// 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)
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)
// container.
type ContainerRunner struct {
Docker ThinDockerClient
+ client *arvados.Client
ArvClient IArvadosClient
Kc IKeepClient
arvados.Container
CrunchLog *ThrottledLogger
Stdout io.WriteCloser
Stderr io.WriteCloser
- LogCollection *CollectionWriter
+ LogCollection arvados.CollectionFileSystem
LogsPDH *string
RunArvMount
MkTempDir
}
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
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),
PollPeriod: runner.statInterval,
}
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 {
}
}
-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
- }
-
- readlinktgt, err = os.Readlink(nextlink)
- if err != nil {
- return
- }
-
- 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
- }
-
- 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):]
-
- tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info)
- if derefErr != nil && derefErr != ErrNotInOutputDir {
- return "", derefErr
- }
-
- // 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)
- 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
- }
-
- if info.Mode().IsRegular() {
- return "", walkUpload.UploadFile(relocated, tgt)
- }
-
- 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
- }
-
- 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)
- }
- }
- sort.Strings(binds)
-
- // Delete secret mounts so they don't get saved to the output collection.
- for bind := range runner.SecretMounts {
- if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
- err = os.Remove(runner.HostOutputDir + bind[len(runner.Container.OutputPath):])
- if err != nil {
- return fmt.Errorf("Unable to remove secret mount: %v", err)
- }
- }
- }
-
- 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 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
- }
-
- // append to manifest_text
- m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
- 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)
+ return err
+ }
+ 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)
}()
return nil
}
- mt, err := runner.LogCollection.ManifestText()
+ mt, err := runner.LogCollection.MarshalManifest(".")
if err != nil {
return fmt.Errorf("While creating log manifest: %v", err)
}
}
// 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.
return
}
runner.setupSignals()
- runner.startHoststat()
+ err = runner.startHoststat()
+ 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 {
}
// 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
cl.ApiToken = token
return cl, nil
}
- cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
+ 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)
- return cr
+ return cr, nil
}
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)
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