X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a8378b8deaa2bbf9d2c154d9d9bb072538c288cc..2ebd44960d1e7a0431d6ad612298012627c5019c:/services/crunch-run/crunchrun.go diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go index 062126d6ff..7ed5be998b 100644 --- a/services/crunch-run/crunchrun.go +++ b/services/crunch-run/crunchrun.go @@ -1,6 +1,8 @@ package main import ( + "bytes" + "context" "encoding/json" "errors" "flag" @@ -24,7 +26,11 @@ import ( "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" + + 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. @@ -55,14 +61,62 @@ 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 - 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) + 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) +} + +// ThinDockerClientProxy is a proxy implementation of ThinDockerClient +// that executes the docker requests on dockerclient.Client +type ThinDockerClientProxy struct { + Docker *dockerclient.Client +} + +// 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) +} + +// 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) +} + +// 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) +} + +// 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) +} + +// 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 @@ -72,8 +126,8 @@ type ContainerRunner struct { ArvClient IArvadosClient Kc IKeepClient arvados.Container - dockerclient.ContainerConfig - dockerclient.HostConfig + ContainerConfig dockercontainer.Config + dockercontainer.HostConfig token string ContainerID string ExitCode *int @@ -81,7 +135,7 @@ type ContainerRunner struct { loggingDone chan bool CrunchLog *ThrottledLogger Stdout io.WriteCloser - Stderr *ThrottledLogger + Stderr io.WriteCloser LogCollection *CollectionWriter LogsPDH *string RunArvMount @@ -146,7 +200,8 @@ func (runner *ContainerRunner) stop() { } runner.cCancelled = true if runner.cStarted { - err := runner.Docker.StopContainer(runner.ContainerID, 10) + timeout := time.Duration(10) + err := runner.Docker.ContainerStop(context.TODO(), runner.ContainerID, &(timeout)) if err != nil { log.Printf("StopContainer failed: %s", err) } @@ -177,7 +232,7 @@ func (runner *ContainerRunner) LoadImage() (err error) { 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") @@ -187,10 +242,11 @@ func (runner *ContainerRunner) LoadImage() (err error) { 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") } @@ -290,10 +346,10 @@ func (runner *ContainerRunner) SetupMounts() (err error) { for _, bind := range binds { mnt := runner.Container.Mounts[bind] - if bind == "stdout" { + if bind == "stdout" || bind == "stderr" { // 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) + return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind) } // Does path start with OutputPath? @@ -302,7 +358,14 @@ func (runner *ContainerRunner) SetupMounts() (err error) { prefix += "/" } if !strings.HasPrefix(mnt.Path, prefix) { - return fmt.Errorf("Stdout path does not start with OutputPath: %s, %s", 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) } } @@ -602,15 +665,46 @@ func (runner *ContainerRunner) LogContainerRecord() (err error) { 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. +// 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) + } + + defer stdinRdr.Close() + } 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) } @@ -618,37 +712,75 @@ func (runner *ContainerRunner) AttachStreams() (err error) { 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)) + stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path) if err != nil { - return fmt.Errorf("While creating stdout file: %v", err) + return err } runner.Stdout = stdoutFile } else { runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout")) } - runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr")) - go runner.ProcessDockerAttach(containerReader) + 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")) + } + + 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() + } + response.Conn.Close() + }() + } 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.Conn.Close() + }() + } + + go runner.ProcessDockerAttach(response.Reader) return nil } +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") @@ -662,10 +794,10 @@ func (runner *ContainerRunner) CreateContainer() error { runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v) } - runner.HostConfig = dockerclient.HostConfig{ - Binds: runner.Binds, - CgroupParent: runner.setCgroupParent, - LogConfig: dockerclient.LogConfig{ + runner.HostConfig = dockercontainer.HostConfig{ + Binds: runner.Binds, + Cgroup: dockercontainer.CgroupSpec(runner.setCgroupParent), + LogConfig: dockercontainer.LogConfig{ Type: "none", }, } @@ -680,21 +812,22 @@ func (runner *ContainerRunner) CreateContainer() error { "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"), "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"), ) - runner.HostConfig.NetworkMode = runner.networkMode + runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode) } else { if runner.enableNetwork == "always" { - runner.HostConfig.NetworkMode = runner.networkMode + runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode) } else { - runner.HostConfig.NetworkMode = "none" + runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none") } } - var err error - runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil) + 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) } + runner.ContainerID = createdBody.ID + return runner.AttachStreams() } @@ -706,7 +839,8 @@ func (runner *ContainerRunner) StartContainer() error { if runner.cCancelled { return ErrCancelled } - err := runner.Docker.StartContainer(runner.ContainerID, &runner.HostConfig) + err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID, + dockertypes.ContainerStartOptions{}) if err != nil { return fmt.Errorf("could not start container: %v", err) } @@ -719,21 +853,22 @@ func (runner *ContainerRunner) StartContainer() error { func (runner *ContainerRunner) WaitFinish() error { runner.CrunchLog.Print("Waiting for container to finish") - waitDocker := runner.Docker.Wait(runner.ContainerID) + 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 - for waitDocker != nil { - select { - case err := <-waitMount: - runner.CrunchLog.Printf("arv-mount exited before container finished: %v", err) - waitMount = nil - runner.stop() - case wr := <-waitDocker: - if wr.Error != nil { - return fmt.Errorf("While waiting for container to finish: %v", wr.Error) - } - runner.ExitCode = &wr.ExitCode - waitDocker = nil - } + select { + case err := <-waitMount: + runner.CrunchLog.Printf("arv-mount exited before container finished: %v", err) + waitMount = nil + runner.stop() + default: } // wait for stdout/stderr to complete @@ -1186,13 +1321,17 @@ func main() { } 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