seg := range fn.segments { + if seg, ok := seg.(*memSegment); ok && seg.flushing != nil { + pending = append(pending, seg.flushing) } } + fn.Unlock() + for _, p := range pending { + <-p + } } type dirnode struct { @@ -549,112 +690,300 @@ func (dn *dirnode) Child(name string, replace func(inode) (inode, error)) (inode return dn.treenode.Child(name, replace) } -// sync flushes in-memory data (for the children with the given names, -// which must be children of dn) to persistent storage. Caller must -// have write lock on dn and the named children. -func (dn *dirnode) sync(names []string) error { - type shortBlock struct { - fn *filenode - idx int - } - var pending []shortBlock - var pendingLen int +type fnSegmentRef struct { + fn *filenode + idx int +} - flush := func(sbs []shortBlock) error { - if len(sbs) == 0 { +// commitBlock concatenates the data from the given filenode segments +// (which must be *memSegments), writes the data out to Keep as a +// single block, and replaces the filenodes' *memSegments with +// storedSegments that reference the relevant portions of the new +// block. +// +// bufsize is the total data size in refs. It is used to preallocate +// the correct amount of memory when len(refs)>1. +// +// If sync is false, commitBlock returns right away, after starting a +// goroutine to do the writes, reacquire the filenodes' locks, and +// swap out the *memSegments. Some filenodes' segments might get +// modified/rearranged in the meantime, in which case commitBlock +// won't replace them. +// +// Caller must have write lock. +func (dn *dirnode) commitBlock(ctx context.Context, refs []fnSegmentRef, bufsize int, sync bool) error { + if len(refs) == 0 { + return nil + } + if err := ctx.Err(); err != nil { + return err + } + done := make(chan struct{}) + var block []byte + segs := make([]*memSegment, 0, len(refs)) + offsets := make([]int, 0, len(refs)) // location of segment's data within block + for _, ref := range refs { + seg := ref.fn.segments[ref.idx].(*memSegment) + if !sync && seg.flushingUnfinished() { + // Let the other flushing goroutine finish. If + // it fails, we'll try again next time. + close(done) return nil + } else { + // In sync mode, we proceed regardless of + // whether another flush is in progress: It + // can't finish before we do, because we hold + // fn's lock until we finish our own writes. } - block := make([]byte, 0, maxBlockSize) - for _, sb := range sbs { - block = append(block, sb.fn.segments[sb.idx].(*memSegment).buf...) + seg.flushing = done + offsets = append(offsets, len(block)) + if len(refs) == 1 { + block = seg.buf + } else if block == nil { + block = append(make([]byte, 0, bufsize), seg.buf...) + } else { + block = append(block, seg.buf...) } + segs = append(segs, seg) + } + blocksize := len(block) + dn.fs.throttle().Acquire() + errs := make(chan error, 1) + go func() { + defer close(done) + defer close(errs) locator, _, err := dn.fs.PutB(block) + dn.fs.throttle().Release() if err != nil { - return err + errs <- err + return } - off := 0 - for _, sb := range sbs { - data := sb.fn.segments[sb.idx].(*memSegment).buf - sb.fn.segments[sb.idx] = storedSegment{ + for idx, ref := range refs { + if !sync { + ref.fn.Lock() + // In async mode, fn's lock was + // released while we were waiting for + // PutB(); lots of things might have + // changed. + if len(ref.fn.segments) <= ref.idx { + // file segments have + // rearranged or changed in + // some way + ref.fn.Unlock() + continue + } else if seg, ok := ref.fn.segments[ref.idx].(*memSegment); !ok || seg != segs[idx] { + // segment has been replaced + ref.fn.Unlock() + continue + } else if seg.flushing != done { + // seg.buf has been replaced + ref.fn.Unlock() + continue + } + } + data := ref.fn.segments[ref.idx].(*memSegment).buf + ref.fn.segments[ref.idx] = storedSegment{ kc: dn.fs, locator: locator, - size: len(block), - offset: off, + size: blocksize, + offset: offsets[idx], length: len(data), } - off += len(data) - sb.fn.memsize -= int64(len(data)) + // atomic is needed here despite caller having + // lock: caller might be running concurrent + // commitBlock() goroutines using the same + // lock, writing different segments from the + // same file. + atomic.AddInt64(&ref.fn.memsize, -int64(len(data))) + if !sync { + ref.fn.Unlock() + } } + }() + if sync { + return <-errs + } else { return nil } +} + +type flushOpts struct { + sync bool + shortBlocks bool +} +// flush in-memory data and remote-cluster block references (for the +// children with the given names, which must be children of dn) to +// local-cluster persistent storage. +// +// Caller must have write lock on dn and the named children. +// +// If any children are dirs, they will be flushed recursively. +func (dn *dirnode) flush(ctx context.Context, names []string, opts flushOpts) error { + cg := newContextGroup(ctx) + defer cg.Cancel() + + goCommit := func(refs []fnSegmentRef, bufsize int) { + cg.Go(func() error { + return dn.commitBlock(cg.Context(), refs, bufsize, opts.sync) + }) + } + + var pending []fnSegmentRef + var pendingLen int = 0 + localLocator := map[string]string{} for _, name := range names { - fn, ok := dn.inodes[name].(*filenode) - if !ok { - continue - } - for idx, seg := range fn.segments { - seg, ok := seg.(*memSegment) - if !ok { - continue - } - if seg.Len() > maxBlockSize/2 { - if err := flush([]shortBlock{{fn, idx}}); err != nil { - return err - } - continue + switch node := dn.inodes[name].(type) { + case *dirnode: + grandchildNames := node.sortedNames() + for _, grandchildName := range grandchildNames { + grandchild := node.inodes[grandchildName] + grandchild.Lock() + defer grandchild.Unlock() } - if pendingLen+seg.Len() > maxBlockSize { - if err := flush(pending); err != nil { - return err + cg.Go(func() error { return node.flush(cg.Context(), grandchildNames, opts) }) + case *filenode: + for idx, seg := range node.segments { + switch seg := seg.(type) { + case storedSegment: + loc, ok := localLocator[seg.locator] + if !ok { + var err error + loc, err = dn.fs.LocalLocator(seg.locator) + if err != nil { + return err + } + localLocator[seg.locator] = loc + } + seg.locator = loc + node.segments[idx] = seg + case *memSegment: + if seg.Len() > maxBlockSize/2 { + goCommit([]fnSegmentRef{{node, idx}}, seg.Len()) + continue + } + if pendingLen+seg.Len() > maxBlockSize { + goCommit(pending, pendingLen) + pending = nil + pendingLen = 0 + } + pending = append(pending, fnSegmentRef{node, idx}) + pendingLen += seg.Len() + default: + panic(fmt.Sprintf("can't sync segment type %T", seg)) } - pending = nil - pendingLen = 0 } - pending = append(pending, shortBlock{fn, idx}) - pendingLen += seg.Len() } } - return flush(pending) + if opts.shortBlocks { + goCommit(pending, pendingLen) + } + return cg.Wait() } -// caller must have read lock. -func (dn *dirnode) marshalManifest(prefix string) (string, error) { - var streamLen int64 - type filepart struct { - name string - offset int64 - length int64 +// caller must have write lock. +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() + case *filenode: + for _, seg := range node.segments { + switch seg := seg.(type) { + case *memSegment: + size += int64(seg.Len()) + } + } + } } - var fileparts []filepart - var subdirs string - var blocks []string + return +} +// caller must have write lock. +func (dn *dirnode) sortedNames() []string { names := make([]string, 0, len(dn.inodes)) for name := range dn.inodes { names = append(names, name) } sort.Strings(names) + return names +} + +// caller must have write lock. +func (dn *dirnode) marshalManifest(ctx context.Context, prefix string) (string, error) { + cg := newContextGroup(ctx) + defer cg.Cancel() + + if len(dn.inodes) == 0 { + if prefix == "." { + return "", nil + } + // Express the existence of an empty directory by + // adding an empty file named `\056`, which (unlike + // the more obvious spelling `.`) is accepted by the + // API's manifest validator. + return manifestEscape(prefix) + " d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n", nil + } + + names := dn.sortedNames() + + // Wait for children to finish any pending write operations + // before locking them. for _, name := range names { node := dn.inodes[name] - node.Lock() - defer node.Unlock() - } - if err := dn.sync(names); err != nil { - return "", err + if fn, ok := node.(*filenode); ok { + fn.waitPrune() + } } + + var dirnames []string + var filenames []string for _, name := range names { - switch node := dn.inodes[name].(type) { + node := dn.inodes[name] + node.Lock() + defer node.Unlock() + switch node := node.(type) { case *dirnode: - subdir, err := node.marshalManifest(prefix + "/" + name) - if err != nil { - return "", err - } - subdirs = subdirs + subdir + dirnames = append(dirnames, name) case *filenode: + filenames = append(filenames, name) + default: + panic(fmt.Sprintf("can't marshal inode type %T", node)) + } + } + + subdirs := make([]string, len(dirnames)) + rootdir := "" + for i, name := range dirnames { + i, name := i, name + cg.Go(func() error { + txt, err := dn.inodes[name].(*dirnode).marshalManifest(cg.Context(), prefix+"/"+name) + subdirs[i] = txt + return err + }) + } + + cg.Go(func() error { + var streamLen int64 + type filepart struct { + name string + offset int64 + length int64 + } + + var fileparts []filepart + var blocks []string + if err := dn.flush(cg.Context(), filenames, flushOpts{sync: true, shortBlocks: true}); err != nil { + return err + } + for _, name := range filenames { + node := dn.inodes[name].(*filenode) if len(node.segments) == 0 { fileparts = append(fileparts, filepart{name: name}) - break + continue } for _, seg := range node.segments { switch seg := seg.(type) { @@ -680,24 +1009,25 @@ func (dn *dirnode) marshalManifest(prefix string) (string, error) { default: // This can't happen: we // haven't unlocked since - // calling sync(). + // calling flush(sync=true). panic(fmt.Sprintf("can't marshal segment type %T", seg)) } } - default: - panic(fmt.Sprintf("can't marshal inode type %T", node)) } - } - var filetokens []string - for _, s := range fileparts { - filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name))) - } - if len(filetokens) == 0 { - return subdirs, nil - } else if len(blocks) == 0 { - blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"} - } - return manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + subdirs, nil + var filetokens []string + for _, s := range fileparts { + filetokens = append(filetokens, fmt.Sprintf("%d:%d:%s", s.offset, s.length, manifestEscape(s.name))) + } + if len(filetokens) == 0 { + return nil + } else if len(blocks) == 0 { + blocks = []string{"d41d8cd98f00b204e9800998ecf8427e+0"} + } + rootdir = manifestEscape(prefix) + " " + strings.Join(blocks, " ") + " " + strings.Join(filetokens, " ") + "\n" + return nil + }) + err := cg.Wait() + return rootdir + strings.Join(subdirs, ""), err } func (dn *dirnode) loadManifest(txt string) error { @@ -758,8 +1088,14 @@ func (dn *dirnode) loadManifest(txt string) error { } name := dirname + "/" + manifestUnescape(toks[2]) fnode, err := dn.createFileAndParents(name) - if err != nil { - return fmt.Errorf("line %d: cannot use path %q: %s", lineno, name, err) + if fnode == nil && err == nil && length == 0 { + // Special case: an empty file used as + // a marker to preserve an otherwise + // empty directory in a manifest. + 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) } // Map the stream offset/range coordinates to // block/offset/range coordinates and add @@ -771,9 +1107,9 @@ func (dn *dirnode) loadManifest(txt string) error { // situation might be rare anyway) segIdx, pos = 0, 0 } - for next := int64(0); segIdx < len(segments); segIdx++ { + for ; segIdx < len(segments); segIdx++ { seg := segments[segIdx] - next = pos + int64(seg.Len()) + next := pos + int64(seg.Len()) if next <= offset || seg.Len() == 0 { pos = next continue @@ -817,15 +1153,14 @@ func (dn *dirnode) loadManifest(txt string) error { return nil } -// only safe to call from loadManifest -- no locking +// only safe to call from loadManifest -- no locking. +// +// 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) { var node inode = dn names := strings.Split(path, "/") basename := names[len(names)-1] - if !permittedName(basename) { - err = fmt.Errorf("invalid file part %q in path %q", basename, path) - return - } for _, name := range names[:len(names)-1] { switch name { case "", ".": @@ -856,6 +1191,12 @@ func (dn *dirnode) createFileAndParents(path string) (fn *filenode, err error) { return } } + if basename == "." { + return + } else if !permittedName(basename) { + err = fmt.Errorf("invalid file part %q in path %q", basename, path) + return + } _, err = node.Child(basename, func(child inode) (inode, error) { switch child := child.(type) { case nil: @@ -902,6 +1243,24 @@ type segment interface { type memSegment struct { buf []byte + // If flushing is not nil and not ready/closed, then a) buf is + // being shared by a pruneMemSegments goroutine, and must be + // copied on write; and b) the flushing channel will close + // when the goroutine finishes, whether it succeeds or not. + flushing <-chan struct{} +} + +func (me *memSegment) flushingUnfinished() bool { + if me.flushing == nil { + return false + } + select { + case <-me.flushing: + me.flushing = nil + return false + default: + return true + } } func (me *memSegment) Len() int { @@ -918,28 +1277,31 @@ func (me *memSegment) Slice(off, length int) segment { } func (me *memSegment) Truncate(n int) { - if n > cap(me.buf) { + if n > cap(me.buf) || (me.flushing != nil && n > len(me.buf)) { newsize := 1024 for newsize < n { newsize = newsize << 2 } newbuf := make([]byte, n, newsize) copy(newbuf, me.buf) - me.buf = newbuf + me.buf, me.flushing = newbuf, nil } else { - // Zero unused part when shrinking, in case we grow - // and start using it again later. - for i := n; i < len(me.buf); i++ { + // reclaim existing capacity, and zero reclaimed part + oldlen := len(me.buf) + me.buf = me.buf[:n] + for i := oldlen; i < n; i++ { me.buf[i] = 0 } } - me.buf = me.buf[:n] } func (me *memSegment) WriteAt(p []byte, off int) { if off+len(p) > len(me.buf) { panic("overflowed segment") } + if me.flushing != nil { + me.buf, me.flushing = append([]byte(nil), me.buf...), nil + } copy(me.buf[off:], p) }