+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package main
import (
+ "bytes"
+ "context"
"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"
"io/ioutil"
"log"
"os/signal"
"path"
"path/filepath"
+ "runtime"
+ "runtime/pprof"
"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.
Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) 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)
}
// 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) (arvados.File, error)
+ ClearBlockCache()
}
// NewLogWriter is a factory function to create a new log writer.
// 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, 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
ArvClient IArvadosClient
Kc IKeepClient
arvados.Container
- dockerclient.ContainerConfig
- dockerclient.HostConfig
+ ContainerConfig dockercontainer.Config
+ dockercontainer.HostConfig
token string
ContainerID string
ExitCode *int
loggingDone chan bool
CrunchLog *ThrottledLogger
Stdout io.WriteCloser
- Stderr *ThrottledLogger
+ 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
- trashLifetime time.Duration
statLogger io.WriteCloser
statReporter *crunchstat.Reporter
// 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
+ arvMountLog *ThrottledLogger
}
-// SetupSignals sets up signal handling to gracefully terminate the underlying
+// 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() {
+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 {
- if !runner.Cancelled {
- runner.CancelLock.Lock()
- runner.Cancelled = true
- if runner.ContainerID != "" {
- runner.Docker.StopContainer(runner.ContainerID, 10)
+ go func(sig chan os.Signal) {
+ s := <-sig
+ if s != nil {
+ runner.CrunchLog.Printf("Caught signal %v", s)
+ }
+ runner.stop()
+ }(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 {
+ runner.CrunchLog.Printf("StopContainer failed: %s", err)
+ }
+ // Suppress multiple calls to stop()
+ runner.cStarted = false
+ }
+}
+
+func (runner *ContainerRunner) stopSignals() {
+ if runner.SigChan != nil {
+ signal.Stop(runner.SigChan)
+ close(runner.SigChan)
+ }
+}
+
+var errorBlacklist = []string{"Cannot connect to the Docker daemon"}
+var brokenNodeHook *string = flag.String("broken-node-hook", "", "Script to run if node is detected to be broken (for example, Docker daemon is not running)")
+
+func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
+ for _, d := range errorBlacklist {
+ if strings.Index(goterr.Error(), d) != -1 {
+ runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
+ if *brokenNodeHook == "" {
+ runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
+ } else {
+ runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
+ // run killme script
+ c := exec.Command(*brokenNodeHook)
+ c.Stdout = runner.CrunchLog
+ c.Stderr = runner.CrunchLog
+ err := c.Run()
+ if err != nil {
+ runner.CrunchLog.Printf("Error running broken node hook: %v", err)
}
- runner.CancelLock.Unlock()
}
+ return true
}
- }(runner.SigChan)
+ }
+ return false
}
// LoadImage determines the docker image id from the container record and
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, true)
if err != nil {
return fmt.Errorf("While loading container image into Docker: %v", err)
}
+
+ defer response.Body.Close()
+ rbody, err := ioutil.ReadAll(response.Body)
+ if err != nil {
+ return fmt.Errorf("Reading response to image load: %v", err)
+ }
+ runner.CrunchLog.Printf("Docker response: %s", rbody)
} else {
runner.CrunchLog.Print("Docker image is available")
}
runner.ContainerConfig.Image = imageID
+ runner.Kc.ClearBlockCache()
+
return nil
}
}
c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
- nt := NewThrottledLogger(runner.NewLogWriter("arv-mount"))
- c.Stdout = nt
- c.Stderr = nt
+ runner.arvMountLog = NewThrottledLogger(runner.NewLogWriter("arv-mount"))
+ c.Stdout = runner.arvMountLog
+ c.Stderr = runner.arvMountLog
+
+ runner.CrunchLog.Printf("Running %v", c.Args)
err = c.Start()
if err != nil {
}()
go func() {
- runner.ArvMountExit <- c.Wait()
+ mnterr := c.Wait()
+ if mnterr != nil {
+ runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
+ }
+ runner.ArvMountExit <- mnterr
close(runner.ArvMountExit)
}()
return c, nil
}
-var tmpBackedOutputDir = false
-
func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
if runner.ArvMountPoint == "" {
runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
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", "--allow-other", "--read-write"}
+ arvMountCmd := []string{
+ "--foreground",
+ "--allow-other",
+ "--read-write",
+ fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
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 {
+ 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" {
+ 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?
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)
}
}
}
switch {
- case mnt.Kind == "collection":
+ 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")
}
collectionPaths = append(collectionPaths, src)
- case mnt.Kind == "tmp" && bind == runner.Container.OutputPath:
- runner.HostOutputDir, err = runner.MkTempDir("", "")
+ case mnt.Kind == "tmp":
+ var tmpdir string
+ tmpdir, err = runner.MkTempDir("", "")
if err != nil {
return fmt.Errorf("While creating mount temp dir: %v", err)
}
- st, staterr := os.Stat(runner.HostOutputDir)
+ st, staterr := os.Stat(tmpdir)
if staterr != nil {
return fmt.Errorf("While Stat on temp dir: %v", staterr)
}
- err = os.Chmod(runner.HostOutputDir, st.Mode()|os.ModeSetgid|0777)
+ err = os.Chmod(tmpdir, 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))
- tmpBackedOutputDir = true
-
- case mnt.Kind == "tmp":
- runner.Binds = append(runner.Binds, bind)
+ runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
+ if bind == runner.Container.OutputPath {
+ runner.HostOutputDir = tmpdir
+ }
case mnt.Kind == "json":
jsondata, err := json.Marshal(mnt.Content)
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.
+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{
+ {
+ label: "Host Information",
+ cmd: []string{"uname", "-a"},
+ },
+ {
+ label: "CPU Information",
+ cmd: []string{"cat", "/proc/cpuinfo"},
+ },
+ {
+ label: "Memory Information",
+ cmd: []string{"cat", "/proc/meminfo"},
+ },
+ {
+ label: "Disk Space",
+ cmd: []string{"df", "-m", "/", os.TempDir()},
+ },
+ {
+ 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()
+
+ 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)
+ }
+ // 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 arvados.File
+ 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)
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()
+ }
+ 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
}
+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 := filepath.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(filepath.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")
for k, v := range runner.Container.Environment {
runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
}
+
+ runner.ContainerConfig.Volumes = runner.Volumes
+
+ runner.HostConfig = dockercontainer.HostConfig{
+ Binds: runner.Binds,
+ LogConfig: dockercontainer.LogConfig{
+ Type: "none",
+ },
+ Resources: dockercontainer.Resources{
+ CgroupParent: runner.setCgroupParent,
+ },
+ }
+
if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
tok, err := runner.ContainerToken()
if err != nil {
"ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
"ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
)
- runner.ContainerConfig.NetworkDisabled = false
+ runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
} else {
- runner.ContainerConfig.NetworkDisabled = true
+ if runner.enableNetwork == "always" {
+ runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
+ } else {
+ runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
+ }
}
- var err error
- 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)
}
- runner.HostConfig = dockerclient.HostConfig{
- Binds: runner.Binds,
- CgroupParent: runner.setCgroupParent,
- LogConfig: dockerclient.LogConfig{
- Type: "none",
- },
- }
+ 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, &runner.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("could not start container: %v", err)
+ var advice string
+ if strings.Contains(err.Error(), "no such file or directory") {
+ advice = fmt.Sprintf("\nPossible causes: command %q is missing, the interpreter given in #! is missing, or script has Windows line endings.", runner.Container.Command[0])
+ }
+ 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() error {
+func (runner *ContainerRunner) WaitFinish() (err 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)
+ waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, "not-running")
+
+ go func() {
+ <-runner.ArvMountExit
+ if runner.cStarted {
+ runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
+ runner.stop()
+ }
+ }()
+
+ 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.ExitCode = &wr.ExitCode
+
+ 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")
+
+func (runner *ContainerRunner) derefOutputSymlink(path string, startinfo os.FileInfo) (tgt string, readlinktgt string, info os.FileInfo, err error) {
+ // Follow symlinks if necessary
+ info = startinfo
+ tgt = path
+ readlinktgt = ""
+ nextlink := path
+ for followed := 0; info.Mode()&os.ModeSymlink != 0; followed++ {
+ if followed >= limitFollowSymlinks {
+ // Got stuck in a loop or just a pathological number of links, give up.
+ err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
+ return
+ }
+
+ readlinktgt, err = os.Readlink(nextlink)
+ if err != nil {
+ return
+ }
+
+ tgt = readlinktgt
+ if !strings.HasPrefix(tgt, "/") {
+ // Relative symlink, resolve it to host path
+ tgt = filepath.Join(filepath.Dir(path), tgt)
+ }
+ if strings.HasPrefix(tgt, runner.Container.OutputPath+"/") && !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
+ // Absolute symlink to container output path, adjust it to host output path.
+ tgt = filepath.Join(runner.HostOutputDir, tgt[len(runner.Container.OutputPath):])
+ }
+ if !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
+ // After dereferencing, symlink target must either be
+ // within output directory, or must point to a
+ // collection mount.
+ err = ErrNotInOutputDir
+ return
+ }
+
+ info, err = os.Lstat(tgt)
+ if err != nil {
+ // tgt
+ err = fmt.Errorf("Symlink in output %q points to invalid location %q: %v",
+ path[len(runner.HostOutputDir):], readlinktgt, err)
+ return
+ }
+
+ nextlink = tgt
+ }
+
+ return
+}
+
+var limitFollowSymlinks = 10
+
+// UploadFile uploads files within the output directory, with special handling
+// for symlinks. If the symlink leads to a keep mount, copy the manifest text
+// from the keep mount into the output manifestText. Ensure that whether
+// symlinks are relative or absolute, every symlink target (even targets that
+// are symlinks themselves) must point to a path in either the output directory
+// or a collection mount.
+//
+// Assumes initial value of "path" is absolute, and located within runner.HostOutputDir.
+func (runner *ContainerRunner) UploadOutputFile(
+ path string,
+ info os.FileInfo,
+ infoerr error,
+ binds []string,
+ walkUpload *WalkUpload,
+ relocateFrom string,
+ relocateTo string,
+ followed int) (manifestText string, err error) {
+
+ if info.Mode().IsDir() {
+ return
+ }
+
+ if infoerr != nil {
+ return "", infoerr
+ }
+
+ if followed >= limitFollowSymlinks {
+ // Got stuck in a loop or just a pathological number of
+ // directory links, give up.
+ err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
+ return
+ }
+
+ // When following symlinks, the source path may need to be logically
+ // relocated to some other path within the output collection. Remove
+ // the relocateFrom prefix and replace it with relocateTo.
+ relocated := relocateTo + path[len(relocateFrom):]
+
+ tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info)
+ if derefErr != nil && derefErr != ErrNotInOutputDir {
+ return "", derefErr
+ }
+
+ // go through mounts and try reverse map to collection reference
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
+ if tgt == bind || strings.HasPrefix(tgt, bind+"/") {
+ // get path relative to bind
+ targetSuffix := tgt[len(bind):]
+
+ // Copy mount and adjust the path to add path relative to the bind
+ adjustedMount := mnt
+ adjustedMount.Path = filepath.Join(adjustedMount.Path, targetSuffix)
+
+ // Terminates in this keep mount, so add the
+ // manifest text at appropriate location.
+ outputSuffix := path[len(runner.HostOutputDir):]
+ manifestText, err = runner.getCollectionManifestForPath(adjustedMount, outputSuffix)
+ return
+ }
+ }
+
+ // If target is not a collection mount, it must be located within the
+ // output directory, otherwise it is an error.
+ if derefErr == ErrNotInOutputDir {
+ err = fmt.Errorf("Symlink in output %q points to invalid location %q, must point to path within the output directory.",
+ path[len(runner.HostOutputDir):], readlinktgt)
+ return
+ }
+
+ if info.Mode().IsRegular() {
+ return "", walkUpload.UploadFile(relocated, tgt)
+ }
+
+ if info.Mode().IsDir() {
+ // Symlink leads to directory. Walk() doesn't follow
+ // directory symlinks, so we walk the target directory
+ // instead. Within the walk, file paths are relocated
+ // so they appear under the original symlink path.
+ err = filepath.Walk(tgt, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
+ var m string
+ m, walkerr = runner.UploadOutputFile(walkpath, walkinfo, walkerr,
+ binds, walkUpload, tgt, relocated, followed+1)
+ if walkerr == nil {
+ manifestText = manifestText + m
+ }
+ return walkerr
+ })
+ return
+ }
+
+ return
+}
+
// HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
func (runner *ContainerRunner) CaptureOutput() error {
if runner.finalState != "Complete" {
return fmt.Errorf("While checking host output path: %v", err)
}
+ // Pre-populate output from the configured mount points
+ var binds []string
+ for bind, mnt := range runner.Container.Mounts {
+ if mnt.Kind == "collection" {
+ binds = append(binds, bind)
+ }
+ }
+ sort.Strings(binds)
+
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)
+
+ cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
+ walkUpload := cw.BeginUpload(runner.HostOutputDir, runner.CrunchLog.Logger)
+
+ var m string
+ err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error {
+ m, err = runner.UploadOutputFile(path, info, err, binds, walkUpload, "", "", 0)
+ if err == nil {
+ manifestText = manifestText + m
+ }
+ return err
+ })
+
+ cw.EndUpload(walkUpload)
+
+ if err != nil {
+ return fmt.Errorf("While uploading output files: %v", err)
+ }
+
+ m, err = cw.ManifestText()
+ manifestText = manifestText + m
if err != nil {
return fmt.Errorf("While uploading output files: %v", err)
}
manifestText = rec.ManifestText
}
- // 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]
continue
}
- if strings.Index(bindSuffix, "/") != 0 {
- return fmt.Errorf("Expected bind to be of the format '%v/*' but found: %v", runner.Container.OutputPath, bind)
- }
-
- jsondata, err := json.Marshal(mnt.Content)
- if err != nil {
- return fmt.Errorf("While marshal of mount content: %v", err)
- }
- var content map[string]interface{}
- err = json.Unmarshal(jsondata, &content)
- if err != nil {
- return fmt.Errorf("While unmarshal of mount content: %v", err)
- }
-
- if content["exclude_from_output"] == true {
+ if mnt.ExcludeFromOutput == true {
continue
}
- idx := strings.Index(mnt.PortableDataHash, "/")
- if idx > 0 {
- mnt.Path = mnt.PortableDataHash[idx:]
- mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
- }
-
// append to manifest_text
m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
if err != nil {
// 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{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "output for " + runner.Container.UUID,
"manifest_text": manifestText}},
&response)
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.
// "path":"/subdir1/subdir2"
// "path":"/subdir/filename" etc
func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
- var collection arvados.Collection
- err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
- if err != nil {
- return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
- }
-
- manifestText := ""
- if mnt.Path == "" || mnt.Path == "/" {
- // no path specified; return the entire manifest text
- manifestText = collection.ManifestText
- manifestText = strings.Replace(manifestText, "./", "."+bindSuffix+"/", -1)
- manifestText = strings.Replace(manifestText, ". ", "."+bindSuffix+" ", -1)
- } else {
- // either a single stream or file from a stream is being sought
- bindIdx := strings.LastIndex(bindSuffix, "/")
- var bindSubdir, bindFileName string
- if bindIdx >= 0 {
- bindSubdir = "." + bindSuffix[0:bindIdx]
- bindFileName = bindSuffix[bindIdx+1:]
- }
- pathIdx := strings.LastIndex(mnt.Path, "/")
- var pathSubdir, pathFileName string
- if pathIdx >= 0 {
- pathSubdir = "." + mnt.Path[0:pathIdx]
- pathFileName = mnt.Path[pathIdx+1:]
- }
- streams := strings.Split(collection.ManifestText, "\n")
- for _, stream := range streams {
- tokens := strings.Split(stream, " ")
- if tokens[0] == "."+mnt.Path {
- // path refers to this complete stream
- adjustedStream := strings.Replace(stream, "."+mnt.Path, "."+bindSuffix, -1)
- manifestText = adjustedStream + "\n"
- break
- } else {
- // look for a matching file in this stream
- if tokens[0] == pathSubdir {
- // path refers to a file in this stream
- for _, token := range tokens {
- if strings.Index(token, ":"+pathFileName) > 0 {
- // found the file in the stream; discard all other file tokens
- for _, t := range tokens {
- if strings.Index(t, ":") == -1 {
- manifestText += (" " + t)
- } else {
- break // done reading all non-file tokens
- }
- }
- manifestText = strings.Trim(manifestText, " ")
- token = strings.Replace(token, ":"+pathFileName, ":"+bindFileName, -1)
- manifestText += (" " + token + "\n")
- manifestText = strings.Replace(manifestText, pathSubdir, bindSubdir, -1)
- break
- }
- }
- }
- }
+ 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
}
- return manifestText, nil
-}
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ return "", nil
+ }
-func (runner *ContainerRunner) loadDiscoveryVars() {
- tl, err := runner.ArvClient.Discovery("defaultTrashLifetime")
- if err != nil {
- log.Fatalf("getting defaultTrashLifetime from discovery document: %s", err)
+ 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())
}
- runner.trashLifetime = time.Duration(tl.(float64)) * time.Second
+ return extracted.Text, nil
}
func (runner *ContainerRunner) CleanupDirs() {
if runner.ArvMount != nil {
- umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
- umnterr := umount.Run()
+ var delay int64 = 8
+ umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
+ umount.Stdout = runner.CrunchLog
+ umount.Stderr = runner.CrunchLog
+ runner.CrunchLog.Printf("Running %v", umount.Args)
+ umnterr := umount.Start()
+
if umnterr != nil {
- runner.CrunchLog.Printf("While running fusermount: %v", umnterr)
+ runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
+ } else {
+ // If arv-mount --unmount gets stuck for any reason, we
+ // don't want to wait for it forever. Do Wait() in a goroutine
+ // so it doesn't block crunch-run.
+ umountExit := make(chan error)
+ go func() {
+ mnterr := umount.Wait()
+ if mnterr != nil {
+ runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
+ }
+ umountExit <- mnterr
+ }()
+
+ for again := true; again; {
+ again = false
+ select {
+ case <-umountExit:
+ umount = nil
+ again = true
+ case <-runner.ArvMountExit:
+ break
+ case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
+ runner.CrunchLog.Printf("Timed out waiting for unmount")
+ if umount != nil {
+ umount.Process.Kill()
+ }
+ runner.ArvMount.Process.Kill()
+ }
+ }
}
+ }
- mnterr := <-runner.ArvMountExit
- if mnterr != nil {
- runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
+ if runner.ArvMountPoint != "" {
+ if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
+ runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
}
}
for _, tmpdir := range runner.CleanupTempDir {
- rmerr := os.RemoveAll(tmpdir)
- if rmerr != nil {
+ if rmerr := os.RemoveAll(tmpdir); 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)
+
+ if runner.arvMountLog != nil {
+ runner.arvMountLog.Close()
+ }
runner.CrunchLog.Close()
- // Closing CrunchLog above allows it to be committed to Keep at this
+ // Closing CrunchLog above allows them to be committed to Keep at this
// 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.Container.UUID,
- "crunch-run", nil})
+ // other further errors (such as failing to write the log to Keep!)
+ // while shutting down
+ runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient,
+ UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: nil})
+ runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
if runner.LogsPDH != nil {
// If we have already assigned something to LogsPDH,
var response arvados.Collection
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
+ "ensure_unique_name": true,
"collection": arvadosclient.Dict{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "logs for " + runner.Container.UUID,
"manifest_text": mt}},
&response)
// UpdateContainerRunning updates the container state to "Running"
func (runner *ContainerRunner) UpdateContainerRunning() error {
- runner.CancelLock.Lock()
- defer runner.CancelLock.Unlock()
- if runner.Cancelled {
+ runner.cStateLock.Lock()
+ defer runner.cStateLock.Unlock()
+ if runner.cCancelled {
return ErrCancelled
}
return runner.ArvClient.Update("containers", runner.Container.UUID,
// IsCancelled returns the value of Cancelled, with goroutine safety.
func (runner *ContainerRunner) IsCancelled() bool {
- runner.CancelLock.Lock()
- defer runner.CancelLock.Unlock()
- return runner.Cancelled
+ 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.Container.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.
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()
-
runner.finalState = "Queued"
+ defer func() {
+ runner.stopSignals()
+ runner.CleanupDirs()
+
+ runner.CrunchLog.Printf("crunch-run finished")
+ runner.CrunchLog.Close()
+ }()
+
defer func() {
// checkErr prints e (unless it's nil) and sets err to
// e (unless err is already non-nil). Thus, if err
if err == nil {
err = e
}
+ if runner.finalState == "Complete" {
+ // There was an error in the finalization.
+ runner.finalState = "Cancelled"
+ }
}
// Log the error encountered in Run(), if any
checkErr(err)
if runner.finalState == "Queued" {
- runner.CrunchLog.Close()
runner.UpdateContainerFinal()
return
}
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()
}()
- err = runner.ArvClient.Get("containers", runner.Container.UUID, nil, &runner.Container)
+ err = runner.fetchContainerRecord()
if err != nil {
- err = fmt.Errorf("While getting container record: %v", err)
return
}
// setup signal handling
- runner.SetupSignals()
+ runner.setupSignals()
// check for and/or load image
err = runner.LoadImage()
if err != nil {
- runner.finalState = "Cancelled"
+ if !runner.checkBrokenNode(err) {
+ // Failed to load image but not due to a "broken node"
+ // condition, probably user error.
+ runner.finalState = "Cancelled"
+ }
err = fmt.Errorf("While loading container image: %v", err)
return
}
return
}
- runner.StartCrunchstat()
+ // 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 {
+ return
+ }
if runner.IsCancelled() {
return
}
runner.finalState = "Cancelled"
+ runner.StartCrunchstat()
+
err = runner.StartContainer()
if err != nil {
+ runner.checkBrokenNode(err)
return
}
return
}
+// Fetch the current container record (uuid = runner.Container.UUID)
+// into runner.Container.
+func (runner *ContainerRunner) fetchContainerRecord() error {
+ reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
+ if err != nil {
+ return fmt.Errorf("error fetching container record: %v", err)
+ }
+ defer reader.Close()
+
+ dec := json.NewDecoder(reader)
+ dec.UseNumber()
+ err = dec.Decode(&runner.Container)
+ if err != nil {
+ return fmt.Errorf("error decoding container record: %v", err)
+ }
+ return nil
+}
+
// NewContainerRunner creates a new container runner.
func NewContainerRunner(api IArvadosClient,
kc IKeepClient,
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
cr.MkTempDir = ioutil.TempDir
- cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
+ 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)
- cr.loadDiscoveryVars()
+
+ loadLogThrottleParams(api)
+
return cr
}
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).
+ `)
+ memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container")
flag.Parse()
containerId := flag.Arg(0)
}
api.Retries = 8
- var kc *keepclient.KeepClient
- kc, err = keepclient.MakeKeepClient(api)
- if err != nil {
- log.Fatalf("%s: %v", containerId, err)
- }
- kc.Retries = 4
+ kc, kcerr := keepclient.MakeKeepClient(api)
- var docker *dockerclient.DockerClient
- docker, err = dockerclient.NewDockerClient("unix:///var/run/docker.sock", nil)
- if err != nil {
- log.Fatalf("%s: %v", containerId, err)
+ // 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)
+
+ if kcerr != nil {
+ cr.CrunchLog.Printf("%s: %v", containerId, kcerr)
+ cr.CrunchLog.Close()
+ os.Exit(1)
+ }
+ if dockererr != nil {
+ cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
+ cr.checkBrokenNode(dockererr)
+ cr.CrunchLog.Close()
+ os.Exit(1)
}
- cr := NewContainerRunner(api, kc, docker, containerId)
+ kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
+ kc.Retries = 4
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 {
- log.Fatalf("%s: %v", containerId, err)
+ runerr := cr.Run()
+
+ if *memprofile != "" {
+ f, err := os.Create(*memprofile)
+ if err != nil {
+ log.Printf("could not create memory profile: ", err)
+ }
+ runtime.GC() // get up-to-date statistics
+ if err := pprof.WriteHeapProfile(f); err != nil {
+ log.Printf("could not write memory profile: ", err)
+ }
+ closeerr := f.Close()
+ if closeerr != nil {
+ log.Printf("closing memprofile file: ", err)
+ }
}
+ if runerr != nil {
+ log.Fatalf("%s: %v", containerId, runerr)
+ }
}
projects / arvados.git / blobdiff