package main
import (
+ "encoding/json"
"errors"
"flag"
+ "fmt"
+ "git.curoverse.com/arvados.git/lib/crunchstat"
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
"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/curoverse/dockerclient"
"io"
- "ioutil"
+ "io/ioutil"
"log"
"os"
"os/exec"
"os/signal"
+ "path"
"strings"
"sync"
"syscall"
+ "time"
)
// IArvadosClient is the minimal Arvados API methods used by crunch-run.
Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error)
+ Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) (err error)
}
// ErrCancelled is the error returned when the container is cancelled.
ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error)
}
-// Mount describes the mount points to create inside the container.
-type Mount struct {
- Kind string `json:"kind"`
- Writable bool `json:"writable"`
- PortableDataHash string `json:"portable_data_hash"`
- UUID string `json:"uuid"`
- DeviceType string `json:"device_type"`
-}
-
-// Collection record returned by the API server.
-type Collection struct {
- ManifestText string `json:"manifest_text"`
-}
-
-// ContainerRecord is the container record returned by the API server.
-type ContainerRecord struct {
- UUID string `json:"uuid"`
- Command []string `json:"command"`
- ContainerImage string `json:"container_image"`
- Cwd string `json:"cwd"`
- Environment map[string]string `json:"environment"`
- Mounts map[string]Mount `json:"mounts"`
- OutputPath string `json:"output_path"`
- Priority int `json:"priority"`
- RuntimeConstraints map[string]interface{} `json:"runtime_constraints"`
- State string `json:"state"`
-}
-
// NewLogWriter is a factory function to create a new log writer.
type NewLogWriter func(name string) io.WriteCloser
+type RunArvMount func(args []string, tok 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)
}
Docker ThinDockerClient
ArvClient IArvadosClient
Kc IKeepClient
- ContainerRecord
+ arvados.Container
dockerclient.ContainerConfig
+ dockerclient.HostConfig
+ token string
ContainerID string
ExitCode *int
NewLogWriter
loggingDone chan bool
CrunchLog *ThrottledLogger
- Stdout *ThrottledLogger
+ Stdout io.WriteCloser
Stderr *ThrottledLogger
LogCollection *CollectionWriter
LogsPDH *string
- ArvMount *exec.Cmd
- ArvMountPoint 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
+
+ statLogger io.WriteCloser
+ statReporter *crunchstat.Reporter
+ statInterval time.Duration
+ cgroupRoot string
+ cgroupParent 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)
signal.Notify(runner.SigChan, syscall.SIGQUIT)
go func(sig <-chan os.Signal) {
- for _ = range sig {
+ for range sig {
if !runner.Cancelled {
runner.CancelLock.Lock()
runner.Cancelled = true
}
}
}(runner.SigChan)
-
- return nil
}
// LoadImage determines the docker image id from the container record and
// the image from Keep.
func (runner *ContainerRunner) LoadImage() (err error) {
- runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.ContainerRecord.ContainerImage)
+ runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
- var collection Collection
- err = runner.ArvClient.Get("collections", runner.ContainerRecord.ContainerImage, nil, &collection)
+ var collection arvados.Collection
+ err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
if err != nil {
- return err
+ return fmt.Errorf("While getting container image collection: %v", err)
}
manifest := manifest.Manifest{Text: collection.ManifestText}
var img, imageID string
for ms := range manifest.StreamIter() {
img = ms.FileStreamSegments[0].Name
if !strings.HasSuffix(img, ".tar") {
- return errors.New("First file in the collection does not end in .tar")
+ return fmt.Errorf("First file in the container image collection does not end in .tar")
}
imageID = img[:len(img)-4]
}
var readCloser io.ReadCloser
readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
if err != nil {
- return err
+ return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
}
err = runner.Docker.LoadImage(readCloser)
if err != nil {
- return err
+ return fmt.Errorf("While loading container image into Docker: %v", err)
}
} else {
runner.CrunchLog.Print("Docker image is available")
return nil
}
-func (runner *ContainerRunner) SetupMounts(hostConfig *dockerclient.HostConfig) (err error) {
- runner.ArvMountPoint = ioutil.TempDir("", "keep")
+func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
+ c = exec.Command("arv-mount", arvMountCmd...)
+
+ // Copy our environment, but override ARVADOS_API_TOKEN with
+ // the container auth token.
+ c.Env = nil
+ for _, s := range os.Environ() {
+ if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
+ c.Env = append(c.Env, s)
+ }
+ }
+ c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
+
+ 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 = 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"}
- collections := []string{}
+ arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
+ collectionPaths := []string{}
+ runner.Binds = nil
+
+ for bind, mnt := range runner.Container.Mounts {
+ if bind == "stdout" {
+ // Is it a "file" mount kind?
+ if mnt.Kind != "file" {
+ return fmt.Errorf("Unsupported mount kind '%s' for stdout. Only 'file' is supported.", mnt.Kind)
+ }
+
+ // Does path start with OutputPath?
+ prefix := runner.Container.OutputPath
+ if !strings.HasSuffix(prefix, "/") {
+ prefix += "/"
+ }
+ if !strings.HasPrefix(mnt.Path, prefix) {
+ return fmt.Errorf("Stdout path does not start with OutputPath: %s, %s", mnt.Path, prefix)
+ }
+ }
- for bind, mnt := range runner.ContainerRecord.Mounts {
if mnt.Kind == "collection" {
var src string
if mnt.UUID != "" && mnt.PortableDataHash != "" {
- return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection")
+ return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
}
if mnt.UUID != "" {
if mnt.Writable {
- return fmt.Errorf("Writing to collection currently not permitted.")
+ return fmt.Errorf("Writing to existing collections currently not permitted.")
}
pdhOnly = false
- src = fmt.Sprintf("%s/by_id/%s", arvMountPoint, mnt.UUID)
+ src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
} else if mnt.PortableDataHash != "" {
if mnt.Writable {
return fmt.Errorf("Can never write to a collection specified by portable data hash")
}
- src = fmt.Sprintf("%s/by_id/%s", arvMountPoint, mnt.PortableDataHash)
+ src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
} else {
- src = fmt.Sprintf("%s/tmp%i", 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 {
- hostConfig.Binds = append(hostConfig.Binds, fmt.Sprintf("%s:%s", src, bind))
+ if bind == runner.Container.OutputPath {
+ runner.HostOutputDir = src
+ }
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
} else {
- hostConfig.Binds = append(hostConfig.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
}
- collections = append(collections, src)
+ collectionPaths = append(collectionPaths, src)
} else if mnt.Kind == "tmp" {
- hostConfig.Binds = append(hostConfig.Binds, bind)
- } else {
- return fmt.Errorf("Unknown mount kind '%s'", mnt.Kind)
+ if bind == runner.Container.OutputPath {
+ 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)
+ }
}
}
+ if runner.HostOutputDir == "" {
+ return fmt.Errorf("Output path does not correspond to a writable mount point")
+ }
+
if pdhOnly {
arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
} else {
arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
}
- arvMountCmd = append(arvMountCmd, arvMountPoint)
+ arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
- runner.ArvMount = exec.Command("arv-mount", arvMountCmd)
- err = runner.ArvMount.Start()
+ token, err := runner.ContainerToken()
if err != nil {
- return err
+ return fmt.Errorf("could not get container token: %s", err)
}
- // XXX need to go through and os.Stat() each file or dir in "sources"
- // to make sure they show up for Docker.
+ runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
+ if err != nil {
+ return fmt.Errorf("While trying to start arv-mount: %v", err)
+ }
+
+ for _, p := range collectionPaths {
+ _, err = os.Stat(p)
+ if err != nil {
+ return fmt.Errorf("While checking that input files exist: %v", err)
+ }
+ }
+
+ return nil
}
-// StartContainer creates the container and runs it.
-func (runner *ContainerRunner) StartContainer() (err error) {
- runner.CrunchLog.Print("Creating Docker container")
+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
- runner.CancelLock.Lock()
- defer runner.CancelLock.Unlock()
+ header := make([]byte, 8)
+ for {
+ _, readerr := io.ReadAtLeast(containerReader, header, 8)
- if runner.Cancelled {
- return ErrCancelled
- }
+ 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)
+ }
+ }
- runner.ContainerConfig.Cmd = runner.ContainerRecord.Command
- if runner.ContainerRecord.Cwd != "." {
- runner.ContainerConfig.WorkingDir = runner.ContainerRecord.Cwd
- }
- for k, v := range runner.ContainerRecord.Environment {
- runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
+ 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)
+ }
+
+ if runner.statReporter != nil {
+ runner.statReporter.Stop()
+ closeerr = runner.statLogger.Close()
+ if closeerr != nil {
+ runner.CrunchLog.Printf("While closing crunchstat logs: %v", closeerr)
+ }
+ }
+
+ runner.loggingDone <- true
+ close(runner.loggingDone)
+ return
+ }
}
- runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
- if err != nil {
- return
+}
+
+func (runner *ContainerRunner) StartCrunchstat() {
+ runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
+ runner.statReporter = &crunchstat.Reporter{
+ CID: runner.ContainerID,
+ Logger: log.New(runner.statLogger, "", 0),
+ CgroupParent: runner.cgroupParent,
+ CgroupRoot: runner.cgroupRoot,
+ PollPeriod: runner.statInterval,
}
- hostConfig := &dockerclient.HostConfig{}
+ runner.statReporter.Start()
+}
+
+// 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")
- err = runner.SetupMounts(hostConfig)
+ var containerReader io.Reader
+ containerReader, err = runner.Docker.AttachContainer(runner.ContainerID,
+ &dockerclient.AttachOptions{Stream: true, Stdout: true, Stderr: true})
if err != nil {
- return
+ return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
}
- runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
- err = runner.Docker.StartContainer(runner.ContainerID, hostConfig)
- if err != nil {
- return
+ runner.loggingDone = make(chan bool)
+
+ if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
+ stdoutPath := stdoutMnt.Path[len(runner.Container.OutputPath):]
+ index := strings.LastIndex(stdoutPath, "/")
+ if index > 0 {
+ subdirs := stdoutPath[:index]
+ if subdirs != "" {
+ st, err := os.Stat(runner.HostOutputDir)
+ if err != nil {
+ return fmt.Errorf("While Stat on temp dir: %v", err)
+ }
+ stdoutPath := path.Join(runner.HostOutputDir, subdirs)
+ err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
+ if err != nil {
+ return fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
+ }
+ }
+ }
+ stdoutFile, err := os.Create(path.Join(runner.HostOutputDir, stdoutPath))
+ if err != nil {
+ return fmt.Errorf("While creating stdout file: %v", err)
+ }
+ runner.Stdout = stdoutFile
+ } else {
+ runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
}
+ runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
+
+ go runner.ProcessDockerAttach(containerReader)
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) {
+// CreateContainer creates the docker container.
+func (runner *ContainerRunner) CreateContainer() error {
+ runner.CrunchLog.Print("Creating Docker container")
- runner.CrunchLog.Print("Attaching container logs")
+ runner.ContainerConfig.Cmd = runner.Container.Command
+ if runner.Container.Cwd != "." {
+ runner.ContainerConfig.WorkingDir = runner.Container.Cwd
+ }
- var stderrReader, stdoutReader io.Reader
- stderrReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stderr: true})
- if err != nil {
- return
+ for k, v := range runner.Container.Environment {
+ runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
+ }
+ if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
+ tok, err := runner.ContainerToken()
+ if err != nil {
+ return err
+ }
+ runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
+ "ARVADOS_API_TOKEN="+tok,
+ "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
+ "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
+ )
+ runner.ContainerConfig.NetworkDisabled = false
+ } else {
+ runner.ContainerConfig.NetworkDisabled = true
}
- stdoutReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stdout: true})
+
+ var err error
+ runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
if err != nil {
- return
+ return fmt.Errorf("While creating container: %v", err)
}
- runner.loggingDone = make(chan bool)
+ runner.HostConfig = dockerclient.HostConfig{Binds: runner.Binds,
+ LogConfig: dockerclient.LogConfig{Type: "none"}}
- 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 runner.AttachStreams()
+}
+// StartContainer starts the docker container created by CreateContainer.
+func (runner *ContainerRunner) StartContainer() error {
+ runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
+ err := runner.Docker.StartContainer(runner.ContainerID, &runner.HostConfig)
+ if err != nil {
+ return fmt.Errorf("could not start container: %v", err)
+ }
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 {
- return wr.Error
+ return fmt.Errorf("While waiting for container to finish: %v", wr.Error)
}
runner.ExitCode = &wr.ExitCode
- // drain stdout/stderr
- <-runner.loggingDone
+ // wait for stdout/stderr to complete
<-runner.loggingDone
- runner.Stdout.Close()
- runner.Stderr.Close()
+ return nil
+}
- umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
- umount.Run()
+// HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
+func (runner *ContainerRunner) CaptureOutput() error {
+ if runner.finalState != "Complete" {
+ return nil
+ }
+
+ if runner.HostOutputDir == "" {
+ return nil
+ }
+
+ _, err := os.Stat(runner.HostOutputDir)
+ if err != nil {
+ return fmt.Errorf("While checking host output path: %v", err)
+ }
+
+ var manifestText string
+
+ collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
+ _, err = os.Stat(collectionMetafile)
+ if err != nil {
+ // Regular directory
+ cw := CollectionWriter{runner.Kc, nil, sync.Mutex{}}
+ manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
+ 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
+ }
+
+ var response arvados.Collection
+ err = runner.ArvClient.Create("collections",
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "manifest_text": manifestText}},
+ &response)
+ if err != nil {
+ return fmt.Errorf("While creating output collection: %v", err)
+ }
+
+ runner.OutputPDH = new(string)
+ *runner.OutputPDH = response.PortableDataHash
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)
// point, but re-open crunch log with ArvClient in case there are any
// other further (such as failing to write the log to Keep!) while
// shutting down
- runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{runner.ArvClient, runner.ContainerRecord.UUID,
+ runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{runner.ArvClient, runner.Container.UUID,
"crunch-run", nil})
+ if runner.LogsPDH != nil {
+ // If we have already assigned something to LogsPDH,
+ // we must be closing the re-opened log, which won't
+ // end up getting attached to the container record and
+ // therefore doesn't need to be saved as a collection
+ // -- it exists only to send logs to other channels.
+ return nil
+ }
+
mt, err := runner.LogCollection.ManifestText()
if err != nil {
- return err
+ return fmt.Errorf("While creating log manifest: %v", err)
}
- response := make(map[string]string)
+ var response arvados.Collection
err = runner.ArvClient.Create("collections",
- arvadosclient.Dict{"name": "logs for " + runner.ContainerRecord.UUID,
- "manifest_text": mt},
- response)
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "name": "logs for " + runner.Container.UUID,
+ "manifest_text": mt}},
+ &response)
if err != nil {
- return err
+ return fmt.Errorf("While creating log collection: %v", err)
}
- runner.LogsPDH = new(string)
- *runner.LogsPDH = response["portable_data_hash"]
+ runner.LogsPDH = &response.PortableDataHash
return nil
}
-// 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)
+// UpdateContainerRunning updates the container state to "Running"
+func (runner *ContainerRunner) UpdateContainerRunning() error {
+ runner.CancelLock.Lock()
+ defer runner.CancelLock.Unlock()
+ if runner.Cancelled {
+ return ErrCancelled
+ }
+ return runner.ArvClient.Update("containers", runner.Container.UUID,
+ arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
}
-// UpdateContainerRecordComplete updates the container record state on API
-// server to "Complete" or "Cancelled"
-func (runner *ContainerRunner) UpdateContainerRecordComplete() error {
- update := arvadosclient.Dict{}
- if runner.LogsPDH != nil {
- update["log"] = *runner.LogsPDH
+// ContainerToken returns the api_token the container (and any
+// arv-mount processes) are allowed to use.
+func (runner *ContainerRunner) ContainerToken() (string, error) {
+ if runner.token != "" {
+ return runner.token, nil
}
- if runner.ExitCode != nil {
- update["exit_code"] = *runner.ExitCode
+
+ var auth arvados.APIClientAuthorization
+ err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
+ if err != nil {
+ return "", err
}
+ runner.token = auth.APIToken
+ return runner.token, nil
+}
+// UpdateContainerComplete updates the container record state on API
+// server to "Complete" or "Cancelled"
+func (runner *ContainerRunner) UpdateContainerFinal() error {
+ update := arvadosclient.Dict{}
update["state"] = runner.finalState
+ if runner.finalState == "Complete" {
+ if runner.LogsPDH != nil {
+ update["log"] = *runner.LogsPDH
+ }
+ if runner.ExitCode != nil {
+ update["exit_code"] = *runner.ExitCode
+ }
+ if runner.OutputPDH != nil {
+ update["output"] = *runner.OutputPDH
+ }
+ }
+ return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
+}
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, update, nil)
+// IsCancelled returns the value of Cancelled, with goroutine safety.
+func (runner *ContainerRunner) IsCancelled() bool {
+ runner.CancelLock.Lock()
+ defer runner.CancelLock.Unlock()
+ return runner.Cancelled
}
// NewArvLogWriter creates an ArvLogWriter
func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser {
- return &ArvLogWriter{runner.ArvClient, runner.ContainerRecord.UUID, name, runner.LogCollection.Open(name + ".txt")}
+ return &ArvLogWriter{runner.ArvClient, runner.Container.UUID, name, runner.LogCollection.Open(name + ".txt")}
}
// 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.Container.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)
+ }
+
+ // Clean up temporary directories _after_ finalizing
+ // everything (if we've made any by then)
+ defer runner.CleanupDirs()
- var runerr, waiterr error
+ runner.finalState = "Queued"
defer func() {
- if err != nil {
- runner.CrunchLog.Print(err)
+ // checkErr prints e (unless it's nil) and sets err to
+ // e (unless err is already non-nil). Thus, if err
+ // 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) {
+ if e == nil {
+ return
+ }
+ runner.CrunchLog.Print(e)
+ if err == nil {
+ err = e
+ }
}
- if runner.Cancelled {
- runner.finalState = "Cancelled"
- } else {
- runner.finalState = "Complete"
- }
+ // Log the error encountered in Run(), if any
+ checkErr(err)
- // (6) write logs
- logerr := runner.CommitLogs()
- if logerr != nil {
- runner.CrunchLog.Print(logerr)
+ if runner.finalState == "Queued" {
+ runner.UpdateContainerFinal()
+ return
}
- // (7) update container record with results
- updateerr := runner.UpdateContainerRecordComplete()
- if updateerr != nil {
- runner.CrunchLog.Print(updateerr)
+ if runner.IsCancelled() {
+ runner.finalState = "Cancelled"
+ // but don't return yet -- we still want to
+ // capture partial output and write logs
}
- runner.CrunchLog.Close()
+ checkErr(runner.CaptureOutput())
+ checkErr(runner.CommitLogs())
+ checkErr(runner.UpdateContainerFinal())
- if err == nil {
- if runerr != nil {
- err = runerr
- } else if waiterr != nil {
- err = runerr
- } else if logerr != nil {
- err = logerr
- } else if updateerr != nil {
- err = updateerr
- }
- }
+ // The real log is already closed, but then we opened
+ // a new one in case we needed to log anything while
+ // finalizing.
+ runner.CrunchLog.Close()
}()
- err = runner.ArvClient.Get("containers", containerUUID, nil, &runner.ContainerRecord)
+ err = runner.ArvClient.Get("containers", runner.Container.UUID, nil, &runner.Container)
if err != nil {
+ err = fmt.Errorf("While getting container record: %v", err)
return
}
- // (0) setup signal handling
- err = runner.SetupSignals()
+ // setup signal handling
+ runner.SetupSignals()
+
+ // check for and/or load image
+ err = runner.LoadImage()
if err != nil {
+ err = fmt.Errorf("While loading container image: %v", err)
return
}
- // (1) check for and/or load image
- err = runner.LoadImage()
+ // set up FUSE mount and binds
+ err = runner.SetupMounts()
if err != nil {
+ err = fmt.Errorf("While setting up mounts: %v", err)
return
}
- // (2) start container
- err = runner.StartContainer()
+ err = runner.CreateContainer()
if err != nil {
- if err == ErrCancelled {
- err = nil
- }
return
}
- // (3) update container record state
- err = runner.UpdateContainerRecordRunning()
- if err != nil {
- runner.CrunchLog.Print(err)
+ runner.StartCrunchstat()
+
+ if runner.IsCancelled() {
+ return
}
- // (4) attach container logs
- runerr = runner.AttachLogs()
- if runerr != nil {
- runner.CrunchLog.Print(runerr)
+ err = runner.UpdateContainerRunning()
+ if err != nil {
+ return
}
+ runner.finalState = "Cancelled"
- // (5) wait for container to finish
- waiterr = runner.WaitFinish()
+ err = runner.StartContainer()
+ if err != nil {
+ return
+ }
+ err = runner.WaitFinish()
+ if err == nil {
+ runner.finalState = "Complete"
+ }
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.LogCollection = &CollectionWriter{kc, nil}
+ cr.RunArvMount = cr.ArvMountCmd
+ cr.MkTempDir = ioutil.TempDir
+ cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
+ cr.Container.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
+ cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
return cr
}
func main() {
+ statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
+ cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
+ cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup")
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)
+ cr.statInterval = *statInterval
+ cr.cgroupRoot = *cgroupRoot
+ cr.cgroupParent = *cgroupParent
- 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