"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"
// 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)
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
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
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
}
}
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)
}
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)
}
runner.ContainerConfig.Image = imageID
- runner.Kc.ClearBlockCache()
+ kc.ClearBlockCache()
return nil
}
}
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
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" {
}
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)
}
}
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")
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 {
// 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{
{
}
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))
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 {
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 {
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{
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:
// 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
}
}
- 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
// 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)
}()
// -- 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"
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
}
}
// 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.
// 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
}
}
// Log the error encountered in Run(), if any
- checkErr(err)
+ checkErr("Run", err)
if runner.finalState == "Queued" {
runner.UpdateContainerFinal()
// 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()
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()
}
runner.finalState = "Cancelled"
- runner.startCrunchstat()
+ err = runner.startCrunchstat()
+ if err != nil {
+ return
+ }
err = runner.StartContainer()
if err != nil {
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() {
`)
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
// 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)
cr.expectCgroupParent = *cgroupParent
cr.enableNetwork = *enableNetwork
cr.networkMode = *networkMode
+ cr.checkContainerd = *checkContainerd
if *cgroupParentSubsystem != "" {
p := findCgroup(*cgroupParentSubsystem)
cr.setCgroupParent = p
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)
}
}
projects / arvados.git / blobdiff