"strings"
"sync"
"syscall"
+ "time"
)
// IArvadosClient is the minimal Arvados API methods used by crunch-run.
// NewLogWriter is a factory function to create a new log writer.
type NewLogWriter func(name string) io.WriteCloser
+type RunArvMount func([]string) (*exec.Cmd, error)
+
+type MkTempDir func(string, string) (string, error)
+
// ThinDockerClient is the minimal Docker client interface used by crunch-run.
type ThinDockerClient interface {
StopContainer(id string, timeout int) error
LoadImage(reader io.Reader) error
CreateContainer(config *dockerclient.ContainerConfig, name string, authConfig *dockerclient.AuthConfig) (string, error)
StartContainer(id string, config *dockerclient.HostConfig) error
- ContainerLogs(id string, options *dockerclient.LogOptions) (io.ReadCloser, error)
+ AttachContainer(id string, options *dockerclient.AttachOptions) (io.ReadCloser, error)
Wait(id string) <-chan dockerclient.WaitResult
RemoveImage(name string, force bool) ([]*dockerclient.ImageDelete, error)
}
Stderr *ThrottledLogger
LogCollection *CollectionWriter
LogsPDH *string
- ArvMount *exec.Cmd
- ArvMountPoint string
- HostOutputDir string
- Binds []string
- OutputPDH *string
- CancelLock sync.Mutex
- Cancelled bool
- SigChan chan os.Signal
- finalState string
+ RunArvMount
+ MkTempDir
+ ArvMount *exec.Cmd
+ ArvMountPoint string
+ HostOutputDir string
+ CleanupTempDir []string
+ Binds []string
+ OutputPDH *string
+ CancelLock sync.Mutex
+ Cancelled bool
+ SigChan chan os.Signal
+ ArvMountExit chan error
+ finalState string
}
// SetupSignals sets up signal handling to gracefully terminate the underlying
// Docker container and update state when receiving a TERM, INT or QUIT signal.
-func (runner *ContainerRunner) SetupSignals() error {
+func (runner *ContainerRunner) SetupSignals() {
runner.SigChan = make(chan os.Signal, 1)
signal.Notify(runner.SigChan, syscall.SIGTERM)
signal.Notify(runner.SigChan, syscall.SIGINT)
}
}
}(runner.SigChan)
-
- return nil
}
// LoadImage determines the docker image id from the container record and
return nil
}
+func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string) (c *exec.Cmd, err error) {
+ c = exec.Command("arv-mount", arvMountCmd...)
+ nt := NewThrottledLogger(runner.NewLogWriter("arv-mount"))
+ c.Stdout = nt
+ c.Stderr = nt
+
+ err = c.Start()
+ if err != nil {
+ return nil, err
+ }
+
+ statReadme := make(chan bool)
+ runner.ArvMountExit = make(chan error)
+
+ keepStatting := true
+ go func() {
+ for keepStatting {
+ time.Sleep(100 * time.Millisecond)
+ _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
+ if err == nil {
+ keepStatting = false
+ statReadme <- true
+ }
+ }
+ close(statReadme)
+ }()
+
+ go func() {
+ runner.ArvMountExit <- c.Wait()
+ close(runner.ArvMountExit)
+ }()
+
+ select {
+ case <-statReadme:
+ break
+ case err := <-runner.ArvMountExit:
+ runner.ArvMount = nil
+ keepStatting = false
+ return nil, err
+ }
+
+ return c, nil
+}
+
func (runner *ContainerRunner) SetupMounts() (err error) {
- runner.ArvMountPoint, err = ioutil.TempDir("", "keep")
+ runner.ArvMountPoint, err = runner.MkTempDir("", "keep")
if err != nil {
return fmt.Errorf("While creating keep mount temp dir: %v", err)
}
+ runner.CleanupTempDir = append(runner.CleanupTempDir, runner.ArvMountPoint)
+
pdhOnly := true
tmpcount := 0
- arvMountCmd := []string{"--foreground"}
+ arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
collectionPaths := []string{}
+ runner.Binds = nil
for bind, mnt := range runner.ContainerRecord.Mounts {
if mnt.Kind == "collection" {
}
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
} else {
- src = fmt.Sprintf("%s/tmp%i", runner.ArvMountPoint, tmpcount)
+ src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp")
- arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%i", tmpcount))
+ arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
tmpcount += 1
}
if mnt.Writable {
collectionPaths = append(collectionPaths, src)
} else if mnt.Kind == "tmp" {
if bind == runner.ContainerRecord.OutputPath {
- runner.HostOutputDir, err = ioutil.TempDir("", "")
+ runner.HostOutputDir, err = runner.MkTempDir("", "")
if err != nil {
return fmt.Errorf("While creating mount temp dir: %v", err)
}
-
+ st, staterr := os.Stat(runner.HostOutputDir)
+ if staterr != nil {
+ return fmt.Errorf("While Stat on temp dir: %v", staterr)
+ }
+ err = os.Chmod(runner.HostOutputDir, st.Mode()|os.ModeSetgid|0777)
+ if staterr != nil {
+ return fmt.Errorf("While Chmod temp dir: %v", err)
+ }
+ runner.CleanupTempDir = append(runner.CleanupTempDir, runner.HostOutputDir)
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", runner.HostOutputDir, bind))
} else {
runner.Binds = append(runner.Binds, bind)
}
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
- runner.ArvMount = exec.Command("arv-mount", arvMountCmd...)
- err = runner.ArvMount.Start()
+ runner.ArvMount, err = runner.RunArvMount(arvMountCmd)
if err != nil {
- runner.ArvMount = nil
return fmt.Errorf("While trying to start arv-mount: %v", err)
}
return nil
}
+func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
+ // Handle docker log protocol
+ // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
+
+ header := make([]byte, 8)
+ for {
+ _, readerr := io.ReadAtLeast(containerReader, header, 8)
+
+ if readerr == nil {
+ readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
+ if header[0] == 1 {
+ // stdout
+ _, readerr = io.CopyN(runner.Stdout, containerReader, readsize)
+ } else {
+ // stderr
+ _, readerr = io.CopyN(runner.Stderr, containerReader, readsize)
+ }
+ }
+
+ if readerr != nil {
+ if readerr != io.EOF {
+ runner.CrunchLog.Printf("While reading docker logs: %v", readerr)
+ }
+
+ closeerr := runner.Stdout.Close()
+ if closeerr != nil {
+ runner.CrunchLog.Printf("While closing stdout logs: %v", closeerr)
+ }
+
+ closeerr = runner.Stderr.Close()
+ if closeerr != nil {
+ runner.CrunchLog.Printf("While closing stderr logs: %v", closeerr)
+ }
+
+ runner.loggingDone <- true
+ close(runner.loggingDone)
+ return
+ }
+ }
+}
+
+// AttachLogs connects the docker container stdout and stderr logs to the
+// Arvados logger which logs to Keep and the API server logs table.
+func (runner *ContainerRunner) AttachStreams() (err error) {
+
+ runner.CrunchLog.Print("Attaching container streams")
+
+ var containerReader io.Reader
+ containerReader, err = runner.Docker.AttachContainer(runner.ContainerID,
+ &dockerclient.AttachOptions{Stream: true, Stdout: true, Stderr: true})
+ if err != nil {
+ return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
+ }
+
+ runner.loggingDone = make(chan bool)
+
+ runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
+ runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
+
+ go runner.ProcessDockerAttach(containerReader)
+
+ return nil
+}
+
// StartContainer creates the container and runs it.
func (runner *ContainerRunner) StartContainer() (err error) {
runner.CrunchLog.Print("Creating Docker container")
if err != nil {
return fmt.Errorf("While creating container: %v", err)
}
- hostConfig := &dockerclient.HostConfig{Binds: runner.Binds}
+ hostConfig := &dockerclient.HostConfig{Binds: runner.Binds,
+ LogConfig: dockerclient.LogConfig{Type: "none"}}
- runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
- err = runner.Docker.StartContainer(runner.ContainerID, hostConfig)
+ err = runner.AttachStreams()
if err != nil {
- return fmt.Errorf("While starting container: %v", err)
+ return err
}
- return nil
-}
-
-// AttachLogs connects the docker container stdout and stderr logs to the
-// Arvados logger which logs to Keep and the API server logs table.
-func (runner *ContainerRunner) AttachLogs() (err error) {
-
- runner.CrunchLog.Print("Attaching container logs")
-
- var stderrReader, stdoutReader io.Reader
- stderrReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stderr: true})
- if err != nil {
- return fmt.Errorf("While getting container standard error: %v", err)
- }
- stdoutReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stdout: true})
+ runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
+ err = runner.Docker.StartContainer(runner.ContainerID, hostConfig)
if err != nil {
- return fmt.Errorf("While getting container standard output: %v", err)
+ return fmt.Errorf("While starting container: %v", err)
}
- runner.loggingDone = make(chan bool)
-
- runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
- runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
- go ReadWriteLines(stdoutReader, runner.Stdout, runner.loggingDone)
- go ReadWriteLines(stderrReader, runner.Stderr, runner.loggingDone)
-
return nil
}
// WaitFinish waits for the container to terminate, capture the exit code, and
// close the stdout/stderr logging.
func (runner *ContainerRunner) WaitFinish() error {
+ runner.CrunchLog.Print("Waiting for container to finish")
+
result := runner.Docker.Wait(runner.ContainerID)
wr := <-result
if wr.Error != nil {
}
runner.ExitCode = &wr.ExitCode
- // drain stdout/stderr
+ // wait for stdout/stderr to complete
<-runner.loggingDone
- <-runner.loggingDone
-
- runner.Stdout.Close()
- runner.Stderr.Close()
return nil
}
-// HandleOutput sets the output and unmounts the FUSE mount.
+// HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
func (runner *ContainerRunner) CaptureOutput() error {
- if runner.ArvMount != nil {
- defer func() {
- umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
- umount.Run()
- }()
- }
-
if runner.finalState != "Complete" {
return nil
}
var response CollectionRecord
err = runner.ArvClient.Create("collections",
- arvadosclient.Dict{"manifest_text": manifestText},
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "manifest_text": manifestText}},
&response)
if err != nil {
return fmt.Errorf("While creating output collection: %v", err)
return nil
}
+func (runner *ContainerRunner) CleanupDirs() {
+ if runner.ArvMount != nil {
+ umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
+ umnterr := umount.Run()
+ if umnterr != nil {
+ runner.CrunchLog.Printf("While running fusermount: %v", umnterr)
+ }
+
+ mnterr := <-runner.ArvMountExit
+ if mnterr != nil {
+ runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
+ }
+ }
+
+ for _, tmpdir := range runner.CleanupTempDir {
+ rmerr := os.RemoveAll(tmpdir)
+ if rmerr != nil {
+ runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", tmpdir, rmerr)
+ }
+ }
+}
+
// CommitLogs posts the collection containing the final container logs.
func (runner *ContainerRunner) CommitLogs() error {
runner.CrunchLog.Print(runner.finalState)
var response CollectionRecord
err = runner.ArvClient.Create("collections",
- arvadosclient.Dict{"name": "logs for " + runner.ContainerRecord.UUID,
- "manifest_text": mt},
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "name": "logs for " + runner.ContainerRecord.UUID,
+ "manifest_text": mt}},
&response)
if err != nil {
return fmt.Errorf("While creating log collection: %v", err)
// UpdateContainerRecordRunning updates the container state to "Running"
func (runner *ContainerRunner) UpdateContainerRecordRunning() error {
- update := arvadosclient.Dict{"state": "Running"}
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, update, nil)
+ return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID,
+ arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
}
// UpdateContainerRecordComplete updates the container record state on API
update["state"] = runner.finalState
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, update, nil)
+ return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, arvadosclient.Dict{"container": update}, nil)
}
// NewArvLogWriter creates an ArvLogWriter
}
// Run the full container lifecycle.
-func (runner *ContainerRunner) Run(containerUUID string) (err error) {
- runner.CrunchLog.Printf("Executing container '%s'", containerUUID)
+func (runner *ContainerRunner) Run() (err error) {
+ runner.CrunchLog.Printf("Executing container '%s'", runner.ContainerRecord.UUID)
+
+ hostname, hosterr := os.Hostname()
+ if hosterr != nil {
+ runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
+ } else {
+ runner.CrunchLog.Printf("Executing on host '%s'", hostname)
+ }
var runerr, waiterr error
runner.finalState = "Complete"
}
- // (7) capture output
+ // (6) capture output
outputerr := runner.CaptureOutput()
if outputerr != nil {
runner.CrunchLog.Print(outputerr)
}
+ // (7) clean up temporary directories
+ runner.CleanupDirs()
+
// (8) write logs
logerr := runner.CommitLogs()
if logerr != nil {
if runerr != nil {
err = runerr
} else if waiterr != nil {
- err = runerr
+ err = waiterr
} else if logerr != nil {
err = logerr
} else if updateerr != nil {
}
}()
- err = runner.ArvClient.Get("containers", containerUUID, nil, &runner.ContainerRecord)
+ err = runner.ArvClient.Get("containers", runner.ContainerRecord.UUID, nil, &runner.ContainerRecord)
if err != nil {
return fmt.Errorf("While getting container record: %v", err)
}
// (1) setup signal handling
- err = runner.SetupSignals()
- if err != nil {
- return fmt.Errorf("While setting up signal handling: %v", err)
- }
+ runner.SetupSignals()
// (2) check for and/or load image
err = runner.LoadImage()
runner.CrunchLog.Print(err)
}
- // (5) attach container logs
- runerr = runner.AttachLogs()
- if runerr != nil {
- runner.CrunchLog.Print(runerr)
- }
-
- // (6) wait for container to finish
+ // (5) wait for container to finish
waiterr = runner.WaitFinish()
return
// NewContainerRunner creates a new container runner.
func NewContainerRunner(api IArvadosClient,
kc IKeepClient,
- docker ThinDockerClient) *ContainerRunner {
+ docker ThinDockerClient,
+ containerUUID string) *ContainerRunner {
cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
cr.NewLogWriter = cr.NewArvLogWriter
+ cr.RunArvMount = cr.ArvMountCmd
+ cr.MkTempDir = ioutil.TempDir
cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
+ cr.ContainerRecord.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
+ cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
return cr
}
func main() {
flag.Parse()
+ containerId := flag.Arg(0)
+
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
- log.Fatal(err)
+ log.Fatalf("%s: %v", containerId, err)
}
api.Retries = 8
var kc *keepclient.KeepClient
kc, err = keepclient.MakeKeepClient(&api)
if err != nil {
- log.Fatal(err)
+ log.Fatalf("%s: %v", containerId, err)
}
kc.Retries = 4
var docker *dockerclient.DockerClient
docker, err = dockerclient.NewDockerClient("unix:///var/run/docker.sock", nil)
if err != nil {
- log.Fatal(err)
+ log.Fatalf("%s: %v", containerId, err)
}
- cr := NewContainerRunner(api, kc, docker)
+ cr := NewContainerRunner(api, kc, docker, containerId)
- err = cr.Run(flag.Arg(0))
+ err = cr.Run()
if err != nil {
- log.Fatal(err)
+ log.Fatalf("%s: %v", containerId, err)
}
}
projects / arvados.git / blobdiff