X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5d164d74505c232cfa232d69a56273da2d02b72a..516685e09227ab64c2d4f7fd04d4b60a75fc5d0f:/services/crunch-run/crunchrun.go diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go index 653e0b4949..1deb740316 100644 --- a/services/crunch-run/crunchrun.go +++ b/services/crunch-run/crunchrun.go @@ -32,6 +32,7 @@ import ( "git.curoverse.com/arvados.git/sdk/go/arvadosclient" "git.curoverse.com/arvados.git/sdk/go/keepclient" "git.curoverse.com/arvados.git/sdk/go/manifest" + "github.com/shirou/gopsutil/process" "golang.org/x/net/context" dockertypes "github.com/docker/docker/api/types" @@ -57,13 +58,15 @@ var ErrCancelled = errors.New("Cancelled") // IKeepClient is the minimal Keep API methods used by crunch-run. type IKeepClient interface { - PutHB(hash string, buf []byte) (string, int, error) + PutB(buf []byte) (string, int, error) + ReadAt(locator string, p []byte, off int) (int, error) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) + LocalLocator(locator string) (string, error) ClearBlockCache() } // NewLogWriter is a factory function to create a new log writer. -type NewLogWriter func(name string) io.WriteCloser +type NewLogWriter func(name string) (io.WriteCloser, error) type RunArvMount func(args []string, tok string) (*exec.Cmd, error) @@ -77,42 +80,54 @@ type ThinDockerClient interface { ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) + ContainerInspect(ctx context.Context, id string) (dockertypes.ContainerJSON, error) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) } +type PsProcess interface { + CmdlineSlice() ([]string, error) +} + // ContainerRunner is the main stateful struct used for a single execution of a // container. type ContainerRunner struct { - Docker ThinDockerClient - ArvClient IArvadosClient - Kc IKeepClient - arvados.Container + Docker ThinDockerClient + client *arvados.Client + ArvClient IArvadosClient + Kc IKeepClient + Container arvados.Container ContainerConfig dockercontainer.Config - dockercontainer.HostConfig - token string - ContainerID string - ExitCode *int - NewLogWriter - loggingDone chan bool - CrunchLog *ThrottledLogger - Stdout io.WriteCloser - Stderr io.WriteCloser - LogCollection *CollectionWriter - LogsPDH *string - RunArvMount - MkTempDir - ArvMount *exec.Cmd - ArvMountPoint string - HostOutputDir string - Binds []string - Volumes map[string]struct{} - OutputPDH *string - SigChan chan os.Signal - ArvMountExit chan error - finalState string - parentTemp string + HostConfig dockercontainer.HostConfig + token string + ContainerID string + ExitCode *int + NewLogWriter NewLogWriter + loggingDone chan bool + CrunchLog *ThrottledLogger + Stdout io.WriteCloser + Stderr io.WriteCloser + logUUID string + logMtx sync.Mutex + LogCollection arvados.CollectionFileSystem + LogsPDH *string + RunArvMount RunArvMount + MkTempDir MkTempDir + ArvMount *exec.Cmd + ArvMountPoint string + HostOutputDir string + Binds []string + Volumes map[string]struct{} + OutputPDH *string + SigChan chan os.Signal + ArvMountExit chan error + SecretMounts map[string]arvados.Mount + MkArvClient func(token string) (IArvadosClient, IKeepClient, error) + finalState string + parentTemp string + + ListProcesses func() ([]PsProcess, error) statLogger io.WriteCloser statReporter *crunchstat.Reporter @@ -136,10 +151,14 @@ type ContainerRunner struct { cStateLock sync.Mutex cCancelled bool // StopContainer() invoked + cRemoved bool // docker confirmed the container no longer exists - enableNetwork string // one of "default" or "always" - networkMode string // passed through to HostConfig.NetworkMode - arvMountLog *ThrottledLogger + enableNetwork string // one of "default" or "always" + networkMode string // passed through to HostConfig.NetworkMode + arvMountLog *ThrottledLogger + checkContainerd time.Duration + + containerWatchdogInterval time.Duration } // setupSignals sets up signal handling to gracefully terminate the underlying @@ -173,31 +192,39 @@ func (runner *ContainerRunner) stop(sig os.Signal) { if err != nil { runner.CrunchLog.Printf("error removing container: %s", err) } + if err == nil || strings.Contains(err.Error(), "No such container: "+runner.ContainerID) { + runner.cRemoved = true + } } var errorBlacklist = []string{ "(?ms).*[Cc]annot connect to the Docker daemon.*", "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*", + "(?ms).*grpc: the connection is unavailable.*", } var brokenNodeHook *string = flag.String("broken-node-hook", "", "Script to run if node is detected to be broken (for example, Docker daemon is not running)") +func (runner *ContainerRunner) runBrokenNodeHook() { + if *brokenNodeHook == "" { + runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.") + } else { + runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook) + // run killme script + c := exec.Command(*brokenNodeHook) + c.Stdout = runner.CrunchLog + c.Stderr = runner.CrunchLog + err := c.Run() + if err != nil { + runner.CrunchLog.Printf("Error running broken node hook: %v", err) + } + } +} + func (runner *ContainerRunner) checkBrokenNode(goterr error) bool { for _, d := range errorBlacklist { if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil { runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr) - if *brokenNodeHook == "" { - runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.") - } else { - runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook) - // run killme script - c := exec.Command(*brokenNodeHook) - c.Stdout = runner.CrunchLog - c.Stderr = runner.CrunchLog - err := c.Run() - if err != nil { - runner.CrunchLog.Printf("Error running broken node hook: %v", err) - } - } + runner.runBrokenNodeHook() return true } } @@ -211,8 +238,17 @@ func (runner *ContainerRunner) LoadImage() (err error) { runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage) + tok, err := runner.ContainerToken() + if err != nil { + return fmt.Errorf("While getting container token (LoadImage): %v", err) + } + arvClient, kc, err := runner.MkArvClient(tok) + if err != nil { + return fmt.Errorf("While creating arv client (LoadImage): %v", err) + } + var collection arvados.Collection - err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection) + err = arvClient.Get("collections", runner.Container.ContainerImage, nil, &collection) if err != nil { return fmt.Errorf("While getting container image collection: %v", err) } @@ -233,7 +269,7 @@ func (runner *ContainerRunner) LoadImage() (err error) { runner.CrunchLog.Print("Loading Docker image from keep") var readCloser io.ReadCloser - readCloser, err = runner.Kc.ManifestFileReader(manifest, img) + readCloser, err = kc.ManifestFileReader(manifest, img) if err != nil { return fmt.Errorf("While creating ManifestFileReader for container image: %v", err) } @@ -255,7 +291,7 @@ func (runner *ContainerRunner) LoadImage() (err error) { runner.ContainerConfig.Image = imageID - runner.Kc.ClearBlockCache() + kc.ClearBlockCache() return nil } @@ -273,7 +309,11 @@ func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) ( } c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token) - runner.arvMountLog = NewThrottledLogger(runner.NewLogWriter("arv-mount")) + w, err := runner.NewLogWriter("arv-mount") + if err != nil { + return nil, err + } + runner.arvMountLog = NewThrottledLogger(w) c.Stdout = runner.arvMountLog c.Stderr = runner.arvMountLog @@ -396,10 +436,24 @@ func (runner *ContainerRunner) SetupMounts() (err error) { for bind := range runner.Container.Mounts { binds = append(binds, bind) } + for bind := range runner.SecretMounts { + if _, ok := runner.Container.Mounts[bind]; ok { + return fmt.Errorf("Secret mount %q conflicts with regular mount", bind) + } + if runner.SecretMounts[bind].Kind != "json" && + runner.SecretMounts[bind].Kind != "text" { + return fmt.Errorf("Secret mount %q type is %q but only 'json' and 'text' are permitted.", + bind, runner.SecretMounts[bind].Kind) + } + binds = append(binds, bind) + } sort.Strings(binds) for _, bind := range binds { - mnt := runner.Container.Mounts[bind] + mnt, ok := runner.Container.Mounts[bind] + if !ok { + mnt = runner.SecretMounts[bind] + } if bind == "stdout" || bind == "stderr" { // Is it a "file" mount kind? if mnt.Kind != "file" { @@ -428,8 +482,8 @@ func (runner *ContainerRunner) SetupMounts() (err error) { } if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" { - if mnt.Kind != "collection" { - return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind) + if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" { + return fmt.Errorf("Only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind) } } @@ -503,26 +557,35 @@ func (runner *ContainerRunner) SetupMounts() (err error) { runner.HostOutputDir = tmpdir } - case mnt.Kind == "json": - jsondata, err := json.Marshal(mnt.Content) - if err != nil { - return fmt.Errorf("encoding json data: %v", err) + case mnt.Kind == "json" || mnt.Kind == "text": + var filedata []byte + if mnt.Kind == "json" { + filedata, err = json.Marshal(mnt.Content) + if err != nil { + return fmt.Errorf("encoding json data: %v", err) + } + } else { + text, ok := mnt.Content.(string) + if !ok { + return fmt.Errorf("content for mount %q must be a string", bind) + } + filedata = []byte(text) } - // Create a tempdir with a single file - // (instead of just a tempfile): this way we - // can ensure the file is world-readable - // inside the container, without having to - // make it world-readable on the docker host. - tmpdir, err := runner.MkTempDir(runner.parentTemp, "json") + + tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind) if err != nil { return fmt.Errorf("creating temp dir: %v", err) } - tmpfn := filepath.Join(tmpdir, "mountdata.json") - err = ioutil.WriteFile(tmpfn, jsondata, 0644) + tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind) + err = ioutil.WriteFile(tmpfn, filedata, 0444) if err != nil { return fmt.Errorf("writing temp file: %v", err) } - runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind)) + if strings.HasPrefix(bind, runner.Container.OutputPath+"/") { + copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]}) + } else { + runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind)) + } case mnt.Kind == "git_tree": tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree") @@ -671,26 +734,37 @@ func (runner *ContainerRunner) stopHoststat() error { return nil } -func (runner *ContainerRunner) startHoststat() { - runner.hoststatLogger = NewThrottledLogger(runner.NewLogWriter("hoststat")) +func (runner *ContainerRunner) startHoststat() error { + w, err := runner.NewLogWriter("hoststat") + if err != nil { + return err + } + runner.hoststatLogger = NewThrottledLogger(w) runner.hoststatReporter = &crunchstat.Reporter{ Logger: log.New(runner.hoststatLogger, "", 0), CgroupRoot: runner.cgroupRoot, PollPeriod: runner.statInterval, } runner.hoststatReporter.Start() + return nil } -func (runner *ContainerRunner) startCrunchstat() { - runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat")) +func (runner *ContainerRunner) startCrunchstat() error { + w, err := runner.NewLogWriter("crunchstat") + if err != nil { + return err + } + runner.statLogger = NewThrottledLogger(w) runner.statReporter = &crunchstat.Reporter{ CID: runner.ContainerID, Logger: log.New(runner.statLogger, "", 0), CgroupParent: runner.expectCgroupParent, CgroupRoot: runner.cgroupRoot, PollPeriod: runner.statInterval, + TempDir: runner.parentTemp, } runner.statReporter.Start() + return nil } type infoCommand struct { @@ -704,7 +778,10 @@ type infoCommand struct { // might differ from what's described in the node record (see // LogNodeRecord). func (runner *ContainerRunner) LogHostInfo() (err error) { - w := runner.NewLogWriter("node-info") + w, err := runner.NewLogWriter("node-info") + if err != nil { + return + } commands := []infoCommand{ { @@ -777,11 +854,15 @@ func (runner *ContainerRunner) LogNodeRecord() error { } func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) { + writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666) + if err != nil { + return false, err + } w := &ArvLogWriter{ ArvClient: runner.ArvClient, UUID: runner.Container.UUID, loggingStream: label, - writeCloser: runner.LogCollection.Open(label + ".json"), + writeCloser: writer, } reader, err := runner.ArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params)) @@ -868,8 +949,10 @@ func (runner *ContainerRunner) AttachStreams() (err error) { return err } runner.Stdout = stdoutFile + } else if w, err := runner.NewLogWriter("stdout"); err != nil { + return err } else { - runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout")) + runner.Stdout = NewThrottledLogger(w) } if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok { @@ -878,8 +961,10 @@ func (runner *ContainerRunner) AttachStreams() (err error) { return err } runner.Stderr = stderrFile + } else if w, err := runner.NewLogWriter("stderr"); err != nil { + return err } else { - runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr")) + runner.Stderr = NewThrottledLogger(w) } if stdinRdr != nil { @@ -949,6 +1034,10 @@ func (runner *ContainerRunner) CreateContainer() error { runner.ContainerConfig.Volumes = runner.Volumes maxRAM := int64(runner.Container.RuntimeConstraints.RAM) + if maxRAM < 4*1024*1024 { + // Docker daemon won't let you set a limit less than 4 MiB + maxRAM = 4 * 1024 * 1024 + } runner.HostConfig = dockercontainer.HostConfig{ Binds: runner.Binds, LogConfig: dockercontainer.LogConfig{ @@ -1019,13 +1108,86 @@ func (runner *ContainerRunner) StartContainer() error { return nil } +// checkContainerd checks if "containerd" is present in the process list. +func (runner *ContainerRunner) CheckContainerd() error { + if runner.checkContainerd == 0 { + return nil + } + p, _ := runner.ListProcesses() + for _, i := range p { + e, _ := i.CmdlineSlice() + if len(e) > 0 { + if strings.Index(e[0], "containerd") > -1 { + return nil + } + } + } + + // Not found + runner.runBrokenNodeHook() + runner.stop(nil) + return fmt.Errorf("'containerd' not found in process list.") +} + // WaitFinish waits for the container to terminate, capture the exit code, and // close the stdout/stderr logging. func (runner *ContainerRunner) WaitFinish() error { + var runTimeExceeded <-chan time.Time runner.CrunchLog.Print("Waiting for container to finish") waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning) arvMountExit := runner.ArvMountExit + if timeout := runner.Container.SchedulingParameters.MaxRunTime; timeout > 0 { + runTimeExceeded = time.After(time.Duration(timeout) * time.Second) + } + + containerGone := make(chan struct{}) + go func() { + defer close(containerGone) + if runner.containerWatchdogInterval < 1 { + runner.containerWatchdogInterval = time.Minute + } + for range time.NewTicker(runner.containerWatchdogInterval).C { + ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(runner.containerWatchdogInterval)) + ctr, err := runner.Docker.ContainerInspect(ctx, runner.ContainerID) + cancel() + runner.cStateLock.Lock() + done := runner.cRemoved || runner.ExitCode != nil + runner.cStateLock.Unlock() + if done { + return + } else if err != nil { + runner.CrunchLog.Printf("Error inspecting container: %s", err) + runner.checkBrokenNode(err) + return + } else if ctr.State == nil || !(ctr.State.Running || ctr.State.Status == "created") { + runner.CrunchLog.Printf("Container is not running: State=%v", ctr.State) + return + } + } + }() + + containerdGone := make(chan error) + defer close(containerdGone) + if runner.checkContainerd > 0 { + go func() { + ticker := time.NewTicker(time.Duration(runner.checkContainerd)) + defer ticker.Stop() + for { + select { + case <-ticker.C: + if ck := runner.CheckContainerd(); ck != nil { + containerdGone <- ck + return + } + case <-containerdGone: + // Channel closed, quit goroutine + return + } + } + }() + } + for { select { case waitBody := <-waitOk: @@ -1046,185 +1208,71 @@ func (runner *ContainerRunner) WaitFinish() error { // arvMountExit will always be ready now that // it's closed, but that doesn't interest us. arvMountExit = nil - } - } -} -var ErrNotInOutputDir = fmt.Errorf("Must point to path within the output directory") - -func (runner *ContainerRunner) derefOutputSymlink(path string, startinfo os.FileInfo) (tgt string, readlinktgt string, info os.FileInfo, err error) { - // Follow symlinks if necessary - info = startinfo - tgt = path - readlinktgt = "" - nextlink := path - for followed := 0; info.Mode()&os.ModeSymlink != 0; followed++ { - if followed >= limitFollowSymlinks { - // Got stuck in a loop or just a pathological number of links, give up. - err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path) - return - } + case <-runTimeExceeded: + runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.") + runner.stop(nil) + runTimeExceeded = nil - readlinktgt, err = os.Readlink(nextlink) - if err != nil { - return - } + case <-containerGone: + return errors.New("docker client never returned status") - tgt = readlinktgt - if !strings.HasPrefix(tgt, "/") { - // Relative symlink, resolve it to host path - tgt = filepath.Join(filepath.Dir(path), tgt) - } - if strings.HasPrefix(tgt, runner.Container.OutputPath+"/") && !strings.HasPrefix(tgt, runner.HostOutputDir+"/") { - // Absolute symlink to container output path, adjust it to host output path. - tgt = filepath.Join(runner.HostOutputDir, tgt[len(runner.Container.OutputPath):]) - } - if !strings.HasPrefix(tgt, runner.HostOutputDir+"/") { - // After dereferencing, symlink target must either be - // within output directory, or must point to a - // collection mount. - err = ErrNotInOutputDir - return - } - - info, err = os.Lstat(tgt) - if err != nil { - // tgt - err = fmt.Errorf("Symlink in output %q points to invalid location %q: %v", - path[len(runner.HostOutputDir):], readlinktgt, err) - return + case err := <-containerdGone: + return err } - - nextlink = tgt } - - return } -var limitFollowSymlinks = 10 - -// UploadFile uploads files within the output directory, with special handling -// for symlinks. If the symlink leads to a keep mount, copy the manifest text -// from the keep mount into the output manifestText. Ensure that whether -// symlinks are relative or absolute, every symlink target (even targets that -// are symlinks themselves) must point to a path in either the output directory -// or a collection mount. -// -// Assumes initial value of "path" is absolute, and located within runner.HostOutputDir. -func (runner *ContainerRunner) UploadOutputFile( - path string, - info os.FileInfo, - infoerr error, - binds []string, - walkUpload *WalkUpload, - relocateFrom string, - relocateTo string, - followed int) (manifestText string, err error) { - - if infoerr != nil { - return "", infoerr - } - - if info.Mode().IsDir() { - // if empty, need to create a .keep file - dir, direrr := os.Open(path) - if direrr != nil { - return "", direrr - } - defer dir.Close() - names, eof := dir.Readdirnames(1) - if len(names) == 0 && eof == io.EOF && path != runner.HostOutputDir { - containerPath := runner.OutputPath + path[len(runner.HostOutputDir):] - for _, bind := range binds { - mnt := runner.Container.Mounts[bind] - // Check if there is a bind for this - // directory, in which case assume we don't need .keep - if (containerPath == bind || strings.HasPrefix(containerPath, bind+"/")) && mnt.PortableDataHash != "d41d8cd98f00b204e9800998ecf8427e+0" { - return - } - } - outputSuffix := path[len(runner.HostOutputDir)+1:] - return fmt.Sprintf("./%v d41d8cd98f00b204e9800998ecf8427e+0 0:0:.keep\n", outputSuffix), nil - } - return - } - - if followed >= limitFollowSymlinks { - // Got stuck in a loop or just a pathological number of - // directory links, give up. - err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path) - return - } - - // "path" is the actual path we are visiting - // "tgt" is the target of "path" (a non-symlink) after following symlinks - // "relocated" is the path in the output manifest where the file should be placed, - // but has HostOutputDir as a prefix. - - // The destination path in the output manifest may need to be - // logically relocated to some other path in order to appear - // in the correct location as a result of following a symlink. - // Remove the relocateFrom prefix and replace it with - // relocateTo. - relocated := relocateTo + path[len(relocateFrom):] +func (runner *ContainerRunner) updateLogs() { + ticker := time.NewTicker(crunchLogUpdatePeriod / 360) + defer ticker.Stop() - tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info) - if derefErr != nil && derefErr != ErrNotInOutputDir { - return "", derefErr - } + sigusr1 := make(chan os.Signal, 1) + signal.Notify(sigusr1, syscall.SIGUSR1) + defer signal.Stop(sigusr1) - // go through mounts and try reverse map to collection reference - for _, bind := range binds { - mnt := runner.Container.Mounts[bind] - if (tgt == bind || strings.HasPrefix(tgt, bind+"/")) && !mnt.Writable { - // get path relative to bind - targetSuffix := tgt[len(bind):] - - // Copy mount and adjust the path to add path relative to the bind - adjustedMount := mnt - adjustedMount.Path = filepath.Join(adjustedMount.Path, targetSuffix) - - // Terminates in this keep mount, so add the - // manifest text at appropriate location. - outputSuffix := relocated[len(runner.HostOutputDir):] - manifestText, err = runner.getCollectionManifestForPath(adjustedMount, outputSuffix) + saveAtTime := time.Now().Add(crunchLogUpdatePeriod) + saveAtSize := crunchLogUpdateSize + var savedSize int64 + for { + select { + case <-ticker.C: + case <-sigusr1: + saveAtTime = time.Now() + } + runner.logMtx.Lock() + done := runner.LogsPDH != nil + runner.logMtx.Unlock() + if done { return } - } - - // If target is not a collection mount, it must be located within the - // output directory, otherwise it is an error. - if derefErr == ErrNotInOutputDir { - err = fmt.Errorf("Symlink in output %q points to invalid location %q, must point to path within the output directory.", - path[len(runner.HostOutputDir):], readlinktgt) - return - } + size := runner.LogCollection.Size() + if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) { + continue + } + saveAtTime = time.Now().Add(crunchLogUpdatePeriod) + saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize + saved, err := runner.saveLogCollection(false) + if err != nil { + runner.CrunchLog.Printf("error updating log collection: %s", err) + continue + } - if info.Mode().IsRegular() { - return "", walkUpload.UploadFile(relocated, tgt) - } + var updated arvados.Container + err = runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{ + "container": arvadosclient.Dict{"log": saved.PortableDataHash}, + }, &updated) + if err != nil { + runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err) + continue + } - if info.Mode().IsDir() { - // Symlink leads to directory. Walk() doesn't follow - // directory symlinks, so we walk the target directory - // instead. Within the walk, file paths are relocated - // so they appear under the original symlink path. - err = filepath.Walk(tgt, func(walkpath string, walkinfo os.FileInfo, walkerr error) error { - var m string - m, walkerr = runner.UploadOutputFile(walkpath, walkinfo, walkerr, - binds, walkUpload, tgt, relocated, followed+1) - if walkerr == nil { - manifestText = manifestText + m - } - return walkerr - }) - return + savedSize = size } - - return } -// HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories +// CaptureOutput saves data from the container's output directory if +// needed, and updates the container output accordingly. func (runner *ContainerRunner) CaptureOutput() error { if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI { // Output may have been set directly by the container, so @@ -1241,153 +1289,47 @@ func (runner *ContainerRunner) CaptureOutput() error { } } - if runner.HostOutputDir == "" { - return nil - } - - _, err := os.Stat(runner.HostOutputDir) + txt, err := (&copier{ + client: runner.client, + arvClient: runner.ArvClient, + keepClient: runner.Kc, + hostOutputDir: runner.HostOutputDir, + ctrOutputDir: runner.Container.OutputPath, + binds: runner.Binds, + mounts: runner.Container.Mounts, + secretMounts: runner.SecretMounts, + logger: runner.CrunchLog, + }).Copy() if err != nil { - return fmt.Errorf("While checking host output path: %v", err) - } - - // Pre-populate output from the configured mount points - var binds []string - for bind, mnt := range runner.Container.Mounts { - if mnt.Kind == "collection" { - binds = append(binds, bind) - } + return err } - sort.Strings(binds) - - var manifestText string - - collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir) - _, err = os.Stat(collectionMetafile) - if err != nil { - // Regular directory - - cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}} - walkUpload := cw.BeginUpload(runner.HostOutputDir, runner.CrunchLog.Logger) - - var m string - err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error { - m, err = runner.UploadOutputFile(path, info, err, binds, walkUpload, "", "", 0) - if err == nil { - manifestText = manifestText + m - } - return err - }) - - cw.EndUpload(walkUpload) - + if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 { + runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n) + fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.client, runner.Kc) if err != nil { - return fmt.Errorf("While uploading output files: %v", err) - } - - m, err = cw.ManifestText() - manifestText = manifestText + m - if err != nil { - return fmt.Errorf("While uploading output files: %v", err) - } - } else { - // FUSE mount directory - file, openerr := os.Open(collectionMetafile) - if openerr != nil { - return fmt.Errorf("While opening FUSE metafile: %v", err) - } - defer file.Close() - - var rec arvados.Collection - err = json.NewDecoder(file).Decode(&rec) - if err != nil { - return fmt.Errorf("While reading FUSE metafile: %v", err) - } - manifestText = rec.ManifestText - } - - for _, bind := range binds { - mnt := runner.Container.Mounts[bind] - - bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath) - - if bindSuffix == bind || len(bindSuffix) <= 0 { - // either does not start with OutputPath or is OutputPath itself - continue - } - - if mnt.ExcludeFromOutput == true || mnt.Writable { - continue + return err } - - // append to manifest_text - m, err := runner.getCollectionManifestForPath(mnt, bindSuffix) + txt, err = fs.MarshalManifest(".") if err != nil { return err } - - manifestText = manifestText + m } - - // Save output - var response arvados.Collection - manifest := manifest.Manifest{Text: manifestText} - manifestText = manifest.Extract(".", ".").Text - err = runner.ArvClient.Create("collections", - arvadosclient.Dict{ - "ensure_unique_name": true, - "collection": arvadosclient.Dict{ - "is_trashed": true, - "name": "output for " + runner.Container.UUID, - "manifest_text": manifestText}}, - &response) + var resp arvados.Collection + err = runner.ArvClient.Create("collections", arvadosclient.Dict{ + "ensure_unique_name": true, + "collection": arvadosclient.Dict{ + "is_trashed": true, + "name": "output for " + runner.Container.UUID, + "manifest_text": txt, + }, + }, &resp) if err != nil { - return fmt.Errorf("While creating output collection: %v", err) + return fmt.Errorf("error creating output collection: %v", err) } - runner.OutputPDH = &response.PortableDataHash + runner.OutputPDH = &resp.PortableDataHash return nil } -var outputCollections = make(map[string]arvados.Collection) - -// Fetch the collection for the mnt.PortableDataHash -// Return the manifest_text fragment corresponding to the specified mnt.Path -// after making any required updates. -// Ex: -// If mnt.Path is not specified, -// return the entire manifest_text after replacing any "." with bindSuffix -// If mnt.Path corresponds to one stream, -// return the manifest_text for that stream after replacing that stream name with bindSuffix -// Otherwise, check if a filename in any one stream is being sought. Return the manifest_text -// for that stream after replacing stream name with bindSuffix minus the last word -// and the file name with last word of the bindSuffix -// Allowed path examples: -// "path":"/" -// "path":"/subdir1" -// "path":"/subdir1/subdir2" -// "path":"/subdir/filename" etc -func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) { - collection := outputCollections[mnt.PortableDataHash] - if collection.PortableDataHash == "" { - err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection) - if err != nil { - return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err) - } - outputCollections[mnt.PortableDataHash] = collection - } - - if collection.ManifestText == "" { - runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash) - return "", nil - } - - mft := manifest.Manifest{Text: collection.ManifestText} - extracted := mft.Extract(mnt.Path, bindSuffix) - if extracted.Err != nil { - return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error()) - } - return extracted.Text, nil -} - func (runner *ContainerRunner) CleanupDirs() { if runner.ArvMount != nil { var delay int64 = 8 @@ -1460,8 +1402,12 @@ func (runner *ContainerRunner) CommitLogs() error { // point, but re-open crunch log with ArvClient in case there are any // other further errors (such as failing to write the log to Keep!) // while shutting down - runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient, - UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: nil}) + runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ + ArvClient: runner.ArvClient, + UUID: runner.Container.UUID, + loggingStream: "crunch-run", + writeCloser: nil, + }) runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0) }() @@ -1473,26 +1419,51 @@ func (runner *ContainerRunner) CommitLogs() error { // -- it exists only to send logs to other channels. return nil } + saved, err := runner.saveLogCollection(true) + if err != nil { + return fmt.Errorf("error saving log collection: %s", err) + } + runner.logMtx.Lock() + defer runner.logMtx.Unlock() + runner.LogsPDH = &saved.PortableDataHash + return nil +} - mt, err := runner.LogCollection.ManifestText() +func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) { + runner.logMtx.Lock() + defer runner.logMtx.Unlock() + if runner.LogsPDH != nil { + // Already finalized. + return + } + mt, err := runner.LogCollection.MarshalManifest(".") if err != nil { - return fmt.Errorf("While creating log manifest: %v", err) - } - - var response arvados.Collection - err = runner.ArvClient.Create("collections", - arvadosclient.Dict{ - "ensure_unique_name": true, - "collection": arvadosclient.Dict{ - "is_trashed": true, - "name": "logs for " + runner.Container.UUID, - "manifest_text": mt}}, - &response) + err = fmt.Errorf("error creating log manifest: %v", err) + return + } + updates := arvadosclient.Dict{ + "name": "logs for " + runner.Container.UUID, + "manifest_text": mt, + } + if final { + updates["is_trashed"] = true + } else { + exp := time.Now().Add(crunchLogUpdatePeriod * 24) + updates["trash_at"] = exp + updates["delete_at"] = exp + } + reqBody := arvadosclient.Dict{"collection": updates} + if runner.logUUID == "" { + reqBody["ensure_unique_name"] = true + err = runner.ArvClient.Create("collections", reqBody, &response) + } else { + err = runner.ArvClient.Update("collections", runner.logUUID, reqBody, &response) + } if err != nil { - return fmt.Errorf("While creating log collection: %v", err) + return } - runner.LogsPDH = &response.PortableDataHash - return nil + runner.logUUID = response.UUID + return } // UpdateContainerRunning updates the container state to "Running" @@ -1518,7 +1489,7 @@ func (runner *ContainerRunner) ContainerToken() (string, error) { if err != nil { return "", err } - runner.token = auth.APIToken + runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID) return runner.token, nil } @@ -1549,12 +1520,17 @@ func (runner *ContainerRunner) IsCancelled() bool { } // NewArvLogWriter creates an ArvLogWriter -func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser { +func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) { + writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666) + if err != nil { + return nil, err + } return &ArvLogWriter{ ArvClient: runner.ArvClient, UUID: runner.Container.UUID, loggingStream: name, - writeCloser: runner.LogCollection.Open(name + ".txt")} + writeCloser: writer, + }, nil } // Run the full container lifecycle. @@ -1584,11 +1560,11 @@ func (runner *ContainerRunner) Run() (err error) { // hasn't already been assigned when Run() returns, // this cleanup func will cause Run() to return the // first non-nil error that is passed to checkErr(). - checkErr := func(e error) { + checkErr := func(errorIn string, e error) { if e == nil { return } - runner.CrunchLog.Print(e) + runner.CrunchLog.Printf("error in %s: %v", errorIn, e) if err == nil { err = e } @@ -1599,7 +1575,7 @@ func (runner *ContainerRunner) Run() (err error) { } // Log the error encountered in Run(), if any - checkErr(err) + checkErr("Run", err) if runner.finalState == "Queued" { runner.UpdateContainerFinal() @@ -1612,10 +1588,10 @@ func (runner *ContainerRunner) Run() (err error) { // capture partial output and write logs } - checkErr(runner.CaptureOutput()) - checkErr(runner.stopHoststat()) - checkErr(runner.CommitLogs()) - checkErr(runner.UpdateContainerFinal()) + checkErr("CaptureOutput", runner.CaptureOutput()) + checkErr("stopHoststat", runner.stopHoststat()) + checkErr("CommitLogs", runner.CommitLogs()) + checkErr("UpdateContainerFinal", runner.UpdateContainerFinal()) }() err = runner.fetchContainerRecord() @@ -1623,7 +1599,16 @@ func (runner *ContainerRunner) Run() (err error) { return } runner.setupSignals() - runner.startHoststat() + err = runner.startHoststat() + if err != nil { + return + } + + // Sanity check that containerd is running. + err = runner.CheckContainerd() + if err != nil { + return + } // check for and/or load image err = runner.LoadImage() @@ -1672,7 +1657,10 @@ func (runner *ContainerRunner) Run() (err error) { } runner.finalState = "Cancelled" - runner.startCrunchstat() + err = runner.startCrunchstat() + if err != nil { + return + } err = runner.StartContainer() if err != nil { @@ -1702,27 +1690,85 @@ func (runner *ContainerRunner) fetchContainerRecord() error { if err != nil { return fmt.Errorf("error decoding container record: %v", err) } + + var sm struct { + SecretMounts map[string]arvados.Mount `json:"secret_mounts"` + } + + containerToken, err := runner.ContainerToken() + if err != nil { + return fmt.Errorf("error getting container token: %v", err) + } + + containerClient, _, err := runner.MkArvClient(containerToken) + if err != nil { + return fmt.Errorf("error creating container API client: %v", err) + } + + err = containerClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm) + if err != nil { + if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 { + return fmt.Errorf("error fetching secret_mounts: %v", err) + } + // ok && apierr.HttpStatusCode == 404, which means + // secret_mounts isn't supported by this API server. + } + runner.SecretMounts = sm.SecretMounts + return nil } // NewContainerRunner creates a new container runner. -func NewContainerRunner(api IArvadosClient, - kc IKeepClient, - docker ThinDockerClient, - containerUUID string) *ContainerRunner { - - cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker} +func NewContainerRunner(client *arvados.Client, api IArvadosClient, kc IKeepClient, docker ThinDockerClient, containerUUID string) (*ContainerRunner, error) { + cr := &ContainerRunner{ + client: client, + ArvClient: api, + Kc: kc, + Docker: docker, + } cr.NewLogWriter = cr.NewArvLogWriter cr.RunArvMount = cr.ArvMountCmd cr.MkTempDir = ioutil.TempDir - cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}} + cr.ListProcesses = func() ([]PsProcess, error) { + pr, err := process.Processes() + if err != nil { + return nil, err + } + ps := make([]PsProcess, len(pr)) + for i, j := range pr { + ps[i] = j + } + return ps, nil + } + cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, error) { + cl, err := arvadosclient.MakeArvadosClient() + if err != nil { + return nil, nil, err + } + cl.ApiToken = token + kc, err := keepclient.MakeKeepClient(cl) + if err != nil { + return nil, nil, err + } + return cl, kc, nil + } + var err error + cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.client, cr.Kc) + if err != nil { + return nil, err + } cr.Container.UUID = containerUUID - cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run")) + w, err := cr.NewLogWriter("crunch-run") + if err != nil { + return nil, err + } + cr.CrunchLog = NewThrottledLogger(w) cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0) loadLogThrottleParams(api) + go cr.updateLogs() - return cr + return cr, nil } func main() { @@ -1741,6 +1787,7 @@ func main() { `) memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container") getVersion := flag.Bool("version", false, "Print version information and exit.") + checkContainerd := flag.Duration("check-containerd", 60*time.Second, "Periodic check if (docker-)containerd is running (use 0s to disable).") flag.Parse() // Print version information if requested @@ -1774,7 +1821,10 @@ func main() { // minimum version we want to support. docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil) - cr := NewContainerRunner(api, kc, docker, containerId) + cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, docker, containerId) + if err != nil { + log.Fatal(err) + } if dockererr != nil { cr.CrunchLog.Printf("%s: %v", containerId, dockererr) cr.checkBrokenNode(dockererr) @@ -1793,6 +1843,7 @@ func main() { cr.expectCgroupParent = *cgroupParent cr.enableNetwork = *enableNetwork cr.networkMode = *networkMode + cr.checkContainerd = *checkContainerd if *cgroupParentSubsystem != "" { p := findCgroup(*cgroupParentSubsystem) cr.setCgroupParent = p @@ -1804,15 +1855,15 @@ func main() { if *memprofile != "" { f, err := os.Create(*memprofile) if err != nil { - log.Printf("could not create memory profile: ", err) + log.Printf("could not create memory profile: %s", err) } runtime.GC() // get up-to-date statistics if err := pprof.WriteHeapProfile(f); err != nil { - log.Printf("could not write memory profile: ", err) + log.Printf("could not write memory profile: %s", err) } closeerr := f.Close() if closeerr != nil { - log.Printf("closing memprofile file: ", err) + log.Printf("closing memprofile file: %s", err) } }