// Copyright (C) The Arvados Authors. All rights reserved.
//
// SPDX-License-Identifier: AGPL-3.0
package crunchrun
import (
"bytes"
"encoding/json"
"errors"
"flag"
"fmt"
"io"
"io/ioutil"
"log"
"os"
"os/exec"
"os/signal"
"path"
"path/filepath"
"regexp"
"runtime"
"runtime/pprof"
"sort"
"strings"
"sync"
"syscall"
"time"
"git.arvados.org/arvados.git/lib/cmd"
"git.arvados.org/arvados.git/lib/crunchstat"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/keepclient"
"git.arvados.org/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"
dockernetwork "github.com/docker/docker/api/types/network"
dockerclient "github.com/docker/docker/client"
)
type command struct{}
var Command = command{}
// 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{}) 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.
var ErrCancelled = errors.New("Cancelled")
// IKeepClient is the minimal Keep API methods used by crunch-run.
type IKeepClient interface {
PutB(buf []byte) (string, int, error)
ReadAt(locator string, p []byte, off int) (int, error)
ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
LocalLocator(locator string) (string, error)
ClearBlockCache()
}
// NewLogWriter is a factory function to create a new log writer.
type NewLogWriter func(name string) (io.WriteCloser, error)
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
ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error
ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error)
ContainerInspect(ctx context.Context, id string) (dockertypes.ContainerJSON, 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)
}
type PsProcess interface {
CmdlineSlice() ([]string, error)
}
// ContainerRunner is the main stateful struct used for a single execution of a
// container.
type ContainerRunner struct {
Docker ThinDockerClient
// Dispatcher client is initialized with the Dispatcher token.
// This is a privileged token used to manage container status
// and logs.
//
// We have both dispatcherClient and DispatcherArvClient
// because there are two different incompatible Arvados Go
// SDKs and we have to use both (hopefully this gets fixed in
// #14467)
dispatcherClient *arvados.Client
DispatcherArvClient IArvadosClient
DispatcherKeepClient IKeepClient
// Container client is initialized with the Container token
// This token controls the permissions of the container, and
// must be used for operations such as reading collections.
//
// Same comment as above applies to
// containerClient/ContainerArvClient.
containerClient *arvados.Client
ContainerArvClient IArvadosClient
ContainerKeepClient IKeepClient
Container arvados.Container
ContainerConfig dockercontainer.Config
HostConfig dockercontainer.HostConfig
token string
ContainerID string
ExitCode *int
NewLogWriter NewLogWriter
loggingDone chan bool
CrunchLog *ThrottledLogger
Stdout io.WriteCloser
Stderr io.WriteCloser
logUUID string
logMtx sync.Mutex
LogCollection arvados.CollectionFileSystem
LogsPDH *string
RunArvMount RunArvMount
MkTempDir MkTempDir
ArvMount *exec.Cmd
ArvMountPoint string
HostOutputDir string
Binds []string
Volumes map[string]struct{}
OutputPDH *string
SigChan chan os.Signal
ArvMountExit chan error
SecretMounts map[string]arvados.Mount
MkArvClient func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
finalState string
parentTemp 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
// 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
cCancelled bool // StopContainer() invoked
cRemoved bool // docker confirmed the container no longer exists
enableNetwork string // one of "default" or "always"
networkMode string // passed through to HostConfig.NetworkMode
arvMountLog *ThrottledLogger
containerWatchdogInterval time.Duration
}
// 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() {
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 s := range sig {
runner.stop(s)
}
}(runner.SigChan)
}
// stop the underlying Docker container.
func (runner *ContainerRunner) stop(sig os.Signal) {
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if sig != nil {
runner.CrunchLog.Printf("caught signal: %v", sig)
}
if runner.ContainerID == "" {
return
}
runner.cCancelled = true
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)
}
if err == nil || strings.Contains(err.Error(), "No such container: "+runner.ContainerID) {
runner.cRemoved = true
}
}
var errorBlacklist = []string{
"(?ms).*[Cc]annot connect to the Docker daemon.*",
"(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
"(?ms).*grpc: the connection is unavailable.*",
}
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) runBrokenNodeHook() {
if *brokenNodeHook == "" {
path := filepath.Join(lockdir, brokenfile)
runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
if err != nil {
runner.CrunchLog.Printf("Error writing %s: %s", path, err)
return
}
f.Close()
} 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)
}
}
}
func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
for _, d := range errorBlacklist {
if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
runner.runBrokenNodeHook()
return true
}
}
return false
}
// 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.Container.ContainerImage)
var collection arvados.Collection
err = runner.ContainerArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
if err != nil {
return fmt.Errorf("While getting container image collection: %v", err)
}
manifest := manifest.Manifest{Text: collection.ManifestText}
var img, imageID string
for ms := range manifest.StreamIter() {
img = ms.FileStreamSegments[0].Name
if !strings.HasSuffix(img, ".tar") {
return fmt.Errorf("First file in the container image collection does not end in .tar")
}
imageID = img[:len(img)-4]
}
runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
_, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
if err != nil {
runner.CrunchLog.Print("Loading Docker image from keep")
var readCloser io.ReadCloser
readCloser, err = runner.ContainerKeepClient.ManifestFileReader(manifest, img)
if err != nil {
return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
}
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.ContainerKeepClient.ClearBlockCache()
return nil
}
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)
w, err := runner.NewLogWriter("arv-mount")
if err != nil {
return nil, err
}
runner.arvMountLog = NewThrottledLogger(w)
c.Stdout = runner.arvMountLog
c.Stderr = runner.arvMountLog
runner.CrunchLog.Printf("Running %v", c.Args)
err = c.Start()
if err != nil {
return nil, err
}
statReadme := make(chan bool)
runner.ArvMountExit = make(chan error)
keepStatting := true
go func() {
for keepStatting {
time.Sleep(100 * time.Millisecond)
_, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
if err == nil {
keepStatting = false
statReadme <- true
}
}
close(statReadme)
}()
go func() {
mnterr := c.Wait()
if mnterr != nil {
runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
}
runner.ArvMountExit <- mnterr
close(runner.ArvMountExit)
}()
select {
case <-statReadme:
break
case err := <-runner.ArvMountExit:
runner.ArvMount = nil
keepStatting = false
return nil, err
}
return c, nil
}
func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
if runner.ArvMountPoint == "" {
runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
}
return
}
func copyfile(src string, dst string) (err error) {
srcfile, err := os.Open(src)
if err != nil {
return
}
os.MkdirAll(path.Dir(dst), 0777)
dstfile, err := os.Create(dst)
if err != nil {
return
}
_, err = io.Copy(dstfile, srcfile)
if err != nil {
return
}
err = srcfile.Close()
err2 := dstfile.Close()
if err != nil {
return
}
if err2 != nil {
return err2
}
return nil
}
func (runner *ContainerRunner) SetupMounts() (err error) {
err = runner.SetupArvMountPoint("keep")
if err != nil {
return fmt.Errorf("While creating keep mount temp dir: %v", err)
}
token, err := runner.ContainerToken()
if err != nil {
return fmt.Errorf("could not get container token: %s", err)
}
pdhOnly := true
tmpcount := 0
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
type copyFile struct {
src string
bind string
}
var copyFiles []copyFile
var binds []string
for bind := range runner.Container.Mounts {
binds = append(binds, bind)
}
for bind := range runner.SecretMounts {
if _, ok := runner.Container.Mounts[bind]; ok {
return fmt.Errorf("Secret mount %q conflicts with regular mount", bind)
}
if runner.SecretMounts[bind].Kind != "json" &&
runner.SecretMounts[bind].Kind != "text" {
return fmt.Errorf("Secret mount %q type is %q but only 'json' and 'text' are permitted.",
bind, runner.SecretMounts[bind].Kind)
}
binds = append(binds, bind)
}
sort.Strings(binds)
for _, bind := range binds {
mnt, ok := runner.Container.Mounts[bind]
if !ok {
mnt = runner.SecretMounts[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" && mnt.Kind != "text" && mnt.Kind != "json" {
return fmt.Errorf("Only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
}
}
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.UUID != "" {
if mnt.Writable {
return fmt.Errorf("Writing to existing collections currently not permitted.")
}
pdhOnly = false
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
} else if mnt.PortableDataHash != "" {
if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
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")
arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
tmpcount += 1
}
if mnt.Writable {
if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
} else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
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)
case mnt.Kind == "tmp":
var tmpdir string
tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
if err != nil {
return fmt.Errorf("While creating mount temp dir: %v", err)
}
st, staterr := os.Stat(tmpdir)
if staterr != nil {
return fmt.Errorf("While Stat on temp dir: %v", staterr)
}
err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
if staterr != nil {
return fmt.Errorf("While Chmod temp dir: %v", err)
}
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
if bind == runner.Container.OutputPath {
runner.HostOutputDir = tmpdir
}
case mnt.Kind == "json" || mnt.Kind == "text":
var filedata []byte
if mnt.Kind == "json" {
filedata, err = json.Marshal(mnt.Content)
if err != nil {
return fmt.Errorf("encoding json data: %v", err)
}
} else {
text, ok := mnt.Content.(string)
if !ok {
return fmt.Errorf("content for mount %q must be a string", bind)
}
filedata = []byte(text)
}
tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
if err != nil {
return fmt.Errorf("creating temp dir: %v", err)
}
tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
err = ioutil.WriteFile(tmpfn, filedata, 0444)
if err != nil {
return fmt.Errorf("writing temp file: %v", err)
}
if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
}
case mnt.Kind == "git_tree":
tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
if err != nil {
return fmt.Errorf("creating temp dir: %v", err)
}
err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
if err != nil {
return err
}
runner.Binds = append(runner.Binds, tmpdir+":"+bind+":ro")
}
}
if runner.HostOutputDir == "" {
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, "--mount-by-id", "by_id")
}
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
if err != nil {
return fmt.Errorf("While trying to start arv-mount: %v", err)
}
for _, p := range collectionPaths {
_, err = os.Stat(p)
if err != nil {
return fmt.Errorf("While checking that input files exist: %v", err)
}
}
for _, cp := range copyFiles {
st, err := os.Stat(cp.src)
if err != nil {
return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
if st.IsDir() {
err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
if walkerr != nil {
return walkerr
}
target := path.Join(cp.bind, walkpath[len(cp.src):])
if walkinfo.Mode().IsRegular() {
copyerr := copyfile(walkpath, target)
if copyerr != nil {
return copyerr
}
return os.Chmod(target, walkinfo.Mode()|0777)
} else if walkinfo.Mode().IsDir() {
mkerr := os.MkdirAll(target, 0777)
if mkerr != nil {
return mkerr
}
return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
} else {
return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
}
})
} else if st.Mode().IsRegular() {
err = copyfile(cp.src, cp.bind)
if err == nil {
err = os.Chmod(cp.bind, st.Mode()|0777)
}
}
if err != nil {
return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
}
return nil
}
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)
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 err != nil {
runner.CrunchLog.Printf("error reading docker logs: %v", err)
}
err = runner.Stdout.Close()
if err != nil {
runner.CrunchLog.Printf("error closing stdout logs: %v", err)
}
err = runner.Stderr.Close()
if err != nil {
runner.CrunchLog.Printf("error closing stderr logs: %v", err)
}
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) 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() error {
w, err := runner.NewLogWriter("hoststat")
if err != nil {
return err
}
runner.hoststatLogger = NewThrottledLogger(w)
runner.hoststatReporter = &crunchstat.Reporter{
Logger: log.New(runner.hoststatLogger, "", 0),
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
}
runner.hoststatReporter.Start()
return nil
}
func (runner *ContainerRunner) startCrunchstat() error {
w, err := runner.NewLogWriter("crunchstat")
if err != nil {
return err
}
runner.statLogger = NewThrottledLogger(w)
runner.statReporter = &crunchstat.Reporter{
CID: runner.ContainerID,
Logger: log.New(runner.statLogger, "", 0),
CgroupParent: runner.expectCgroupParent,
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
TempDir: runner.parentTemp,
}
runner.statReporter.Start()
return nil
}
type infoCommand struct {
label string
cmd []string
}
// 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, err := runner.NewLogWriter("node-info")
if err != nil {
return
}
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.
for _, command := range commands {
fmt.Fprintln(w, command.label)
cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
cmd.Stdout = w
cmd.Stderr = w
if err := cmd.Run(); err != nil {
err = fmt.Errorf("While running command %q: %v", command.cmd, err)
fmt.Fprintln(w, err)
return err
}
fmt.Fprintln(w, "")
}
err = w.Close()
if err != nil {
return fmt.Errorf("While closing node-info logs: %v", err)
}
return nil
}
// LogContainerRecord gets and saves the raw JSON container record from the API server
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 the current host's InstanceType config entry (or
// the arvados#node record, if running via crunch-dispatch-slurm).
func (runner *ContainerRunner) LogNodeRecord() error {
if it := os.Getenv("InstanceType"); it != "" {
// Dispatched via arvados-dispatch-cloud. Save
// InstanceType config fragment received from
// dispatcher on stdin.
w, err := runner.LogCollection.OpenFile("node.json", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return err
}
defer w.Close()
_, err = io.WriteString(w, it)
if err != nil {
return err
}
return w.Close()
} else {
// Dispatched via crunch-dispatch-slurm. Look up
// apiserver's node record corresponding to
// $SLURMD_NODENAME.
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) {
writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return false, err
}
w := &ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
UUID: runner.Container.UUID,
loggingStream: label,
writeCloser: writer,
}
reader, err := runner.DispatcherArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
if err != nil {
return false, fmt.Errorf("error getting %s record: %v", label, err)
}
defer reader.Close()
dec := json.NewDecoder(reader)
dec.UseNumber()
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(items[0]); err != nil {
return false, fmt.Errorf("error logging %s record: %v", label, err)
}
err = w.Close()
if err != nil {
return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
}
return true, 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")
// 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.ContainerArvClient.Get("collections", collId, nil, &stdinColl)
if err != nil {
return fmt.Errorf("While getting stdin collection: %v", err)
}
stdinRdr, err = runner.ContainerKeepClient.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 {
stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
if err != nil {
return err
}
runner.Stdout = stdoutFile
} else if w, err := runner.NewLogWriter("stdout"); err != nil {
return err
} else {
runner.Stdout = NewThrottledLogger(w)
}
if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
if err != nil {
return err
}
runner.Stderr = stderrFile
} else if w, err := runner.NewLogWriter("stderr"); err != nil {
return err
} else {
runner.Stderr = NewThrottledLogger(w)
}
if stdinRdr != nil {
go func() {
_, err := io.Copy(response.Conn, stdinRdr)
if err != nil {
runner.CrunchLog.Printf("While writing stdin collection to docker container: %v", err)
runner.stop(nil)
}
stdinRdr.Close()
response.CloseWrite()
}()
} else if len(stdinJson) != 0 {
go func() {
_, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
if err != nil {
runner.CrunchLog.Printf("While writing stdin json to docker container: %v", err)
runner.stop(nil)
}
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")
runner.ContainerConfig.Cmd = runner.Container.Command
if runner.Container.Cwd != "." {
runner.ContainerConfig.WorkingDir = runner.Container.Cwd
}
for k, v := range runner.Container.Environment {
runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
}
runner.ContainerConfig.Volumes = runner.Volumes
maxRAM := int64(runner.Container.RuntimeConstraints.RAM)
minDockerRAM := int64(16)
if maxRAM < minDockerRAM*1024*1024 {
// Docker daemon won't let you set a limit less than ~10 MiB
maxRAM = minDockerRAM * 1024 * 1024
}
runner.HostConfig = dockercontainer.HostConfig{
Binds: runner.Binds,
LogConfig: dockercontainer.LogConfig{
Type: "none",
},
Resources: dockercontainer.Resources{
CgroupParent: runner.setCgroupParent,
NanoCPUs: int64(runner.Container.RuntimeConstraints.VCPUs) * 1000000000,
Memory: maxRAM, // RAM
MemorySwap: maxRAM, // RAM+swap
KernelMemory: maxRAM, // kernel portion
},
}
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")
}
}
_, 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.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)
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 {
var advice string
if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
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)
}
return nil
}
// WaitFinish waits for the container to terminate, capture the exit code, and
// close the stdout/stderr logging.
func (runner *ContainerRunner) WaitFinish() error {
var runTimeExceeded <-chan time.Time
runner.CrunchLog.Print("Waiting for container to finish")
waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning)
arvMountExit := runner.ArvMountExit
if timeout := runner.Container.SchedulingParameters.MaxRunTime; timeout > 0 {
runTimeExceeded = time.After(time.Duration(timeout) * time.Second)
}
containerGone := make(chan struct{})
go func() {
defer close(containerGone)
if runner.containerWatchdogInterval < 1 {
runner.containerWatchdogInterval = time.Minute
}
for range time.NewTicker(runner.containerWatchdogInterval).C {
ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(runner.containerWatchdogInterval))
ctr, err := runner.Docker.ContainerInspect(ctx, runner.ContainerID)
cancel()
runner.cStateLock.Lock()
done := runner.cRemoved || runner.ExitCode != nil
runner.cStateLock.Unlock()
if done {
return
} else if err != nil {
runner.CrunchLog.Printf("Error inspecting container: %s", err)
runner.checkBrokenNode(err)
return
} else if ctr.State == nil || !(ctr.State.Running || ctr.State.Status == "created") {
runner.CrunchLog.Printf("Container is not running: State=%v", ctr.State)
return
}
}
}()
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)
case <-arvMountExit:
runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
runner.stop(nil)
// arvMountExit will always be ready now that
// it's closed, but that doesn't interest us.
arvMountExit = nil
case <-runTimeExceeded:
runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
runner.stop(nil)
runTimeExceeded = nil
case <-containerGone:
return errors.New("docker client never returned status")
}
}
}
func (runner *ContainerRunner) updateLogs() {
ticker := time.NewTicker(crunchLogUpdatePeriod / 360)
defer ticker.Stop()
sigusr1 := make(chan os.Signal, 1)
signal.Notify(sigusr1, syscall.SIGUSR1)
defer signal.Stop(sigusr1)
saveAtTime := time.Now().Add(crunchLogUpdatePeriod)
saveAtSize := crunchLogUpdateSize
var savedSize int64
for {
select {
case <-ticker.C:
case <-sigusr1:
saveAtTime = time.Now()
}
runner.logMtx.Lock()
done := runner.LogsPDH != nil
runner.logMtx.Unlock()
if done {
return
}
size := runner.LogCollection.Size()
if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) {
continue
}
saveAtTime = time.Now().Add(crunchLogUpdatePeriod)
saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize
saved, err := runner.saveLogCollection(false)
if err != nil {
runner.CrunchLog.Printf("error updating log collection: %s", err)
continue
}
var updated arvados.Container
err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
"container": arvadosclient.Dict{"log": saved.PortableDataHash},
}, &updated)
if err != nil {
runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
continue
}
savedSize = size
}
}
// CaptureOutput saves data from the container's output directory if
// needed, and updates the container output accordingly.
func (runner *ContainerRunner) CaptureOutput() error {
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.DispatcherArvClient.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
}
}
txt, err := (&copier{
client: runner.containerClient,
arvClient: runner.ContainerArvClient,
keepClient: runner.ContainerKeepClient,
hostOutputDir: runner.HostOutputDir,
ctrOutputDir: runner.Container.OutputPath,
binds: runner.Binds,
mounts: runner.Container.Mounts,
secretMounts: runner.SecretMounts,
logger: runner.CrunchLog,
}).Copy()
if err != nil {
return err
}
if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 {
runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n)
fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.containerClient, runner.ContainerKeepClient)
if err != nil {
return err
}
txt, err = fs.MarshalManifest(".")
if err != nil {
return err
}
}
var resp arvados.Collection
err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
"ensure_unique_name": true,
"collection": arvadosclient.Dict{
"is_trashed": true,
"name": "output for " + runner.Container.UUID,
"manifest_text": txt,
},
}, &resp)
if err != nil {
return fmt.Errorf("error creating output collection: %v", err)
}
runner.OutputPDH = &resp.PortableDataHash
return nil
}
func (runner *ContainerRunner) CleanupDirs() {
if runner.ArvMount != nil {
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("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()
}
}
}
}
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)
}
}
if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
}
}
// CommitLogs posts the collection containing the final container logs.
func (runner *ContainerRunner) CommitLogs() error {
func() {
// Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
runner.CrunchLog.Print(runner.finalState)
if runner.arvMountLog != nil {
runner.arvMountLog.Close()
}
runner.CrunchLog.Close()
// 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 errors (such as failing to write the log to Keep!)
// while shutting down
runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
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,
// 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
}
saved, err := runner.saveLogCollection(true)
if err != nil {
return fmt.Errorf("error saving log collection: %s", err)
}
runner.logMtx.Lock()
defer runner.logMtx.Unlock()
runner.LogsPDH = &saved.PortableDataHash
return nil
}
func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
runner.logMtx.Lock()
defer runner.logMtx.Unlock()
if runner.LogsPDH != nil {
// Already finalized.
return
}
mt, err := runner.LogCollection.MarshalManifest(".")
if err != nil {
err = fmt.Errorf("error creating log manifest: %v", err)
return
}
updates := arvadosclient.Dict{
"name": "logs for " + runner.Container.UUID,
"manifest_text": mt,
}
if final {
updates["is_trashed"] = true
} else {
exp := time.Now().Add(crunchLogUpdatePeriod * 24)
updates["trash_at"] = exp
updates["delete_at"] = exp
}
reqBody := arvadosclient.Dict{"collection": updates}
if runner.logUUID == "" {
reqBody["ensure_unique_name"] = true
err = runner.DispatcherArvClient.Create("collections", reqBody, &response)
} else {
err = runner.DispatcherArvClient.Update("collections", runner.logUUID, reqBody, &response)
}
if err != nil {
return
}
runner.logUUID = response.UUID
return
}
// 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.DispatcherArvClient.Update("containers", runner.Container.UUID,
arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
}
// 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.DispatcherArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
if err != nil {
return "", err
}
runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID)
return runner.token, nil
}
// UpdateContainerComplete updates the container record state on API
// server to "Complete" or "Cancelled"
func (runner *ContainerRunner) UpdateContainerFinal() error {
update := arvadosclient.Dict{}
update["state"] = runner.finalState
if runner.LogsPDH != nil {
update["log"] = *runner.LogsPDH
}
if runner.finalState == "Complete" {
if runner.ExitCode != nil {
update["exit_code"] = *runner.ExitCode
}
if runner.OutputPDH != nil {
update["output"] = *runner.OutputPDH
}
}
return runner.DispatcherArvClient.Update("containers", runner.Container.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, error) {
writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return nil, err
}
return &ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
UUID: runner.Container.UUID,
loggingStream: name,
writeCloser: writer,
}, nil
}
// Run the full container lifecycle.
func (runner *ContainerRunner) Run() (err error) {
runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
hostname, hosterr := os.Hostname()
if hosterr != nil {
runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
} else {
runner.CrunchLog.Printf("Executing on host '%s'", hostname)
}
runner.finalState = "Queued"
defer func() {
runner.CleanupDirs()
runner.CrunchLog.Printf("crunch-run finished")
runner.CrunchLog.Close()
}()
err = runner.fetchContainerRecord()
if err != nil {
return
}
if runner.Container.State != "Locked" {
return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
}
defer func() {
// 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(errorIn string, e error) {
if e == nil {
return
}
runner.CrunchLog.Printf("error in %s: %v", errorIn, e)
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("Run", err)
if runner.finalState == "Queued" {
runner.UpdateContainerFinal()
return
}
if runner.IsCancelled() {
runner.finalState = "Cancelled"
// but don't return yet -- we still want to
// capture partial output and write logs
}
checkErr("CaptureOutput", runner.CaptureOutput())
checkErr("stopHoststat", runner.stopHoststat())
checkErr("CommitLogs", runner.CommitLogs())
checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
}()
runner.setupSignals()
err = runner.startHoststat()
if err != nil {
return
}
// check for and/or load image
err = runner.LoadImage()
if err != nil {
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
}
// set up FUSE mount and binds
err = runner.SetupMounts()
if err != nil {
runner.finalState = "Cancelled"
err = fmt.Errorf("While setting up mounts: %v", err)
return
}
err = runner.CreateContainer()
if err != nil {
return
}
err = runner.LogHostInfo()
if err != nil {
return
}
err = runner.LogNodeRecord()
if err != nil {
return
}
err = runner.LogContainerRecord()
if err != nil {
return
}
if runner.IsCancelled() {
return
}
err = runner.UpdateContainerRunning()
if err != nil {
return
}
runner.finalState = "Cancelled"
err = runner.startCrunchstat()
if err != nil {
return
}
err = runner.StartContainer()
if err != nil {
runner.checkBrokenNode(err)
return
}
err = runner.WaitFinish()
if err == nil && !runner.IsCancelled() {
runner.finalState = "Complete"
}
return
}
// Fetch the current container record (uuid = runner.Container.UUID)
// into runner.Container.
func (runner *ContainerRunner) fetchContainerRecord() error {
reader, err := runner.DispatcherArvClient.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)
}
var sm struct {
SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
}
containerToken, err := runner.ContainerToken()
if err != nil {
return fmt.Errorf("error getting container token: %v", err)
}
runner.ContainerArvClient, runner.ContainerKeepClient,
runner.containerClient, err = runner.MkArvClient(containerToken)
if err != nil {
return fmt.Errorf("error creating container API client: %v", err)
}
err = runner.ContainerArvClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
if err != nil {
if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
return fmt.Errorf("error fetching secret_mounts: %v", err)
}
// ok && apierr.HttpStatusCode == 404, which means
// secret_mounts isn't supported by this API server.
}
runner.SecretMounts = sm.SecretMounts
return nil
}
// NewContainerRunner creates a new container runner.
func NewContainerRunner(dispatcherClient *arvados.Client,
dispatcherArvClient IArvadosClient,
dispatcherKeepClient IKeepClient,
docker ThinDockerClient,
containerUUID string) (*ContainerRunner, error) {
cr := &ContainerRunner{
dispatcherClient: dispatcherClient,
DispatcherArvClient: dispatcherArvClient,
DispatcherKeepClient: dispatcherKeepClient,
Docker: docker,
}
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
cr.MkTempDir = ioutil.TempDir
cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
cl, err := arvadosclient.MakeArvadosClient()
if err != nil {
return nil, nil, nil, err
}
cl.ApiToken = token
kc, err := keepclient.MakeKeepClient(cl)
if err != nil {
return nil, nil, nil, err
}
c2 := arvados.NewClientFromEnv()
c2.AuthToken = token
return cl, kc, c2, nil
}
var err error
cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.dispatcherClient, cr.DispatcherKeepClient)
if err != nil {
return nil, err
}
cr.Container.UUID = containerUUID
w, err := cr.NewLogWriter("crunch-run")
if err != nil {
return nil, err
}
cr.CrunchLog = NewThrottledLogger(w)
cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
loadLogThrottleParams(dispatcherArvClient)
go cr.updateLogs()
return cr, nil
}
func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
flags := flag.NewFlagSet(prog, flag.ContinueOnError)
statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
stdinEnv := flags.Bool("stdin-env", false, "Load environment variables from JSON message on stdin")
sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
enableNetwork := flags.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 := flags.String("container-network-mode", "default",
`Set networking mode for container. Corresponds to Docker network mode (--net).
`)
memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
ignoreDetachFlag := false
if len(args) > 0 && args[0] == "-no-detach" {
// This process was invoked by a parent process, which
// has passed along its own arguments, including
// -detach, after the leading -no-detach flag. Strip
// the leading -no-detach flag (it's not recognized by
// flags.Parse()) and ignore the -detach flag that
// comes later.
args = args[1:]
ignoreDetachFlag = true
}
if err := flags.Parse(args); err == flag.ErrHelp {
return 0
} else if err != nil {
log.Print(err)
return 1
}
if *stdinEnv && !ignoreDetachFlag {
// Load env vars on stdin if asked (but not in a
// detached child process, in which case stdin is
// /dev/null).
err := loadEnv(os.Stdin)
if err != nil {
log.Print(err)
return 1
}
}
containerId := flags.Arg(0)
switch {
case *detach && !ignoreDetachFlag:
return Detach(containerId, prog, args, os.Stdout, os.Stderr)
case *kill >= 0:
return KillProcess(containerId, syscall.Signal(*kill), os.Stdout, os.Stderr)
case *list:
return ListProcesses(os.Stdout, os.Stderr)
}
if containerId == "" {
log.Printf("usage: %s [options] UUID", prog)
return 1
}
log.Printf("crunch-run %s started", cmd.Version.String())
time.Sleep(*sleep)
if *caCertsPath != "" {
arvadosclient.CertFiles = []string{*caCertsPath}
}
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Printf("%s: %v", containerId, err)
return 1
}
api.Retries = 8
kc, kcerr := keepclient.MakeKeepClient(api)
if kcerr != nil {
log.Printf("%s: %v", containerId, kcerr)
return 1
}
kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
kc.Retries = 4
// 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)
cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, docker, containerId)
if err != nil {
log.Print(err)
return 1
}
if dockererr != nil {
cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
cr.checkBrokenNode(dockererr)
cr.CrunchLog.Close()
return 1
}
parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerId+".")
if tmperr != nil {
log.Printf("%s: %v", containerId, tmperr)
return 1
}
cr.parentTemp = parentTemp
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
}
runerr := cr.Run()
if *memprofile != "" {
f, err := os.Create(*memprofile)
if err != nil {
log.Printf("could not create memory profile: %s", err)
}
runtime.GC() // get up-to-date statistics
if err := pprof.WriteHeapProfile(f); err != nil {
log.Printf("could not write memory profile: %s", err)
}
closeerr := f.Close()
if closeerr != nil {
log.Printf("closing memprofile file: %s", err)
}
}
if runerr != nil {
log.Printf("%s: %v", containerId, runerr)
return 1
}
return 0
}
func loadEnv(rdr io.Reader) error {
buf, err := ioutil.ReadAll(rdr)
if err != nil {
return fmt.Errorf("read stdin: %s", err)
}
var env map[string]string
err = json.Unmarshal(buf, &env)
if err != nil {
return fmt.Errorf("decode stdin: %s", err)
}
for k, v := range env {
err = os.Setenv(k, v)
if err != nil {
return fmt.Errorf("setenv(%q): %s", k, err)
}
}
return nil
}