X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f44a15adce692614ecb816dbe2d0205704d9a4ab..1b7a6c0ca4fa348c313a0862cfca597319cfe08f:/services/crunch-run/crunchrun.go diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go index bb5973d874..705bea486b 100644 --- a/services/crunch-run/crunchrun.go +++ b/services/crunch-run/crunchrun.go @@ -6,7 +6,6 @@ package main import ( "bytes" - "context" "encoding/json" "errors" "flag" @@ -33,6 +32,7 @@ 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" + "golang.org/x/net/context" dockertypes "github.com/docker/docker/api/types" dockercontainer "github.com/docker/docker/api/types/container" @@ -75,60 +75,13 @@ type ThinDockerClient interface { 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 + ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan 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, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) { - return proxy.Docker.ContainerWait(ctx, container, condition) -} - -// 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 // container. type ContainerRunner struct { @@ -161,10 +114,12 @@ type ContainerRunner struct { ArvMountExit chan error finalState string - statLogger io.WriteCloser - statReporter *crunchstat.Reporter - statInterval time.Duration - cgroupRoot string + statLogger io.WriteCloser + statReporter *crunchstat.Reporter + hoststatLogger io.WriteCloser + hoststatReporter *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 @@ -180,7 +135,6 @@ type ContainerRunner struct { setCgroupParent string cStateLock sync.Mutex - cStarted bool // StartContainer() succeeded cCancelled bool // StopContainer() invoked enableNetwork string // one of "default" or "always" @@ -197,11 +151,10 @@ func (runner *ContainerRunner) setupSignals() { signal.Notify(runner.SigChan, syscall.SIGQUIT) go func(sig chan os.Signal) { - s := <-sig - if s != nil { - runner.CrunchLog.Printf("Caught signal %v", s) + for s := range sig { + runner.CrunchLog.Printf("caught signal: %v", s) + runner.stop() } - runner.stop() }(runner.SigChan) } @@ -209,25 +162,20 @@ func (runner *ContainerRunner) setupSignals() { func (runner *ContainerRunner) stop() { runner.cStateLock.Lock() defer runner.cStateLock.Unlock() - if runner.cCancelled { + if runner.ContainerID == "" { return } runner.cCancelled = true - if runner.cStarted { - timeout := time.Duration(10) - err := runner.Docker.ContainerStop(context.TODO(), runner.ContainerID, &(timeout)) - if err != nil { - runner.CrunchLog.Printf("StopContainer failed: %s", err) - } - // Suppress multiple calls to stop() - runner.cStarted = false + runner.CrunchLog.Printf("removing container") + err := runner.Docker.ContainerRemove(context.TODO(), runner.ContainerID, dockertypes.ContainerRemoveOptions{Force: true}) + if err != nil { + runner.CrunchLog.Printf("error removing container: %s", err) } } func (runner *ContainerRunner) stopSignals() { if runner.SigChan != nil { signal.Stop(runner.SigChan) - close(runner.SigChan) } } @@ -597,53 +545,74 @@ func (runner *ContainerRunner) SetupMounts() (err error) { 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 + defer close(runner.loggingDone) header := make([]byte, 8) - for { - _, readerr := io.ReadAtLeast(containerReader, header, 8) - - if readerr == nil { - readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24) - if header[0] == 1 { - // stdout - _, readerr = io.CopyN(runner.Stdout, containerReader, readsize) - } else { - // stderr - _, readerr = io.CopyN(runner.Stderr, containerReader, readsize) + var err error + for err == nil { + _, err = io.ReadAtLeast(containerReader, header, 8) + if err != nil { + if err == io.EOF { + err = nil } + break } + readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24) + if header[0] == 1 { + // stdout + _, err = io.CopyN(runner.Stdout, containerReader, readsize) + } else { + // stderr + _, err = io.CopyN(runner.Stderr, containerReader, readsize) + } + } - if readerr != nil { - if readerr != io.EOF { - runner.CrunchLog.Printf("While reading docker logs: %v", readerr) - } - - closeerr := runner.Stdout.Close() - if closeerr != nil { - runner.CrunchLog.Printf("While closing stdout logs: %v", closeerr) - } + if err != nil { + runner.CrunchLog.Printf("error reading docker logs: %v", err) + } - closeerr = runner.Stderr.Close() - if closeerr != nil { - runner.CrunchLog.Printf("While closing stderr logs: %v", closeerr) - } + err = runner.Stdout.Close() + if err != nil { + runner.CrunchLog.Printf("error closing stdout logs: %v", err) + } - if runner.statReporter != nil { - runner.statReporter.Stop() - closeerr = runner.statLogger.Close() - if closeerr != nil { - runner.CrunchLog.Printf("While closing crunchstat logs: %v", closeerr) - } - } + err = runner.Stderr.Close() + if err != nil { + runner.CrunchLog.Printf("error closing stderr logs: %v", err) + } - runner.loggingDone <- true - close(runner.loggingDone) - return + if runner.statReporter != nil { + runner.statReporter.Stop() + err = runner.statLogger.Close() + if err != nil { + runner.CrunchLog.Printf("error closing crunchstat logs: %v", err) } } } -func (runner *ContainerRunner) StartCrunchstat() { +func (runner *ContainerRunner) stopHoststat() error { + if runner.hoststatReporter == nil { + return nil + } + runner.hoststatReporter.Stop() + err := runner.hoststatLogger.Close() + if err != nil { + return fmt.Errorf("error closing hoststat logs: %v", err) + } + return nil +} + +func (runner *ContainerRunner) startHoststat() { + runner.hoststatLogger = NewThrottledLogger(runner.NewLogWriter("hoststat")) + runner.hoststatReporter = &crunchstat.Reporter{ + Logger: log.New(runner.hoststatLogger, "", 0), + CgroupRoot: runner.cgroupRoot, + PollPeriod: runner.statInterval, + } + runner.hoststatReporter.Start() +} + +func (runner *ContainerRunner) startCrunchstat() { runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat")) runner.statReporter = &crunchstat.Reporter{ CID: runner.ContainerID, @@ -660,9 +629,12 @@ type infoCommand struct { cmd []string } -// LogNodeInfo gathers node information and store it on the log for debugging -// purposes. -func (runner *ContainerRunner) LogNodeInfo() (err error) { +// LogHostInfo logs info about the current host, for debugging and +// accounting purposes. Although it's logged as "node-info", this is +// about the environment where crunch-run is actually running, which +// might differ from what's described in the node record (see +// LogNodeRecord). +func (runner *ContainerRunner) LogHostInfo() (err error) { w := runner.NewLogWriter("node-info") commands := []infoCommand{ @@ -710,38 +682,71 @@ func (runner *ContainerRunner) LogNodeInfo() (err error) { } // LogContainerRecord gets and saves the raw JSON container record from the API server -func (runner *ContainerRunner) LogContainerRecord() (err error) { +func (runner *ContainerRunner) LogContainerRecord() error { + logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil) + if !logged && err == nil { + err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID) + } + return err +} + +// LogNodeRecord logs arvados#node record corresponding to the current host. +func (runner *ContainerRunner) LogNodeRecord() error { + hostname := os.Getenv("SLURMD_NODENAME") + if hostname == "" { + hostname, _ = os.Hostname() + } + _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) { + // The "info" field has admin-only info when obtained + // with a privileged token, and should not be logged. + node, ok := resp.(map[string]interface{}) + if ok { + delete(node, "info") + } + }) + return err +} + +func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) { w := &ArvLogWriter{ ArvClient: runner.ArvClient, UUID: runner.Container.UUID, - loggingStream: "container", - writeCloser: runner.LogCollection.Open("container.json"), + loggingStream: label, + writeCloser: runner.LogCollection.Open(label + ".json"), } - // Get Container record JSON from the API Server - reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil) + reader, err := runner.ArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params)) if err != nil { - return fmt.Errorf("While retrieving container record from the API server: %v", err) + return false, fmt.Errorf("error getting %s record: %v", label, err) } defer reader.Close() dec := json.NewDecoder(reader) dec.UseNumber() - var cr map[string]interface{} - if err = dec.Decode(&cr); err != nil { - return fmt.Errorf("While decoding the container record JSON response: %v", err) + var resp map[string]interface{} + if err = dec.Decode(&resp); err != nil { + return false, fmt.Errorf("error decoding %s list response: %v", label, err) + } + items, ok := resp["items"].([]interface{}) + if !ok { + return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label) + } else if len(items) < 1 { + return false, nil + } + if munge != nil { + munge(items[0]) } // 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) + if err = enc.Encode(items[0]); err != nil { + return false, fmt.Errorf("error logging %s record: %v", label, err) } err = w.Close() if err != nil { - return fmt.Errorf("While closing container.json log: %v", err) + return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err) } - return nil + return true, nil } // AttachStreams connects the docker container stdin, stdout and stderr logs @@ -937,46 +942,38 @@ func (runner *ContainerRunner) StartContainer() error { } return fmt.Errorf("could not start container: %v%s", err, advice) } - runner.cStarted = true return nil } // WaitFinish waits for the container to terminate, capture the exit code, and // close the stdout/stderr logging. -func (runner *ContainerRunner) WaitFinish() (err error) { +func (runner *ContainerRunner) WaitFinish() error { runner.CrunchLog.Print("Waiting for container to finish") - waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, "not-running") + waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning) + arvMountExit := runner.ArvMountExit + for { + select { + case waitBody := <-waitOk: + runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode) + code := int(waitBody.StatusCode) + runner.ExitCode = &code + + // wait for stdout/stderr to complete + <-runner.loggingDone + return nil + + case err := <-waitErr: + return fmt.Errorf("container wait: %v", err) - go func() { - <-runner.ArvMountExit - if runner.cStarted { + case <-arvMountExit: runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.") runner.stop() + // arvMountExit will always be ready now that + // it's closed, but that doesn't interest us. + arvMountExit = nil } - }() - - var waitBody dockercontainer.ContainerWaitOKBody - select { - case waitBody = <-waitOk: - case err = <-waitErr: } - - // Container isn't running any more - runner.cStarted = false - - if err != nil { - return fmt.Errorf("container wait: %v", err) - } - - runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode) - code := int(waitBody.StatusCode) - runner.ExitCode = &code - - // wait for stdout/stderr to complete - <-runner.loggingDone - - return nil } var ErrNotInOutputDir = fmt.Errorf("Must point to path within the output directory") @@ -1155,10 +1152,6 @@ func (runner *ContainerRunner) UploadOutputFile( // HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories func (runner *ContainerRunner) CaptureOutput() error { - if runner.finalState != "Complete" { - 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. @@ -1543,6 +1536,7 @@ func (runner *ContainerRunner) Run() (err error) { } checkErr(runner.CaptureOutput()) + checkErr(runner.stopHoststat()) checkErr(runner.CommitLogs()) checkErr(runner.UpdateContainerFinal()) }() @@ -1551,9 +1545,8 @@ func (runner *ContainerRunner) Run() (err error) { if err != nil { return } - - // setup signal handling runner.setupSignals() + runner.startHoststat() // check for and/or load image err = runner.LoadImage() @@ -1579,13 +1572,14 @@ func (runner *ContainerRunner) Run() (err error) { if err != nil { return } - - // Gather and record node information - err = runner.LogNodeInfo() + err = runner.LogHostInfo() + if err != nil { + return + } + err = runner.LogNodeRecord() if err != nil { return } - // Save container.json record on log collection err = runner.LogContainerRecord() if err != nil { return @@ -1601,7 +1595,7 @@ func (runner *ContainerRunner) Run() (err error) { } runner.finalState = "Cancelled" - runner.StartCrunchstat() + runner.startCrunchstat() err = runner.StartContainer() if err != nil { @@ -1610,7 +1604,7 @@ func (runner *ContainerRunner) Run() (err error) { } err = runner.WaitFinish() - if err == nil { + if err == nil && !runner.IsCancelled() { runner.finalState = "Complete" } return @@ -1702,10 +1696,8 @@ func main() { // API version 1.21 corresponds to Docker 1.9, which is currently the // minimum version we want to support. docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil) - dockerClientProxy := ThinDockerClientProxy{Docker: docker} - - cr := NewContainerRunner(api, kc, dockerClientProxy, containerId) + cr := NewContainerRunner(api, kc, docker, containerId) if dockererr != nil { cr.CrunchLog.Printf("%s: %v", containerId, dockererr) cr.checkBrokenNode(dockererr)