package main
import (
+ "bytes"
+ "context"
"encoding/json"
"errors"
"flag"
"fmt"
- "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"
"io/ioutil"
"log"
"os"
"os/exec"
"os/signal"
+ "path"
+ "path/filepath"
+ "sort"
"strings"
"sync"
"syscall"
"time"
+
+ "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"
+
+ dockertypes "github.com/docker/docker/api/types"
+ dockercontainer "github.com/docker/docker/api/types/container"
+ dockernetwork "github.com/docker/docker/api/types/network"
+ dockerclient "github.com/docker/docker/client"
)
// IArvadosClient is the minimal Arvados API methods used by crunch-run.
type IArvadosClient interface {
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)
+ Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
+ Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
+ CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
+ Discovery(key string) (interface{}, error)
}
// ErrCancelled is the error returned when the container is cancelled.
// IKeepClient is the minimal Keep API methods used by crunch-run.
type IKeepClient interface {
PutHB(hash string, buf []byte) (string, int, error)
- ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error)
+ ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, 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"`
+// 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 {
+ ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error)
+ ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
+ networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error)
+ ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error
+ ContainerStop(ctx context.Context, container string, timeout *time.Duration) error
+ ContainerWait(ctx context.Context, container string) (int64, 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)
}
-// Collection record returned by the API server.
-type CollectionRecord struct {
- ManifestText string `json:"manifest_text"`
- PortableDataHash string `json:"portable_data_hash"`
+// ThinDockerClientProxy is a proxy implementation of ThinDockerClient
+// that executes the docker requests on dockerclient.Client
+type ThinDockerClientProxy struct {
+ Docker *dockerclient.Client
}
-// 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"`
- Output string `json:"output"`
+// ContainerAttach invokes dockerclient.Client.ContainerAttach
+func (proxy ThinDockerClientProxy) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
+ return proxy.Docker.ContainerAttach(ctx, container, options)
}
-// NewLogWriter is a factory function to create a new log writer.
-type NewLogWriter func(name string) io.WriteCloser
+// ContainerCreate invokes dockerclient.Client.ContainerCreate
+func (proxy ThinDockerClientProxy) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
+ networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
+ return proxy.Docker.ContainerCreate(ctx, config, hostConfig, networkingConfig, containerName)
+}
-type RunArvMount func([]string) (*exec.Cmd, error)
+// ContainerStart invokes dockerclient.Client.ContainerStart
+func (proxy ThinDockerClientProxy) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
+ return proxy.Docker.ContainerStart(ctx, container, options)
+}
-type MkTempDir func(string, string) (string, error)
+// ContainerStop invokes dockerclient.Client.ContainerStop
+func (proxy ThinDockerClientProxy) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
+ return proxy.Docker.ContainerStop(ctx, container, timeout)
+}
-// ThinDockerClient is the minimal Docker client interface used by crunch-run.
-type ThinDockerClient interface {
- StopContainer(id string, timeout int) error
- InspectImage(id string) (*dockerclient.ImageInfo, error)
- LoadImage(reader io.Reader) error
- CreateContainer(config *dockerclient.ContainerConfig, name string, authConfig *dockerclient.AuthConfig) (string, error)
- StartContainer(id string, config *dockerclient.HostConfig) error
- AttachContainer(id string, options *dockerclient.AttachOptions) (io.ReadCloser, error)
- Wait(id string) <-chan dockerclient.WaitResult
- RemoveImage(name string, force bool) ([]*dockerclient.ImageDelete, error)
+// ContainerWait invokes dockerclient.Client.ContainerWait
+func (proxy ThinDockerClientProxy) ContainerWait(ctx context.Context, container string) (int64, error) {
+ return proxy.Docker.ContainerWait(ctx, container)
+}
+
+// ImageInspectWithRaw invokes dockerclient.Client.ImageInspectWithRaw
+func (proxy ThinDockerClientProxy) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
+ return proxy.Docker.ImageInspectWithRaw(ctx, image)
+}
+
+// ImageLoad invokes dockerclient.Client.ImageLoad
+func (proxy ThinDockerClientProxy) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
+ return proxy.Docker.ImageLoad(ctx, input, quiet)
+}
+
+// ImageRemove invokes dockerclient.Client.ImageRemove
+func (proxy ThinDockerClientProxy) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
+ return proxy.Docker.ImageRemove(ctx, image, options)
}
// ContainerRunner is the main stateful struct used for a single execution of a
Docker ThinDockerClient
ArvClient IArvadosClient
Kc IKeepClient
- ContainerRecord
- dockerclient.ContainerConfig
+ arvados.Container
+ ContainerConfig dockercontainer.Config
+ dockercontainer.HostConfig
+ token string
ContainerID string
ExitCode *int
NewLogWriter
loggingDone chan bool
CrunchLog *ThrottledLogger
- Stdout *ThrottledLogger
- Stderr *ThrottledLogger
+ Stdout io.WriteCloser
+ Stderr io.WriteCloser
LogCollection *CollectionWriter
LogsPDH *string
RunArvMount
HostOutputDir string
CleanupTempDir []string
Binds []string
+ Volumes map[string]struct{}
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
+ // What we expect the container's cgroup parent to be.
+ expectCgroupParent string
+ // What we tell docker to use as the container's cgroup
+ // parent. Note: Ideally we would use the same field for both
+ // expectCgroupParent and setCgroupParent, and just make it
+ // default to "docker". However, when using docker < 1.10 with
+ // systemd, specifying a non-empty cgroup parent (even the
+ // default value "docker") hits a docker bug
+ // (https://github.com/docker/docker/issues/17126). Using two
+ // separate fields makes it possible to use the "expect cgroup
+ // parent to be X" feature even on sites where the "specify
+ // cgroup parent" feature breaks.
+ setCgroupParent string
+
+ cStateLock sync.Mutex
+ cStarted bool // StartContainer() succeeded
+ cCancelled bool // StopContainer() invoked
+
+ enableNetwork string // one of "default" or "always"
+ networkMode string // passed through to HostConfig.NetworkMode
}
// SetupSignals sets up signal handling to gracefully terminate the underlying
signal.Notify(runner.SigChan, syscall.SIGINT)
signal.Notify(runner.SigChan, syscall.SIGQUIT)
- go func(sig <-chan os.Signal) {
- for _ = range sig {
- if !runner.Cancelled {
- runner.CancelLock.Lock()
- runner.Cancelled = true
- if runner.ContainerID != "" {
- runner.Docker.StopContainer(runner.ContainerID, 10)
- }
- runner.CancelLock.Unlock()
- }
- }
+ go func(sig chan os.Signal) {
+ <-sig
+ runner.stop()
+ signal.Stop(sig)
}(runner.SigChan)
}
+// stop the underlying Docker container.
+func (runner *ContainerRunner) stop() {
+ runner.cStateLock.Lock()
+ defer runner.cStateLock.Unlock()
+ if runner.cCancelled {
+ return
+ }
+ runner.cCancelled = true
+ if runner.cStarted {
+ timeout := time.Duration(10)
+ err := runner.Docker.ContainerStop(context.TODO(), runner.ContainerID, &(timeout))
+ if err != nil {
+ log.Printf("StopContainer failed: %s", err)
+ }
+ }
+}
+
// LoadImage determines the docker image id from the container record and
// checks if it is available in the local Docker image store. If not, it loads
// 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 CollectionRecord
- 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 fmt.Errorf("While getting container image collection: %v", err)
}
runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
- _, err = runner.Docker.InspectImage(imageID)
+ _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
if err != nil {
runner.CrunchLog.Print("Loading Docker image from keep")
return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
}
- err = runner.Docker.LoadImage(readCloser)
+ response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, false)
if err != nil {
return fmt.Errorf("While loading container image into Docker: %v", err)
}
+ response.Body.Close()
} else {
runner.CrunchLog.Print("Docker image is available")
}
return nil
}
-func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string) (c *exec.Cmd, err error) {
+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
return c, nil
}
+func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
+ if runner.ArvMountPoint == "" {
+ runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
+ }
+ return
+}
+
func (runner *ContainerRunner) SetupMounts() (err error) {
- runner.ArvMountPoint, err = runner.MkTempDir("", "keep")
+ err = runner.SetupArvMountPoint("keep")
if err != nil {
return fmt.Errorf("While creating keep mount temp dir: %v", err)
}
pdhOnly := true
tmpcount := 0
arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
+
+ if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
+ arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
+ }
+
collectionPaths := []string{}
runner.Binds = nil
+ runner.Volumes = make(map[string]struct{})
+ needCertMount := true
+
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
+ if bind == "stdout" || bind == "stderr" {
+ // Is it a "file" mount kind?
+ if mnt.Kind != "file" {
+ return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind)
+ }
+
+ // Does path start with OutputPath?
+ prefix := runner.Container.OutputPath
+ if !strings.HasSuffix(prefix, "/") {
+ prefix += "/"
+ }
+ if !strings.HasPrefix(mnt.Path, prefix) {
+ return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
+ }
+ }
+
+ if bind == "stdin" {
+ // Is it a "collection" mount kind?
+ if mnt.Kind != "collection" && mnt.Kind != "json" {
+ return fmt.Errorf("Unsupported mount kind '%s' for stdin. Only 'collection' or 'json' are supported.", mnt.Kind)
+ }
+ }
+
+ if bind == "/etc/arvados/ca-certificates.crt" {
+ needCertMount = false
+ }
+
+ 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)
+ }
+ }
- for bind, mnt := range runner.ContainerRecord.Mounts {
- if mnt.Kind == "collection" {
+ switch {
+ case mnt.Kind == "collection" && bind != "stdin":
var src string
if mnt.UUID != "" && mnt.PortableDataHash != "" {
return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
if mnt.Writable {
return fmt.Errorf("Can never write to a collection specified by portable data hash")
}
+ idx := strings.Index(mnt.PortableDataHash, "/")
+ if idx > 0 {
+ mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
+ mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
+ runner.Container.Mounts[bind] = mnt
+ }
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
+ if mnt.Path != "" && mnt.Path != "." {
+ if strings.HasPrefix(mnt.Path, "./") {
+ mnt.Path = mnt.Path[2:]
+ } else if strings.HasPrefix(mnt.Path, "/") {
+ mnt.Path = mnt.Path[1:]
+ }
+ src += "/" + mnt.Path
+ }
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp")
tmpcount += 1
}
if mnt.Writable {
- if bind == runner.ContainerRecord.OutputPath {
+ if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
+ } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
+ return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind)
}
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
} else {
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
}
collectionPaths = append(collectionPaths, src)
- } else if mnt.Kind == "tmp" {
- if bind == runner.ContainerRecord.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)
+
+ case mnt.Kind == "tmp" && bind == runner.Container.OutputPath:
+ runner.HostOutputDir, err = runner.MkTempDir("", "")
+ if err != nil {
+ return fmt.Errorf("While creating mount temp dir: %v", err)
}
- } else {
- return fmt.Errorf("Unknown mount kind '%s'", mnt.Kind)
+ 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))
+
+ case mnt.Kind == "tmp":
+ runner.Volumes[bind] = struct{}{}
+
+ case mnt.Kind == "json":
+ jsondata, err := json.Marshal(mnt.Content)
+ if err != nil {
+ return fmt.Errorf("encoding json data: %v", err)
+ }
+ // 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("", "")
+ if err != nil {
+ return fmt.Errorf("creating temp dir: %v", err)
+ }
+ runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
+ tmpfn := filepath.Join(tmpdir, "mountdata.json")
+ err = ioutil.WriteFile(tmpfn, jsondata, 0644)
+ if err != nil {
+ return fmt.Errorf("writing temp file: %v", err)
+ }
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
}
}
return fmt.Errorf("Output path does not correspond to a writable mount point")
}
+ if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
+ for _, certfile := range arvadosclient.CertFiles {
+ _, err := os.Stat(certfile)
+ if err == nil {
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
+ break
+ }
+ }
+ }
+
if pdhOnly {
arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
} else {
}
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
- runner.ArvMount, err = runner.RunArvMount(arvMountCmd)
+ token, err := runner.ContainerToken()
+ if err != nil {
+ return fmt.Errorf("could not get container token: %s", err)
+ }
+
+ runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
if err != nil {
return fmt.Errorf("While trying to start arv-mount: %v", err)
}
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
}
}
-// 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) StartCrunchstat() {
+ runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
+ runner.statReporter = &crunchstat.Reporter{
+ CID: runner.ContainerID,
+ Logger: log.New(runner.statLogger, "", 0),
+ CgroupParent: runner.expectCgroupParent,
+ CgroupRoot: runner.cgroupRoot,
+ PollPeriod: runner.statInterval,
+ }
+ runner.statReporter.Start()
+}
+
+type infoCommand struct {
+ label string
+ cmd []string
+}
+
+// Gather node information and store it on the log for debugging
+// purposes.
+func (runner *ContainerRunner) LogNodeInfo() (err error) {
+ w := runner.NewLogWriter("node-info")
+ logger := log.New(w, "node-info", 0)
+
+ commands := []infoCommand{
+ infoCommand{
+ label: "Host Information",
+ cmd: []string{"uname", "-a"},
+ },
+ infoCommand{
+ label: "CPU Information",
+ cmd: []string{"cat", "/proc/cpuinfo"},
+ },
+ infoCommand{
+ label: "Memory Information",
+ cmd: []string{"cat", "/proc/meminfo"},
+ },
+ infoCommand{
+ label: "Disk Space",
+ cmd: []string{"df", "-m", "/", os.TempDir()},
+ },
+ infoCommand{
+ label: "Disk INodes",
+ cmd: []string{"df", "-i", "/", os.TempDir()},
+ },
+ }
+
+ // Run commands with informational output to be logged.
+ var out []byte
+ for _, command := range commands {
+ out, err = exec.Command(command.cmd[0], command.cmd[1:]...).CombinedOutput()
+ if err != nil {
+ return fmt.Errorf("While running command %q: %v",
+ command.cmd, err)
+ }
+ logger.Println(command.label)
+ for _, line := range strings.Split(string(out), "\n") {
+ logger.Println(" ", line)
+ }
+ }
+
+ err = w.Close()
+ if err != nil {
+ return fmt.Errorf("While closing node-info logs: %v", err)
+ }
+ return nil
+}
+
+// Get and save the raw JSON container record from the API server
+func (runner *ContainerRunner) LogContainerRecord() (err error) {
+ w := &ArvLogWriter{
+ ArvClient: runner.ArvClient,
+ UUID: runner.Container.UUID,
+ loggingStream: "container",
+ writeCloser: runner.LogCollection.Open("container.json"),
+ }
+
+ // Get Container record JSON from the API Server
+ reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
+ if err != nil {
+ return fmt.Errorf("While retrieving container record from the API server: %v", err)
+ }
+ defer reader.Close()
+ // Read the API server response as []byte
+ json_bytes, err := ioutil.ReadAll(reader)
+ if err != nil {
+ return fmt.Errorf("While reading container record API server response: %v", err)
+ }
+ // Decode the JSON []byte
+ var cr map[string]interface{}
+ if err = json.Unmarshal(json_bytes, &cr); err != nil {
+ return fmt.Errorf("While decoding the container record JSON response: %v", err)
+ }
+ // Re-encode it using indentation to improve readability
+ enc := json.NewEncoder(w)
+ enc.SetIndent("", " ")
+ if err = enc.Encode(cr); err != nil {
+ return fmt.Errorf("While logging the JSON container record: %v", err)
+ }
+ err = w.Close()
+ if err != nil {
+ return fmt.Errorf("While closing container.json log: %v", err)
+ }
+ return nil
+}
+
+// AttachStreams connects the docker container stdin, 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 stdin mount is provided, attach it to the docker container
+ var stdinRdr keepclient.Reader
+ var stdinJson []byte
+ if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
+ if stdinMnt.Kind == "collection" {
+ var stdinColl arvados.Collection
+ collId := stdinMnt.UUID
+ if collId == "" {
+ collId = stdinMnt.PortableDataHash
+ }
+ err = runner.ArvClient.Get("collections", collId, nil, &stdinColl)
+ if err != nil {
+ return fmt.Errorf("While getting stding collection: %v", err)
+ }
+
+ stdinRdr, err = runner.Kc.ManifestFileReader(manifest.Manifest{Text: stdinColl.ManifestText}, stdinMnt.Path)
+ if os.IsNotExist(err) {
+ return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
+ } else if err != nil {
+ return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
+ }
+ } else if stdinMnt.Kind == "json" {
+ stdinJson, err = json.Marshal(stdinMnt.Content)
+ if err != nil {
+ return fmt.Errorf("While encoding stdin json data: %v", err)
+ }
+ }
+ }
+
+ stdinUsed := stdinRdr != nil || len(stdinJson) != 0
+ response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
+ dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, 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"))
+ if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
+ stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
+ if err != nil {
+ return err
+ }
+ runner.Stdout = stdoutFile
+ } else {
+ runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
+ }
+
+ if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
+ stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
+ if err != nil {
+ return err
+ }
+ runner.Stderr = stderrFile
+ } else {
+ runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
+ }
- go runner.ProcessDockerAttach(containerReader)
+ if stdinRdr != nil {
+ go func() {
+ _, err := io.Copy(response.Conn, stdinRdr)
+ if err != nil {
+ runner.CrunchLog.Print("While writing stdin collection to docker container %q", err)
+ runner.stop()
+ }
+ stdinRdr.Close()
+ response.CloseWrite()
+ }()
+ } else if len(stdinJson) != 0 {
+ go func() {
+ _, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
+ if err != nil {
+ runner.CrunchLog.Print("While writing stdin json to docker container %q", err)
+ runner.stop()
+ }
+ response.CloseWrite()
+ }()
+ }
+
+ go runner.ProcessDockerAttach(response.Reader)
return nil
}
-// StartContainer creates the container and runs it.
-func (runner *ContainerRunner) StartContainer() (err error) {
+func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
+ stdoutPath := mntPath[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 nil, 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 nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
+ }
+ }
+ }
+ stdoutFile, err := os.Create(path.Join(runner.HostOutputDir, stdoutPath))
+ if err != nil {
+ return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
+ }
+
+ return stdoutFile, nil
+}
+
+// CreateContainer creates the docker container.
+func (runner *ContainerRunner) CreateContainer() error {
runner.CrunchLog.Print("Creating Docker container")
- runner.CancelLock.Lock()
- defer runner.CancelLock.Unlock()
+ runner.ContainerConfig.Cmd = runner.Container.Command
+ if runner.Container.Cwd != "." {
+ runner.ContainerConfig.WorkingDir = runner.Container.Cwd
+ }
- if runner.Cancelled {
- return ErrCancelled
+ for k, v := range runner.Container.Environment {
+ runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
}
- runner.ContainerConfig.Cmd = runner.ContainerRecord.Command
- if runner.ContainerRecord.Cwd != "." {
- runner.ContainerConfig.WorkingDir = runner.ContainerRecord.Cwd
+ runner.ContainerConfig.Volumes = runner.Volumes
+
+ runner.HostConfig = dockercontainer.HostConfig{
+ Binds: runner.Binds,
+ Cgroup: dockercontainer.CgroupSpec(runner.setCgroupParent),
+ LogConfig: dockercontainer.LogConfig{
+ Type: "none",
+ },
}
- for k, v := range runner.ContainerRecord.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.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
+ } else {
+ if runner.enableNetwork == "always" {
+ runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
+ } else {
+ runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
+ }
}
- runner.ContainerConfig.NetworkDisabled = true
- runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
+
+ _, stdinUsed := runner.Container.Mounts["stdin"]
+ runner.ContainerConfig.OpenStdin = stdinUsed
+ runner.ContainerConfig.StdinOnce = stdinUsed
+ runner.ContainerConfig.AttachStdin = stdinUsed
+ runner.ContainerConfig.AttachStdout = true
+ runner.ContainerConfig.AttachStderr = true
+
+ createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
if err != nil {
return fmt.Errorf("While creating container: %v", err)
}
- hostConfig := &dockerclient.HostConfig{Binds: runner.Binds,
- LogConfig: dockerclient.LogConfig{Type: "none"}}
- err = runner.AttachStreams()
- if err != nil {
- return err
- }
+ runner.ContainerID = createdBody.ID
+ 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, hostConfig)
+ runner.cStateLock.Lock()
+ defer runner.cStateLock.Unlock()
+ if runner.cCancelled {
+ return ErrCancelled
+ }
+ err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
+ dockertypes.ContainerStartOptions{})
if err != nil {
- return fmt.Errorf("While starting container: %v", err)
+ return fmt.Errorf("could not start container: %v", err)
}
-
+ runner.cStarted = true
return nil
}
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 fmt.Errorf("While waiting for container to finish: %v", wr.Error)
+ waitDocker, err := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID)
+ if err != nil {
+ return fmt.Errorf("container wait: %v", err)
+ }
+
+ runner.CrunchLog.Printf("Container exited with code: %v", waitDocker)
+ code := int(waitDocker)
+ runner.ExitCode = &code
+
+ waitMount := runner.ArvMountExit
+ select {
+ case err := <-waitMount:
+ runner.CrunchLog.Printf("arv-mount exited before container finished: %v", err)
+ waitMount = nil
+ runner.stop()
+ default:
}
- runner.ExitCode = &wr.ExitCode
// wait for stdout/stderr to complete
<-runner.loggingDone
return nil
}
+ if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
+ // Output may have been set directly by the container, so
+ // refresh the container record to check.
+ err := runner.ArvClient.Get("containers", runner.Container.UUID,
+ nil, &runner.Container)
+ if err != nil {
+ return err
+ }
+ if runner.Container.Output != "" {
+ // Container output is already set.
+ runner.OutputPDH = &runner.Container.Output
+ return nil
+ }
+ }
+
if runner.HostOutputDir == "" {
return nil
}
_, err = os.Stat(collectionMetafile)
if err != nil {
// Regular directory
- cw := CollectionWriter{runner.Kc, nil, sync.Mutex{}}
+ cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
if err != nil {
return fmt.Errorf("While uploading output files: %v", err)
}
defer file.Close()
- rec := CollectionRecord{}
+ 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 CollectionRecord
+ // Pre-populate output from the configured mount points
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ 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 {
+ 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)
if err != nil {
return fmt.Errorf("While creating output collection: %v", err)
}
+ runner.OutputPDH = &response.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
+ }
- runner.OutputPDH = new(string)
- *runner.OutputPDH = response.PortableDataHash
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ return "", nil
+ }
- 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() {
// 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,
- "crunch-run", nil})
+ runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient,
+ UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: 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 fmt.Errorf("While creating log manifest: %v", err)
}
- var response CollectionRecord
+ var response arvados.Collection
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
+ "ensure_unique_name": true,
"collection": arvadosclient.Dict{
- "name": "logs for " + runner.ContainerRecord.UUID,
+ "is_trashed": true,
+ "name": "logs for " + runner.Container.UUID,
"manifest_text": mt}},
&response)
if err != nil {
return fmt.Errorf("While creating log collection: %v", err)
}
-
- runner.LogsPDH = new(string)
- *runner.LogsPDH = response.PortableDataHash
-
+ runner.LogsPDH = &response.PortableDataHash
return nil
}
-// UpdateContainerRecordRunning updates the container state to "Running"
-func (runner *ContainerRunner) UpdateContainerRecordRunning() error {
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID,
+// UpdateContainerRunning updates the container state to "Running"
+func (runner *ContainerRunner) UpdateContainerRunning() error {
+ runner.cStateLock.Lock()
+ defer runner.cStateLock.Unlock()
+ if runner.cCancelled {
+ 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
+// 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
+ }
+
+ 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) UpdateContainerRecordComplete() error {
+func (runner *ContainerRunner) UpdateContainerFinal() error {
update := arvadosclient.Dict{}
+ update["state"] = runner.finalState
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
+ if runner.finalState == "Complete" {
+ 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)
+}
- update["state"] = runner.finalState
-
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, arvadosclient.Dict{"container": update}, nil)
+// IsCancelled returns the value of Cancelled, with goroutine safety.
+func (runner *ContainerRunner) IsCancelled() bool {
+ runner.cStateLock.Lock()
+ defer runner.cStateLock.Unlock()
+ return runner.cCancelled
}
// 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{ArvClient: runner.ArvClient, UUID: runner.Container.UUID, loggingStream: name,
+ writeCloser: runner.LogCollection.Open(name + ".txt")}
}
// Run the full container lifecycle.
func (runner *ContainerRunner) Run() (err error) {
- runner.CrunchLog.Printf("Executing container '%s'", runner.ContainerRecord.UUID)
+ runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
hostname, hosterr := os.Hostname()
if hosterr != nil {
runner.CrunchLog.Printf("Executing on host '%s'", hostname)
}
- var runerr, waiterr error
+ // Clean up temporary directories _after_ finalizing
+ // everything (if we've made any by then)
+ defer runner.CleanupDirs()
+
+ 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) capture output
- outputerr := runner.CaptureOutput()
- if outputerr != nil {
- runner.CrunchLog.Print(outputerr)
+ if runner.finalState == "Queued" {
+ runner.CrunchLog.Close()
+ runner.UpdateContainerFinal()
+ return
}
- // (7) clean up temporary directories
- runner.CleanupDirs()
-
- // (8) write logs
- logerr := runner.CommitLogs()
- if logerr != nil {
- runner.CrunchLog.Print(logerr)
+ if runner.IsCancelled() {
+ runner.finalState = "Cancelled"
+ // but don't return yet -- we still want to
+ // capture partial output and write logs
}
- // (9) update container record with results
- updateerr := runner.UpdateContainerRecordComplete()
- if updateerr != nil {
- runner.CrunchLog.Print(updateerr)
- }
+ checkErr(runner.CaptureOutput())
+ checkErr(runner.CommitLogs())
+ checkErr(runner.UpdateContainerFinal())
+ // 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()
-
- if err == nil {
- if runerr != nil {
- err = runerr
- } else if waiterr != nil {
- err = waiterr
- } else if logerr != nil {
- err = logerr
- } else if updateerr != nil {
- err = updateerr
- }
- }
}()
- err = runner.ArvClient.Get("containers", runner.ContainerRecord.UUID, nil, &runner.ContainerRecord)
+ err = runner.ArvClient.Get("containers", runner.Container.UUID, nil, &runner.Container)
if err != nil {
- return fmt.Errorf("While getting container record: %v", err)
+ err = fmt.Errorf("While getting container record: %v", err)
+ return
}
- // (1) setup signal handling
+ // setup signal handling
runner.SetupSignals()
- // (2) check for and/or load image
+ // check for and/or load image
err = runner.LoadImage()
if err != nil {
- return fmt.Errorf("While loading container image: %v", err)
+ runner.finalState = "Cancelled"
+ err = fmt.Errorf("While loading container image: %v", err)
+ return
}
- // (3) set up FUSE mount and binds
+ // set up FUSE mount and binds
err = runner.SetupMounts()
if err != nil {
- return fmt.Errorf("While setting up mounts: %v", err)
+ runner.finalState = "Cancelled"
+ err = fmt.Errorf("While setting up mounts: %v", err)
+ return
}
- // (3) create and start container
- err = runner.StartContainer()
+ err = runner.CreateContainer()
if err != nil {
- if err == ErrCancelled {
- err = nil
- }
return
}
- // (4) update container record state
- err = runner.UpdateContainerRecordRunning()
+ // Gather and record node information
+ err = runner.LogNodeInfo()
+ if err != nil {
+ return
+ }
+ // Save container.json record on log collection
+ err = runner.LogContainerRecord()
if err != nil {
- runner.CrunchLog.Print(err)
+ return
}
- // (5) wait for container to finish
- waiterr = runner.WaitFinish()
+ runner.StartCrunchstat()
+ if runner.IsCancelled() {
+ return
+ }
+
+ err = runner.UpdateContainerRunning()
+ if err != nil {
+ return
+ }
+ runner.finalState = "Cancelled"
+
+ err = runner.StartContainer()
+ if err != nil {
+ return
+ }
+
+ err = runner.WaitFinish()
+ if err == nil {
+ runner.finalState = "Complete"
+ }
return
}
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
cr.MkTempDir = ioutil.TempDir
- cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
- cr.ContainerRecord.UUID = containerUUID
+ cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
+ cr.Container.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
+
+ loadLogThrottleParams(api)
+
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 (ignored if -cgroup-parent-subsystem is used)")
+ cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
+ caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
+ enableNetwork := flag.String("container-enable-networking", "default",
+ `Specify if networking should be enabled for container. One of 'default', 'always':
+ default: only enable networking if container requests it.
+ always: containers always have networking enabled
+ `)
+ networkMode := flag.String("container-network-mode", "default",
+ `Set networking mode for container. Corresponds to Docker network mode (--net).
+ `)
flag.Parse()
containerId := flag.Arg(0)
+ if *caCertsPath != "" {
+ arvadosclient.CertFiles = []string{*caCertsPath}
+ }
+
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Fatalf("%s: %v", containerId, err)
api.Retries = 8
var kc *keepclient.KeepClient
- kc, err = keepclient.MakeKeepClient(&api)
+ kc, err = keepclient.MakeKeepClient(api)
if err != nil {
log.Fatalf("%s: %v", containerId, err)
}
kc.Retries = 4
- var docker *dockerclient.DockerClient
- docker, err = dockerclient.NewDockerClient("unix:///var/run/docker.sock", nil)
+ var docker *dockerclient.Client
+ // API version 1.21 corresponds to Docker 1.9, which is currently the
+ // minimum version we want to support.
+ docker, err = dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
if err != nil {
log.Fatalf("%s: %v", containerId, err)
}
- cr := NewContainerRunner(api, kc, docker, containerId)
+ dockerClientProxy := ThinDockerClientProxy{Docker: docker}
+
+ cr := NewContainerRunner(api, kc, dockerClientProxy, containerId)
+ cr.statInterval = *statInterval
+ cr.cgroupRoot = *cgroupRoot
+ cr.expectCgroupParent = *cgroupParent
+ cr.enableNetwork = *enableNetwork
+ cr.networkMode = *networkMode
+ if *cgroupParentSubsystem != "" {
+ p := findCgroup(*cgroupParentSubsystem)
+ cr.setCgroupParent = p
+ cr.expectCgroupParent = p
+ }
err = cr.Run()
if err != nil {
projects / arvados.git / blobdiff