services/crunch-run/crunchrun.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package main
   6
   7 import (
   8         "bytes"
   9         "context"
  10         "encoding/json"
  11         "errors"
  12         "flag"
  13         "fmt"
  14         "io"
  15         "io/ioutil"
  16         "log"
  17         "os"
  18         "os/exec"
  19         "os/signal"
  20         "path"
  21         "path/filepath"
  22         "regexp"
  23         "runtime"
  24         "runtime/pprof"
  25         "sort"
  26         "strings"
  27         "sync"
  28         "syscall"
  29         "time"
  30
  31         "git.curoverse.com/arvados.git/lib/crunchstat"
  32         "git.curoverse.com/arvados.git/sdk/go/arvados"
  33         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  34         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  35         "git.curoverse.com/arvados.git/sdk/go/manifest"
  36
  37         dockertypes "github.com/docker/docker/api/types"
  38         dockercontainer "github.com/docker/docker/api/types/container"
  39         dockernetwork "github.com/docker/docker/api/types/network"
  40         dockerclient "github.com/docker/docker/client"
  41 )
  42
  43 var version = "dev"
  44
  45 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  46 type IArvadosClient interface {
  47         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  48         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  49         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  50         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  51         CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
  52         Discovery(key string) (interface{}, error)
  53 }
  54
  55 // ErrCancelled is the error returned when the container is cancelled.
  56 var ErrCancelled = errors.New("Cancelled")
  57
  58 // IKeepClient is the minimal Keep API methods used by crunch-run.
  59 type IKeepClient interface {
  60         PutHB(hash string, buf []byte) (string, int, error)
  61         ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
  62         ClearBlockCache()
  63 }
  64
  65 // NewLogWriter is a factory function to create a new log writer.
  66 type NewLogWriter func(name string) io.WriteCloser
  67
  68 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  69
  70 type MkTempDir func(string, string) (string, error)
  71
  72 // ThinDockerClient is the minimal Docker client interface used by crunch-run.
  73 type ThinDockerClient interface {
  74         ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error)
  75         ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
  76                 networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error)
  77         ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error
  78         ContainerStop(ctx context.Context, container string, timeout *time.Duration) error
  79         ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error)
  80         ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error)
  81         ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error)
  82         ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error)
  83 }
  84
  85 // ThinDockerClientProxy is a proxy implementation of ThinDockerClient
  86 // that executes the docker requests on dockerclient.Client
  87 type ThinDockerClientProxy struct {
  88         Docker *dockerclient.Client
  89 }
  90
  91 // ContainerAttach invokes dockerclient.Client.ContainerAttach
  92 func (proxy ThinDockerClientProxy) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
  93         return proxy.Docker.ContainerAttach(ctx, container, options)
  94 }
  95
  96 // ContainerCreate invokes dockerclient.Client.ContainerCreate
  97 func (proxy ThinDockerClientProxy) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
  98         networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
  99         return proxy.Docker.ContainerCreate(ctx, config, hostConfig, networkingConfig, containerName)
 100 }
 101
 102 // ContainerStart invokes dockerclient.Client.ContainerStart
 103 func (proxy ThinDockerClientProxy) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 104         return proxy.Docker.ContainerStart(ctx, container, options)
 105 }
 106
 107 // ContainerStop invokes dockerclient.Client.ContainerStop
 108 func (proxy ThinDockerClientProxy) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
 109         return proxy.Docker.ContainerStop(ctx, container, timeout)
 110 }
 111
 112 // ContainerWait invokes dockerclient.Client.ContainerWait
 113 func (proxy ThinDockerClientProxy) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
 114         return proxy.Docker.ContainerWait(ctx, container, condition)
 115 }
 116
 117 // ImageInspectWithRaw invokes dockerclient.Client.ImageInspectWithRaw
 118 func (proxy ThinDockerClientProxy) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 119         return proxy.Docker.ImageInspectWithRaw(ctx, image)
 120 }
 121
 122 // ImageLoad invokes dockerclient.Client.ImageLoad
 123 func (proxy ThinDockerClientProxy) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 124         return proxy.Docker.ImageLoad(ctx, input, quiet)
 125 }
 126
 127 // ImageRemove invokes dockerclient.Client.ImageRemove
 128 func (proxy ThinDockerClientProxy) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 129         return proxy.Docker.ImageRemove(ctx, image, options)
 130 }
 131
 132 // ContainerRunner is the main stateful struct used for a single execution of a
 133 // container.
 134 type ContainerRunner struct {
 135         Docker    ThinDockerClient
 136         ArvClient IArvadosClient
 137         Kc        IKeepClient
 138         arvados.Container
 139         ContainerConfig dockercontainer.Config
 140         dockercontainer.HostConfig
 141         token       string
 142         ContainerID string
 143         ExitCode    *int
 144         NewLogWriter
 145         loggingDone   chan bool
 146         CrunchLog     *ThrottledLogger
 147         Stdout        io.WriteCloser
 148         Stderr        io.WriteCloser
 149         LogCollection *CollectionWriter
 150         LogsPDH       *string
 151         RunArvMount
 152         MkTempDir
 153         ArvMount       *exec.Cmd
 154         ArvMountPoint  string
 155         HostOutputDir  string
 156         CleanupTempDir []string
 157         Binds          []string
 158         Volumes        map[string]struct{}
 159         OutputPDH      *string
 160         SigChan        chan os.Signal
 161         ArvMountExit   chan error
 162         finalState     string
 163
 164         statLogger   io.WriteCloser
 165         statReporter *crunchstat.Reporter
 166         statInterval time.Duration
 167         cgroupRoot   string
 168         // What we expect the container's cgroup parent to be.
 169         expectCgroupParent string
 170         // What we tell docker to use as the container's cgroup
 171         // parent. Note: Ideally we would use the same field for both
 172         // expectCgroupParent and setCgroupParent, and just make it
 173         // default to "docker". However, when using docker < 1.10 with
 174         // systemd, specifying a non-empty cgroup parent (even the
 175         // default value "docker") hits a docker bug
 176         // (https://github.com/docker/docker/issues/17126). Using two
 177         // separate fields makes it possible to use the "expect cgroup
 178         // parent to be X" feature even on sites where the "specify
 179         // cgroup parent" feature breaks.
 180         setCgroupParent string
 181
 182         cStateLock sync.Mutex
 183         cStarted   bool // StartContainer() succeeded
 184         cCancelled bool // StopContainer() invoked
 185
 186         enableNetwork string // one of "default" or "always"
 187         networkMode   string // passed through to HostConfig.NetworkMode
 188         arvMountLog   *ThrottledLogger
 189 }
 190
 191 // setupSignals sets up signal handling to gracefully terminate the underlying
 192 // Docker container and update state when receiving a TERM, INT or QUIT signal.
 193 func (runner *ContainerRunner) setupSignals() {
 194         runner.SigChan = make(chan os.Signal, 1)
 195         signal.Notify(runner.SigChan, syscall.SIGTERM)
 196         signal.Notify(runner.SigChan, syscall.SIGINT)
 197         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 198
 199         go func(sig chan os.Signal) {
 200                 s := <-sig
 201                 if s != nil {
 202                         runner.CrunchLog.Printf("Caught signal %v", s)
 203                 }
 204                 runner.stop()
 205         }(runner.SigChan)
 206 }
 207
 208 // stop the underlying Docker container.
 209 func (runner *ContainerRunner) stop() {
 210         runner.cStateLock.Lock()
 211         defer runner.cStateLock.Unlock()
 212         if runner.cCancelled {
 213                 return
 214         }
 215         runner.cCancelled = true
 216         if runner.cStarted {
 217                 timeout := time.Duration(10)
 218                 err := runner.Docker.ContainerStop(context.TODO(), runner.ContainerID, &(timeout))
 219                 if err != nil {
 220                         runner.CrunchLog.Printf("StopContainer failed: %s", err)
 221                 }
 222                 // Suppress multiple calls to stop()
 223                 runner.cStarted = false
 224         }
 225 }
 226
 227 func (runner *ContainerRunner) stopSignals() {
 228         if runner.SigChan != nil {
 229                 signal.Stop(runner.SigChan)
 230                 close(runner.SigChan)
 231         }
 232 }
 233
 234 var errorBlacklist = []string{
 235         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 236         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 237 }
 238 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)")
 239
 240 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 241         for _, d := range errorBlacklist {
 242                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 243                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 244                         if *brokenNodeHook == "" {
 245                                 runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
 246                         } else {
 247                                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 248                                 // run killme script
 249                                 c := exec.Command(*brokenNodeHook)
 250                                 c.Stdout = runner.CrunchLog
 251                                 c.Stderr = runner.CrunchLog
 252                                 err := c.Run()
 253                                 if err != nil {
 254                                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 255                                 }
 256                         }
 257                         return true
 258                 }
 259         }
 260         return false
 261 }
 262
 263 // LoadImage determines the docker image id from the container record and
 264 // checks if it is available in the local Docker image store.  If not, it loads
 265 // the image from Keep.
 266 func (runner *ContainerRunner) LoadImage() (err error) {
 267
 268         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 269
 270         var collection arvados.Collection
 271         err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
 272         if err != nil {
 273                 return fmt.Errorf("While getting container image collection: %v", err)
 274         }
 275         manifest := manifest.Manifest{Text: collection.ManifestText}
 276         var img, imageID string
 277         for ms := range manifest.StreamIter() {
 278                 img = ms.FileStreamSegments[0].Name
 279                 if !strings.HasSuffix(img, ".tar") {
 280                         return fmt.Errorf("First file in the container image collection does not end in .tar")
 281                 }
 282                 imageID = img[:len(img)-4]
 283         }
 284
 285         runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
 286
 287         _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
 288         if err != nil {
 289                 runner.CrunchLog.Print("Loading Docker image from keep")
 290
 291                 var readCloser io.ReadCloser
 292                 readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
 293                 if err != nil {
 294                         return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
 295                 }
 296
 297                 response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, true)
 298                 if err != nil {
 299                         return fmt.Errorf("While loading container image into Docker: %v", err)
 300                 }
 301
 302                 defer response.Body.Close()
 303                 rbody, err := ioutil.ReadAll(response.Body)
 304                 if err != nil {
 305                         return fmt.Errorf("Reading response to image load: %v", err)
 306                 }
 307                 runner.CrunchLog.Printf("Docker response: %s", rbody)
 308         } else {
 309                 runner.CrunchLog.Print("Docker image is available")
 310         }
 311
 312         runner.ContainerConfig.Image = imageID
 313
 314         runner.Kc.ClearBlockCache()
 315
 316         return nil
 317 }
 318
 319 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 320         c = exec.Command("arv-mount", arvMountCmd...)
 321
 322         // Copy our environment, but override ARVADOS_API_TOKEN with
 323         // the container auth token.
 324         c.Env = nil
 325         for _, s := range os.Environ() {
 326                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 327                         c.Env = append(c.Env, s)
 328                 }
 329         }
 330         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 331
 332         runner.arvMountLog = NewThrottledLogger(runner.NewLogWriter("arv-mount"))
 333         c.Stdout = runner.arvMountLog
 334         c.Stderr = runner.arvMountLog
 335
 336         runner.CrunchLog.Printf("Running %v", c.Args)
 337
 338         err = c.Start()
 339         if err != nil {
 340                 return nil, err
 341         }
 342
 343         statReadme := make(chan bool)
 344         runner.ArvMountExit = make(chan error)
 345
 346         keepStatting := true
 347         go func() {
 348                 for keepStatting {
 349                         time.Sleep(100 * time.Millisecond)
 350                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 351                         if err == nil {
 352                                 keepStatting = false
 353                                 statReadme <- true
 354                         }
 355                 }
 356                 close(statReadme)
 357         }()
 358
 359         go func() {
 360                 mnterr := c.Wait()
 361                 if mnterr != nil {
 362                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 363                 }
 364                 runner.ArvMountExit <- mnterr
 365                 close(runner.ArvMountExit)
 366         }()
 367
 368         select {
 369         case <-statReadme:
 370                 break
 371         case err := <-runner.ArvMountExit:
 372                 runner.ArvMount = nil
 373                 keepStatting = false
 374                 return nil, err
 375         }
 376
 377         return c, nil
 378 }
 379
 380 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 381         if runner.ArvMountPoint == "" {
 382                 runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
 383         }
 384         return
 385 }
 386
 387 func (runner *ContainerRunner) SetupMounts() (err error) {
 388         err = runner.SetupArvMountPoint("keep")
 389         if err != nil {
 390                 return fmt.Errorf("While creating keep mount temp dir: %v", err)
 391         }
 392
 393         pdhOnly := true
 394         tmpcount := 0
 395         arvMountCmd := []string{
 396                 "--foreground",
 397                 "--allow-other",
 398                 "--read-write",
 399                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 400
 401         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 402                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 403         }
 404
 405         collectionPaths := []string{}
 406         runner.Binds = nil
 407         runner.Volumes = make(map[string]struct{})
 408         needCertMount := true
 409
 410         var binds []string
 411         for bind := range runner.Container.Mounts {
 412                 binds = append(binds, bind)
 413         }
 414         sort.Strings(binds)
 415
 416         for _, bind := range binds {
 417                 mnt := runner.Container.Mounts[bind]
 418                 if bind == "stdout" || bind == "stderr" {
 419                         // Is it a "file" mount kind?
 420                         if mnt.Kind != "file" {
 421                                 return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind)
 422                         }
 423
 424                         // Does path start with OutputPath?
 425                         prefix := runner.Container.OutputPath
 426                         if !strings.HasSuffix(prefix, "/") {
 427                                 prefix += "/"
 428                         }
 429                         if !strings.HasPrefix(mnt.Path, prefix) {
 430                                 return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 431                         }
 432                 }
 433
 434                 if bind == "stdin" {
 435                         // Is it a "collection" mount kind?
 436                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 437                                 return fmt.Errorf("Unsupported mount kind '%s' for stdin. Only 'collection' or 'json' are supported.", mnt.Kind)
 438                         }
 439                 }
 440
 441                 if bind == "/etc/arvados/ca-certificates.crt" {
 442                         needCertMount = false
 443                 }
 444
 445                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 446                         if mnt.Kind != "collection" {
 447                                 return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind)
 448                         }
 449                 }
 450
 451                 switch {
 452                 case mnt.Kind == "collection" && bind != "stdin":
 453                         var src string
 454                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 455                                 return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 456                         }
 457                         if mnt.UUID != "" {
 458                                 if mnt.Writable {
 459                                         return fmt.Errorf("Writing to existing collections currently not permitted.")
 460                                 }
 461                                 pdhOnly = false
 462                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 463                         } else if mnt.PortableDataHash != "" {
 464                                 if mnt.Writable {
 465                                         return fmt.Errorf("Can never write to a collection specified by portable data hash")
 466                                 }
 467                                 idx := strings.Index(mnt.PortableDataHash, "/")
 468                                 if idx > 0 {
 469                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 470                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 471                                         runner.Container.Mounts[bind] = mnt
 472                                 }
 473                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 474                                 if mnt.Path != "" && mnt.Path != "." {
 475                                         if strings.HasPrefix(mnt.Path, "./") {
 476                                                 mnt.Path = mnt.Path[2:]
 477                                         } else if strings.HasPrefix(mnt.Path, "/") {
 478                                                 mnt.Path = mnt.Path[1:]
 479                                         }
 480                                         src += "/" + mnt.Path
 481                                 }
 482                         } else {
 483                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 484                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 485                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 486                                 tmpcount += 1
 487                         }
 488                         if mnt.Writable {
 489                                 if bind == runner.Container.OutputPath {
 490                                         runner.HostOutputDir = src
 491                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 492                                         return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind)
 493                                 }
 494                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 495                         } else {
 496                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
 497                         }
 498                         collectionPaths = append(collectionPaths, src)
 499
 500                 case mnt.Kind == "tmp":
 501                         var tmpdir string
 502                         tmpdir, err = runner.MkTempDir("", "")
 503                         if err != nil {
 504                                 return fmt.Errorf("While creating mount temp dir: %v", err)
 505                         }
 506                         st, staterr := os.Stat(tmpdir)
 507                         if staterr != nil {
 508                                 return fmt.Errorf("While Stat on temp dir: %v", staterr)
 509                         }
 510                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 511                         if staterr != nil {
 512                                 return fmt.Errorf("While Chmod temp dir: %v", err)
 513                         }
 514                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 515                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
 516                         if bind == runner.Container.OutputPath {
 517                                 runner.HostOutputDir = tmpdir
 518                         }
 519
 520                 case mnt.Kind == "json":
 521                         jsondata, err := json.Marshal(mnt.Content)
 522                         if err != nil {
 523                                 return fmt.Errorf("encoding json data: %v", err)
 524                         }
 525                         // Create a tempdir with a single file
 526                         // (instead of just a tempfile): this way we
 527                         // can ensure the file is world-readable
 528                         // inside the container, without having to
 529                         // make it world-readable on the docker host.
 530                         tmpdir, err := runner.MkTempDir("", "")
 531                         if err != nil {
 532                                 return fmt.Errorf("creating temp dir: %v", err)
 533                         }
 534                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 535                         tmpfn := filepath.Join(tmpdir, "mountdata.json")
 536                         err = ioutil.WriteFile(tmpfn, jsondata, 0644)
 537                         if err != nil {
 538                                 return fmt.Errorf("writing temp file: %v", err)
 539                         }
 540                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
 541
 542                 case mnt.Kind == "git_tree":
 543                         tmpdir, err := runner.MkTempDir("", "")
 544                         if err != nil {
 545                                 return fmt.Errorf("creating temp dir: %v", err)
 546                         }
 547                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 548                         err = gitMount(mnt).extractTree(runner.ArvClient, tmpdir)
 549                         if err != nil {
 550                                 return err
 551                         }
 552                         bind := tmpdir + ":" + bind
 553                         if !mnt.Writable {
 554                                 bind = bind + ":ro"
 555                         }
 556                         runner.Binds = append(runner.Binds, bind)
 557                 }
 558         }
 559
 560         if runner.HostOutputDir == "" {
 561                 return fmt.Errorf("Output path does not correspond to a writable mount point")
 562         }
 563
 564         if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
 565                 for _, certfile := range arvadosclient.CertFiles {
 566                         _, err := os.Stat(certfile)
 567                         if err == nil {
 568                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
 569                                 break
 570                         }
 571                 }
 572         }
 573
 574         if pdhOnly {
 575                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 576         } else {
 577                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 578         }
 579         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 580
 581         token, err := runner.ContainerToken()
 582         if err != nil {
 583                 return fmt.Errorf("could not get container token: %s", err)
 584         }
 585
 586         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 587         if err != nil {
 588                 return fmt.Errorf("While trying to start arv-mount: %v", err)
 589         }
 590
 591         for _, p := range collectionPaths {
 592                 _, err = os.Stat(p)
 593                 if err != nil {
 594                         return fmt.Errorf("While checking that input files exist: %v", err)
 595                 }
 596         }
 597
 598         return nil
 599 }
 600
 601 func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
 602         // Handle docker log protocol
 603         // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
 604
 605         header := make([]byte, 8)
 606         for {
 607                 _, readerr := io.ReadAtLeast(containerReader, header, 8)
 608
 609                 if readerr == nil {
 610                         readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
 611                         if header[0] == 1 {
 612                                 // stdout
 613                                 _, readerr = io.CopyN(runner.Stdout, containerReader, readsize)
 614                         } else {
 615                                 // stderr
 616                                 _, readerr = io.CopyN(runner.Stderr, containerReader, readsize)
 617                         }
 618                 }
 619
 620                 if readerr != nil {
 621                         if readerr != io.EOF {
 622                                 runner.CrunchLog.Printf("While reading docker logs: %v", readerr)
 623                         }
 624
 625                         closeerr := runner.Stdout.Close()
 626                         if closeerr != nil {
 627                                 runner.CrunchLog.Printf("While closing stdout logs: %v", closeerr)
 628                         }
 629
 630                         closeerr = runner.Stderr.Close()
 631                         if closeerr != nil {
 632                                 runner.CrunchLog.Printf("While closing stderr logs: %v", closeerr)
 633                         }
 634
 635                         if runner.statReporter != nil {
 636                                 runner.statReporter.Stop()
 637                                 closeerr = runner.statLogger.Close()
 638                                 if closeerr != nil {
 639                                         runner.CrunchLog.Printf("While closing crunchstat logs: %v", closeerr)
 640                                 }
 641                         }
 642
 643                         runner.loggingDone <- true
 644                         close(runner.loggingDone)
 645                         return
 646                 }
 647         }
 648 }
 649
 650 func (runner *ContainerRunner) StartCrunchstat() {
 651         runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
 652         runner.statReporter = &crunchstat.Reporter{
 653                 CID:          runner.ContainerID,
 654                 Logger:       log.New(runner.statLogger, "", 0),
 655                 CgroupParent: runner.expectCgroupParent,
 656                 CgroupRoot:   runner.cgroupRoot,
 657                 PollPeriod:   runner.statInterval,
 658         }
 659         runner.statReporter.Start()
 660 }
 661
 662 type infoCommand struct {
 663         label string
 664         cmd   []string
 665 }
 666
 667 // LogNodeInfo gathers node information and store it on the log for debugging
 668 // purposes.
 669 func (runner *ContainerRunner) LogNodeInfo() (err error) {
 670         w := runner.NewLogWriter("node-info")
 671         logger := log.New(w, "node-info", 0)
 672
 673         commands := []infoCommand{
 674                 {
 675                         label: "Host Information",
 676                         cmd:   []string{"uname", "-a"},
 677                 },
 678                 {
 679                         label: "CPU Information",
 680                         cmd:   []string{"cat", "/proc/cpuinfo"},
 681                 },
 682                 {
 683                         label: "Memory Information",
 684                         cmd:   []string{"cat", "/proc/meminfo"},
 685                 },
 686                 {
 687                         label: "Disk Space",
 688                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 689                 },
 690                 {
 691                         label: "Disk INodes",
 692                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 693                 },
 694         }
 695
 696         // Run commands with informational output to be logged.
 697         var out []byte
 698         for _, command := range commands {
 699                 out, err = exec.Command(command.cmd[0], command.cmd[1:]...).CombinedOutput()
 700                 if err != nil {
 701                         return fmt.Errorf("While running command %q: %v",
 702                                 command.cmd, err)
 703                 }
 704                 logger.Println(command.label)
 705                 for _, line := range strings.Split(string(out), "\n") {
 706                         logger.Println(" ", line)
 707                 }
 708         }
 709
 710         err = w.Close()
 711         if err != nil {
 712                 return fmt.Errorf("While closing node-info logs: %v", err)
 713         }
 714         return nil
 715 }
 716
 717 // LogContainerRecord gets and saves the raw JSON container record from the API server
 718 func (runner *ContainerRunner) LogContainerRecord() (err error) {
 719         w := &ArvLogWriter{
 720                 ArvClient:     runner.ArvClient,
 721                 UUID:          runner.Container.UUID,
 722                 loggingStream: "container",
 723                 writeCloser:   runner.LogCollection.Open("container.json"),
 724         }
 725
 726         // Get Container record JSON from the API Server
 727         reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
 728         if err != nil {
 729                 return fmt.Errorf("While retrieving container record from the API server: %v", err)
 730         }
 731         defer reader.Close()
 732
 733         dec := json.NewDecoder(reader)
 734         dec.UseNumber()
 735         var cr map[string]interface{}
 736         if err = dec.Decode(&cr); err != nil {
 737                 return fmt.Errorf("While decoding the container record JSON response: %v", err)
 738         }
 739         // Re-encode it using indentation to improve readability
 740         enc := json.NewEncoder(w)
 741         enc.SetIndent("", "    ")
 742         if err = enc.Encode(cr); err != nil {
 743                 return fmt.Errorf("While logging the JSON container record: %v", err)
 744         }
 745         err = w.Close()
 746         if err != nil {
 747                 return fmt.Errorf("While closing container.json log: %v", err)
 748         }
 749         return nil
 750 }
 751
 752 // AttachStreams connects the docker container stdin, stdout and stderr logs
 753 // to the Arvados logger which logs to Keep and the API server logs table.
 754 func (runner *ContainerRunner) AttachStreams() (err error) {
 755
 756         runner.CrunchLog.Print("Attaching container streams")
 757
 758         // If stdin mount is provided, attach it to the docker container
 759         var stdinRdr arvados.File
 760         var stdinJson []byte
 761         if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
 762                 if stdinMnt.Kind == "collection" {
 763                         var stdinColl arvados.Collection
 764                         collId := stdinMnt.UUID
 765                         if collId == "" {
 766                                 collId = stdinMnt.PortableDataHash
 767                         }
 768                         err = runner.ArvClient.Get("collections", collId, nil, &stdinColl)
 769                         if err != nil {
 770                                 return fmt.Errorf("While getting stding collection: %v", err)
 771                         }
 772
 773                         stdinRdr, err = runner.Kc.ManifestFileReader(manifest.Manifest{Text: stdinColl.ManifestText}, stdinMnt.Path)
 774                         if os.IsNotExist(err) {
 775                                 return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
 776                         } else if err != nil {
 777                                 return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
 778                         }
 779                 } else if stdinMnt.Kind == "json" {
 780                         stdinJson, err = json.Marshal(stdinMnt.Content)
 781                         if err != nil {
 782                                 return fmt.Errorf("While encoding stdin json data: %v", err)
 783                         }
 784                 }
 785         }
 786
 787         stdinUsed := stdinRdr != nil || len(stdinJson) != 0
 788         response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
 789                 dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, Stdout: true, Stderr: true})
 790         if err != nil {
 791                 return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
 792         }
 793
 794         runner.loggingDone = make(chan bool)
 795
 796         if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
 797                 stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
 798                 if err != nil {
 799                         return err
 800                 }
 801                 runner.Stdout = stdoutFile
 802         } else {
 803                 runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
 804         }
 805
 806         if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
 807                 stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
 808                 if err != nil {
 809                         return err
 810                 }
 811                 runner.Stderr = stderrFile
 812         } else {
 813                 runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
 814         }
 815
 816         if stdinRdr != nil {
 817                 go func() {
 818                         _, err := io.Copy(response.Conn, stdinRdr)
 819                         if err != nil {
 820                                 runner.CrunchLog.Print("While writing stdin collection to docker container %q", err)
 821                                 runner.stop()
 822                         }
 823                         stdinRdr.Close()
 824                         response.CloseWrite()
 825                 }()
 826         } else if len(stdinJson) != 0 {
 827                 go func() {
 828                         _, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
 829                         if err != nil {
 830                                 runner.CrunchLog.Print("While writing stdin json to docker container %q", err)
 831                                 runner.stop()
 832                         }
 833                         response.CloseWrite()
 834                 }()
 835         }
 836
 837         go runner.ProcessDockerAttach(response.Reader)
 838
 839         return nil
 840 }
 841
 842 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 843         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 844         index := strings.LastIndex(stdoutPath, "/")
 845         if index > 0 {
 846                 subdirs := stdoutPath[:index]
 847                 if subdirs != "" {
 848                         st, err := os.Stat(runner.HostOutputDir)
 849                         if err != nil {
 850                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 851                         }
 852                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 853                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 854                         if err != nil {
 855                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 856                         }
 857                 }
 858         }
 859         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 860         if err != nil {
 861                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 862         }
 863
 864         return stdoutFile, nil
 865 }
 866
 867 // CreateContainer creates the docker container.
 868 func (runner *ContainerRunner) CreateContainer() error {
 869         runner.CrunchLog.Print("Creating Docker container")
 870
 871         runner.ContainerConfig.Cmd = runner.Container.Command
 872         if runner.Container.Cwd != "." {
 873                 runner.ContainerConfig.WorkingDir = runner.Container.Cwd
 874         }
 875
 876         for k, v := range runner.Container.Environment {
 877                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
 878         }
 879
 880         runner.ContainerConfig.Volumes = runner.Volumes
 881
 882         runner.HostConfig = dockercontainer.HostConfig{
 883                 Binds: runner.Binds,
 884                 LogConfig: dockercontainer.LogConfig{
 885                         Type: "none",
 886                 },
 887                 Resources: dockercontainer.Resources{
 888                         CgroupParent: runner.setCgroupParent,
 889                 },
 890         }
 891
 892         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
 893                 tok, err := runner.ContainerToken()
 894                 if err != nil {
 895                         return err
 896                 }
 897                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
 898                         "ARVADOS_API_TOKEN="+tok,
 899                         "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
 900                         "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
 901                 )
 902                 runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 903         } else {
 904                 if runner.enableNetwork == "always" {
 905                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 906                 } else {
 907                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
 908                 }
 909         }
 910
 911         _, stdinUsed := runner.Container.Mounts["stdin"]
 912         runner.ContainerConfig.OpenStdin = stdinUsed
 913         runner.ContainerConfig.StdinOnce = stdinUsed
 914         runner.ContainerConfig.AttachStdin = stdinUsed
 915         runner.ContainerConfig.AttachStdout = true
 916         runner.ContainerConfig.AttachStderr = true
 917
 918         createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
 919         if err != nil {
 920                 return fmt.Errorf("While creating container: %v", err)
 921         }
 922
 923         runner.ContainerID = createdBody.ID
 924
 925         return runner.AttachStreams()
 926 }
 927
 928 // StartContainer starts the docker container created by CreateContainer.
 929 func (runner *ContainerRunner) StartContainer() error {
 930         runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
 931         runner.cStateLock.Lock()
 932         defer runner.cStateLock.Unlock()
 933         if runner.cCancelled {
 934                 return ErrCancelled
 935         }
 936         err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
 937                 dockertypes.ContainerStartOptions{})
 938         if err != nil {
 939                 var advice string
 940                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
 941                         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])
 942                 }
 943                 return fmt.Errorf("could not start container: %v%s", err, advice)
 944         }
 945         runner.cStarted = true
 946         return nil
 947 }
 948
 949 // WaitFinish waits for the container to terminate, capture the exit code, and
 950 // close the stdout/stderr logging.
 951 func (runner *ContainerRunner) WaitFinish() (err error) {
 952         runner.CrunchLog.Print("Waiting for container to finish")
 953
 954         waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, "not-running")
 955
 956         go func() {
 957                 <-runner.ArvMountExit
 958                 if runner.cStarted {
 959                         runner.CrunchLog.Printf("arv-mount exited while container is still running.  Stopping container.")
 960                         runner.stop()
 961                 }
 962         }()
 963
 964         var waitBody dockercontainer.ContainerWaitOKBody
 965         select {
 966         case waitBody = <-waitOk:
 967         case err = <-waitErr:
 968         }
 969
 970         // Container isn't running any more
 971         runner.cStarted = false
 972
 973         if err != nil {
 974                 return fmt.Errorf("container wait: %v", err)
 975         }
 976
 977         runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode)
 978         code := int(waitBody.StatusCode)
 979         runner.ExitCode = &code
 980
 981         // wait for stdout/stderr to complete
 982         <-runner.loggingDone
 983
 984         return nil
 985 }
 986
 987 var ErrNotInOutputDir = fmt.Errorf("Must point to path within the output directory")
 988
 989 func (runner *ContainerRunner) derefOutputSymlink(path string, startinfo os.FileInfo) (tgt string, readlinktgt string, info os.FileInfo, err error) {
 990         // Follow symlinks if necessary
 991         info = startinfo
 992         tgt = path
 993         readlinktgt = ""
 994         nextlink := path
 995         for followed := 0; info.Mode()&os.ModeSymlink != 0; followed++ {
 996                 if followed >= limitFollowSymlinks {
 997                         // Got stuck in a loop or just a pathological number of links, give up.
 998                         err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
 999                         return
1000                 }
1001
1002                 readlinktgt, err = os.Readlink(nextlink)
1003                 if err != nil {
1004                         return
1005                 }
1006
1007                 tgt = readlinktgt
1008                 if !strings.HasPrefix(tgt, "/") {
1009                         // Relative symlink, resolve it to host path
1010                         tgt = filepath.Join(filepath.Dir(path), tgt)
1011                 }
1012                 if strings.HasPrefix(tgt, runner.Container.OutputPath+"/") && !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
1013                         // Absolute symlink to container output path, adjust it to host output path.
1014                         tgt = filepath.Join(runner.HostOutputDir, tgt[len(runner.Container.OutputPath):])
1015                 }
1016                 if !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
1017                         // After dereferencing, symlink target must either be
1018                         // within output directory, or must point to a
1019                         // collection mount.
1020                         err = ErrNotInOutputDir
1021                         return
1022                 }
1023
1024                 info, err = os.Lstat(tgt)
1025                 if err != nil {
1026                         // tgt
1027                         err = fmt.Errorf("Symlink in output %q points to invalid location %q: %v",
1028                                 path[len(runner.HostOutputDir):], readlinktgt, err)
1029                         return
1030                 }
1031
1032                 nextlink = tgt
1033         }
1034
1035         return
1036 }
1037
1038 var limitFollowSymlinks = 10
1039
1040 // UploadFile uploads files within the output directory, with special handling
1041 // for symlinks. If the symlink leads to a keep mount, copy the manifest text
1042 // from the keep mount into the output manifestText.  Ensure that whether
1043 // symlinks are relative or absolute, every symlink target (even targets that
1044 // are symlinks themselves) must point to a path in either the output directory
1045 // or a collection mount.
1046 //
1047 // Assumes initial value of "path" is absolute, and located within runner.HostOutputDir.
1048 func (runner *ContainerRunner) UploadOutputFile(
1049         path string,
1050         info os.FileInfo,
1051         infoerr error,
1052         binds []string,
1053         walkUpload *WalkUpload,
1054         relocateFrom string,
1055         relocateTo string,
1056         followed int) (manifestText string, err error) {
1057
1058         if info.Mode().IsDir() {
1059                 return
1060         }
1061
1062         if infoerr != nil {
1063                 return "", infoerr
1064         }
1065
1066         if followed >= limitFollowSymlinks {
1067                 // Got stuck in a loop or just a pathological number of
1068                 // directory links, give up.
1069                 err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
1070                 return
1071         }
1072
1073         // When following symlinks, the source path may need to be logically
1074         // relocated to some other path within the output collection.  Remove
1075         // the relocateFrom prefix and replace it with relocateTo.
1076         relocated := relocateTo + path[len(relocateFrom):]
1077
1078         tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info)
1079         if derefErr != nil && derefErr != ErrNotInOutputDir {
1080                 return "", derefErr
1081         }
1082
1083         // go through mounts and try reverse map to collection reference
1084         for _, bind := range binds {
1085                 mnt := runner.Container.Mounts[bind]
1086                 if tgt == bind || strings.HasPrefix(tgt, bind+"/") {
1087                         // get path relative to bind
1088                         targetSuffix := tgt[len(bind):]
1089
1090                         // Copy mount and adjust the path to add path relative to the bind
1091                         adjustedMount := mnt
1092                         adjustedMount.Path = filepath.Join(adjustedMount.Path, targetSuffix)
1093
1094                         // Terminates in this keep mount, so add the
1095                         // manifest text at appropriate location.
1096                         outputSuffix := path[len(runner.HostOutputDir):]
1097                         manifestText, err = runner.getCollectionManifestForPath(adjustedMount, outputSuffix)
1098                         return
1099                 }
1100         }
1101
1102         // If target is not a collection mount, it must be located within the
1103         // output directory, otherwise it is an error.
1104         if derefErr == ErrNotInOutputDir {
1105                 err = fmt.Errorf("Symlink in output %q points to invalid location %q, must point to path within the output directory.",
1106                         path[len(runner.HostOutputDir):], readlinktgt)
1107                 return
1108         }
1109
1110         if info.Mode().IsRegular() {
1111                 return "", walkUpload.UploadFile(relocated, tgt)
1112         }
1113
1114         if info.Mode().IsDir() {
1115                 // Symlink leads to directory.  Walk() doesn't follow
1116                 // directory symlinks, so we walk the target directory
1117                 // instead.  Within the walk, file paths are relocated
1118                 // so they appear under the original symlink path.
1119                 err = filepath.Walk(tgt, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
1120                         var m string
1121                         m, walkerr = runner.UploadOutputFile(walkpath, walkinfo, walkerr,
1122                                 binds, walkUpload, tgt, relocated, followed+1)
1123                         if walkerr == nil {
1124                                 manifestText = manifestText + m
1125                         }
1126                         return walkerr
1127                 })
1128                 return
1129         }
1130
1131         return
1132 }
1133
1134 // HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
1135 func (runner *ContainerRunner) CaptureOutput() error {
1136         if runner.finalState != "Complete" {
1137                 return nil
1138         }
1139
1140         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
1141                 // Output may have been set directly by the container, so
1142                 // refresh the container record to check.
1143                 err := runner.ArvClient.Get("containers", runner.Container.UUID,
1144                         nil, &runner.Container)
1145                 if err != nil {
1146                         return err
1147                 }
1148                 if runner.Container.Output != "" {
1149                         // Container output is already set.
1150                         runner.OutputPDH = &runner.Container.Output
1151                         return nil
1152                 }
1153         }
1154
1155         if runner.HostOutputDir == "" {
1156                 return nil
1157         }
1158
1159         _, err := os.Stat(runner.HostOutputDir)
1160         if err != nil {
1161                 return fmt.Errorf("While checking host output path: %v", err)
1162         }
1163
1164         // Pre-populate output from the configured mount points
1165         var binds []string
1166         for bind, mnt := range runner.Container.Mounts {
1167                 if mnt.Kind == "collection" {
1168                         binds = append(binds, bind)
1169                 }
1170         }
1171         sort.Strings(binds)
1172
1173         var manifestText string
1174
1175         collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
1176         _, err = os.Stat(collectionMetafile)
1177         if err != nil {
1178                 // Regular directory
1179
1180                 cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
1181                 walkUpload := cw.BeginUpload(runner.HostOutputDir, runner.CrunchLog.Logger)
1182
1183                 var m string
1184                 err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error {
1185                         m, err = runner.UploadOutputFile(path, info, err, binds, walkUpload, "", "", 0)
1186                         if err == nil {
1187                                 manifestText = manifestText + m
1188                         }
1189                         return err
1190                 })
1191
1192                 cw.EndUpload(walkUpload)
1193
1194                 if err != nil {
1195                         return fmt.Errorf("While uploading output files: %v", err)
1196                 }
1197
1198                 m, err = cw.ManifestText()
1199                 manifestText = manifestText + m
1200                 if err != nil {
1201                         return fmt.Errorf("While uploading output files: %v", err)
1202                 }
1203         } else {
1204                 // FUSE mount directory
1205                 file, openerr := os.Open(collectionMetafile)
1206                 if openerr != nil {
1207                         return fmt.Errorf("While opening FUSE metafile: %v", err)
1208                 }
1209                 defer file.Close()
1210
1211                 var rec arvados.Collection
1212                 err = json.NewDecoder(file).Decode(&rec)
1213                 if err != nil {
1214                         return fmt.Errorf("While reading FUSE metafile: %v", err)
1215                 }
1216                 manifestText = rec.ManifestText
1217         }
1218
1219         for _, bind := range binds {
1220                 mnt := runner.Container.Mounts[bind]
1221
1222                 bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
1223
1224                 if bindSuffix == bind || len(bindSuffix) <= 0 {
1225                         // either does not start with OutputPath or is OutputPath itself
1226                         continue
1227                 }
1228
1229                 if mnt.ExcludeFromOutput == true {
1230                         continue
1231                 }
1232
1233                 // append to manifest_text
1234                 m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
1235                 if err != nil {
1236                         return err
1237                 }
1238
1239                 manifestText = manifestText + m
1240         }
1241
1242         // Save output
1243         var response arvados.Collection
1244         manifest := manifest.Manifest{Text: manifestText}
1245         manifestText = manifest.Extract(".", ".").Text
1246         err = runner.ArvClient.Create("collections",
1247                 arvadosclient.Dict{
1248                         "ensure_unique_name": true,
1249                         "collection": arvadosclient.Dict{
1250                                 "is_trashed":    true,
1251                                 "name":          "output for " + runner.Container.UUID,
1252                                 "manifest_text": manifestText}},
1253                 &response)
1254         if err != nil {
1255                 return fmt.Errorf("While creating output collection: %v", err)
1256         }
1257         runner.OutputPDH = &response.PortableDataHash
1258         return nil
1259 }
1260
1261 var outputCollections = make(map[string]arvados.Collection)
1262
1263 // Fetch the collection for the mnt.PortableDataHash
1264 // Return the manifest_text fragment corresponding to the specified mnt.Path
1265 //  after making any required updates.
1266 //  Ex:
1267 //    If mnt.Path is not specified,
1268 //      return the entire manifest_text after replacing any "." with bindSuffix
1269 //    If mnt.Path corresponds to one stream,
1270 //      return the manifest_text for that stream after replacing that stream name with bindSuffix
1271 //    Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
1272 //      for that stream after replacing stream name with bindSuffix minus the last word
1273 //      and the file name with last word of the bindSuffix
1274 //  Allowed path examples:
1275 //    "path":"/"
1276 //    "path":"/subdir1"
1277 //    "path":"/subdir1/subdir2"
1278 //    "path":"/subdir/filename" etc
1279 func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
1280         collection := outputCollections[mnt.PortableDataHash]
1281         if collection.PortableDataHash == "" {
1282                 err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
1283                 if err != nil {
1284                         return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
1285                 }
1286                 outputCollections[mnt.PortableDataHash] = collection
1287         }
1288
1289         if collection.ManifestText == "" {
1290                 runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
1291                 return "", nil
1292         }
1293
1294         mft := manifest.Manifest{Text: collection.ManifestText}
1295         extracted := mft.Extract(mnt.Path, bindSuffix)
1296         if extracted.Err != nil {
1297                 return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
1298         }
1299         return extracted.Text, nil
1300 }
1301
1302 func (runner *ContainerRunner) CleanupDirs() {
1303         if runner.ArvMount != nil {
1304                 var delay int64 = 8
1305                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1306                 umount.Stdout = runner.CrunchLog
1307                 umount.Stderr = runner.CrunchLog
1308                 runner.CrunchLog.Printf("Running %v", umount.Args)
1309                 umnterr := umount.Start()
1310
1311                 if umnterr != nil {
1312                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1313                 } else {
1314                         // If arv-mount --unmount gets stuck for any reason, we
1315                         // don't want to wait for it forever.  Do Wait() in a goroutine
1316                         // so it doesn't block crunch-run.
1317                         umountExit := make(chan error)
1318                         go func() {
1319                                 mnterr := umount.Wait()
1320                                 if mnterr != nil {
1321                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1322                                 }
1323                                 umountExit <- mnterr
1324                         }()
1325
1326                         for again := true; again; {
1327                                 again = false
1328                                 select {
1329                                 case <-umountExit:
1330                                         umount = nil
1331                                         again = true
1332                                 case <-runner.ArvMountExit:
1333                                         break
1334                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1335                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1336                                         if umount != nil {
1337                                                 umount.Process.Kill()
1338                                         }
1339                                         runner.ArvMount.Process.Kill()
1340                                 }
1341                         }
1342                 }
1343         }
1344
1345         if runner.ArvMountPoint != "" {
1346                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1347                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1348                 }
1349         }
1350
1351         for _, tmpdir := range runner.CleanupTempDir {
1352                 if rmerr := os.RemoveAll(tmpdir); rmerr != nil {
1353                         runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", tmpdir, rmerr)
1354                 }
1355         }
1356 }
1357
1358 // CommitLogs posts the collection containing the final container logs.
1359 func (runner *ContainerRunner) CommitLogs() error {
1360         runner.CrunchLog.Print(runner.finalState)
1361
1362         if runner.arvMountLog != nil {
1363                 runner.arvMountLog.Close()
1364         }
1365         runner.CrunchLog.Close()
1366
1367         // Closing CrunchLog above allows them to be committed to Keep at this
1368         // point, but re-open crunch log with ArvClient in case there are any
1369         // other further errors (such as failing to write the log to Keep!)
1370         // while shutting down
1371         runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient,
1372                 UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: nil})
1373         runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1374
1375         if runner.LogsPDH != nil {
1376                 // If we have already assigned something to LogsPDH,
1377                 // we must be closing the re-opened log, which won't
1378                 // end up getting attached to the container record and
1379                 // therefore doesn't need to be saved as a collection
1380                 // -- it exists only to send logs to other channels.
1381                 return nil
1382         }
1383
1384         mt, err := runner.LogCollection.ManifestText()
1385         if err != nil {
1386                 return fmt.Errorf("While creating log manifest: %v", err)
1387         }
1388
1389         var response arvados.Collection
1390         err = runner.ArvClient.Create("collections",
1391                 arvadosclient.Dict{
1392                         "ensure_unique_name": true,
1393                         "collection": arvadosclient.Dict{
1394                                 "is_trashed":    true,
1395                                 "name":          "logs for " + runner.Container.UUID,
1396                                 "manifest_text": mt}},
1397                 &response)
1398         if err != nil {
1399                 return fmt.Errorf("While creating log collection: %v", err)
1400         }
1401         runner.LogsPDH = &response.PortableDataHash
1402         return nil
1403 }
1404
1405 // UpdateContainerRunning updates the container state to "Running"
1406 func (runner *ContainerRunner) UpdateContainerRunning() error {
1407         runner.cStateLock.Lock()
1408         defer runner.cStateLock.Unlock()
1409         if runner.cCancelled {
1410                 return ErrCancelled
1411         }
1412         return runner.ArvClient.Update("containers", runner.Container.UUID,
1413                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
1414 }
1415
1416 // ContainerToken returns the api_token the container (and any
1417 // arv-mount processes) are allowed to use.
1418 func (runner *ContainerRunner) ContainerToken() (string, error) {
1419         if runner.token != "" {
1420                 return runner.token, nil
1421         }
1422
1423         var auth arvados.APIClientAuthorization
1424         err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1425         if err != nil {
1426                 return "", err
1427         }
1428         runner.token = auth.APIToken
1429         return runner.token, nil
1430 }
1431
1432 // UpdateContainerComplete updates the container record state on API
1433 // server to "Complete" or "Cancelled"
1434 func (runner *ContainerRunner) UpdateContainerFinal() error {
1435         update := arvadosclient.Dict{}
1436         update["state"] = runner.finalState
1437         if runner.LogsPDH != nil {
1438                 update["log"] = *runner.LogsPDH
1439         }
1440         if runner.finalState == "Complete" {
1441                 if runner.ExitCode != nil {
1442                         update["exit_code"] = *runner.ExitCode
1443                 }
1444                 if runner.OutputPDH != nil {
1445                         update["output"] = *runner.OutputPDH
1446                 }
1447         }
1448         return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1449 }
1450
1451 // IsCancelled returns the value of Cancelled, with goroutine safety.
1452 func (runner *ContainerRunner) IsCancelled() bool {
1453         runner.cStateLock.Lock()
1454         defer runner.cStateLock.Unlock()
1455         return runner.cCancelled
1456 }
1457
1458 // NewArvLogWriter creates an ArvLogWriter
1459 func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser {
1460         return &ArvLogWriter{
1461                 ArvClient:     runner.ArvClient,
1462                 UUID:          runner.Container.UUID,
1463                 loggingStream: name,
1464                 writeCloser:   runner.LogCollection.Open(name + ".txt")}
1465 }
1466
1467 // Run the full container lifecycle.
1468 func (runner *ContainerRunner) Run() (err error) {
1469         runner.CrunchLog.Printf("crunch-run %s started", version)
1470         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1471
1472         hostname, hosterr := os.Hostname()
1473         if hosterr != nil {
1474                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1475         } else {
1476                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1477         }
1478
1479         runner.finalState = "Queued"
1480
1481         defer func() {
1482                 runner.stopSignals()
1483                 runner.CleanupDirs()
1484
1485                 runner.CrunchLog.Printf("crunch-run finished")
1486                 runner.CrunchLog.Close()
1487         }()
1488
1489         defer func() {
1490                 // checkErr prints e (unless it's nil) and sets err to
1491                 // e (unless err is already non-nil). Thus, if err
1492                 // hasn't already been assigned when Run() returns,
1493                 // this cleanup func will cause Run() to return the
1494                 // first non-nil error that is passed to checkErr().
1495                 checkErr := func(e error) {
1496                         if e == nil {
1497                                 return
1498                         }
1499                         runner.CrunchLog.Print(e)
1500                         if err == nil {
1501                                 err = e
1502                         }
1503                         if runner.finalState == "Complete" {
1504                                 // There was an error in the finalization.
1505                                 runner.finalState = "Cancelled"
1506                         }
1507                 }
1508
1509                 // Log the error encountered in Run(), if any
1510                 checkErr(err)
1511
1512                 if runner.finalState == "Queued" {
1513                         runner.UpdateContainerFinal()
1514                         return
1515                 }
1516
1517                 if runner.IsCancelled() {
1518                         runner.finalState = "Cancelled"
1519                         // but don't return yet -- we still want to
1520                         // capture partial output and write logs
1521                 }
1522
1523                 checkErr(runner.CaptureOutput())
1524                 checkErr(runner.CommitLogs())
1525                 checkErr(runner.UpdateContainerFinal())
1526         }()
1527
1528         err = runner.fetchContainerRecord()
1529         if err != nil {
1530                 return
1531         }
1532
1533         // setup signal handling
1534         runner.setupSignals()
1535
1536         // check for and/or load image
1537         err = runner.LoadImage()
1538         if err != nil {
1539                 if !runner.checkBrokenNode(err) {
1540                         // Failed to load image but not due to a "broken node"
1541                         // condition, probably user error.
1542                         runner.finalState = "Cancelled"
1543                 }
1544                 err = fmt.Errorf("While loading container image: %v", err)
1545                 return
1546         }
1547
1548         // set up FUSE mount and binds
1549         err = runner.SetupMounts()
1550         if err != nil {
1551                 runner.finalState = "Cancelled"
1552                 err = fmt.Errorf("While setting up mounts: %v", err)
1553                 return
1554         }
1555
1556         err = runner.CreateContainer()
1557         if err != nil {
1558                 return
1559         }
1560
1561         // Gather and record node information
1562         err = runner.LogNodeInfo()
1563         if err != nil {
1564                 return
1565         }
1566         // Save container.json record on log collection
1567         err = runner.LogContainerRecord()
1568         if err != nil {
1569                 return
1570         }
1571
1572         if runner.IsCancelled() {
1573                 return
1574         }
1575
1576         err = runner.UpdateContainerRunning()
1577         if err != nil {
1578                 return
1579         }
1580         runner.finalState = "Cancelled"
1581
1582         runner.StartCrunchstat()
1583
1584         err = runner.StartContainer()
1585         if err != nil {
1586                 runner.checkBrokenNode(err)
1587                 return
1588         }
1589
1590         err = runner.WaitFinish()
1591         if err == nil {
1592                 runner.finalState = "Complete"
1593         }
1594         return
1595 }
1596
1597 // Fetch the current container record (uuid = runner.Container.UUID)
1598 // into runner.Container.
1599 func (runner *ContainerRunner) fetchContainerRecord() error {
1600         reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1601         if err != nil {
1602                 return fmt.Errorf("error fetching container record: %v", err)
1603         }
1604         defer reader.Close()
1605
1606         dec := json.NewDecoder(reader)
1607         dec.UseNumber()
1608         err = dec.Decode(&runner.Container)
1609         if err != nil {
1610                 return fmt.Errorf("error decoding container record: %v", err)
1611         }
1612         return nil
1613 }
1614
1615 // NewContainerRunner creates a new container runner.
1616 func NewContainerRunner(api IArvadosClient,
1617         kc IKeepClient,
1618         docker ThinDockerClient,
1619         containerUUID string) *ContainerRunner {
1620
1621         cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
1622         cr.NewLogWriter = cr.NewArvLogWriter
1623         cr.RunArvMount = cr.ArvMountCmd
1624         cr.MkTempDir = ioutil.TempDir
1625         cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
1626         cr.Container.UUID = containerUUID
1627         cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
1628         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1629
1630         loadLogThrottleParams(api)
1631
1632         return cr
1633 }
1634
1635 func main() {
1636         statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1637         cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1638         cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1639         cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1640         caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
1641         enableNetwork := flag.String("container-enable-networking", "default",
1642                 `Specify if networking should be enabled for container.  One of 'default', 'always':
1643         default: only enable networking if container requests it.
1644         always:  containers always have networking enabled
1645         `)
1646         networkMode := flag.String("container-network-mode", "default",
1647                 `Set networking mode for container.  Corresponds to Docker network mode (--net).
1648         `)
1649         memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container")
1650         getVersion := flag.Bool("version", false, "Print version information and exit.")
1651         flag.Parse()
1652
1653         // Print version information if requested
1654         if *getVersion {
1655                 fmt.Printf("crunch-run %s\n", version)
1656                 return
1657         }
1658
1659         log.Printf("crunch-run %s started", version)
1660
1661         containerId := flag.Arg(0)
1662
1663         if *caCertsPath != "" {
1664                 arvadosclient.CertFiles = []string{*caCertsPath}
1665         }
1666
1667         api, err := arvadosclient.MakeArvadosClient()
1668         if err != nil {
1669                 log.Fatalf("%s: %v", containerId, err)
1670         }
1671         api.Retries = 8
1672
1673         kc, kcerr := keepclient.MakeKeepClient(api)
1674         if kcerr != nil {
1675                 log.Fatalf("%s: %v", containerId, kcerr)
1676         }
1677         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1678         kc.Retries = 4
1679
1680         // API version 1.21 corresponds to Docker 1.9, which is currently the
1681         // minimum version we want to support.
1682         docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
1683         dockerClientProxy := ThinDockerClientProxy{Docker: docker}
1684
1685         cr := NewContainerRunner(api, kc, dockerClientProxy, containerId)
1686
1687         if dockererr != nil {
1688                 cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
1689                 cr.checkBrokenNode(dockererr)
1690                 cr.CrunchLog.Close()
1691                 os.Exit(1)
1692         }
1693
1694         cr.statInterval = *statInterval
1695         cr.cgroupRoot = *cgroupRoot
1696         cr.expectCgroupParent = *cgroupParent
1697         cr.enableNetwork = *enableNetwork
1698         cr.networkMode = *networkMode
1699         if *cgroupParentSubsystem != "" {
1700                 p := findCgroup(*cgroupParentSubsystem)
1701                 cr.setCgroupParent = p
1702                 cr.expectCgroupParent = p
1703         }
1704
1705         runerr := cr.Run()
1706
1707         if *memprofile != "" {
1708                 f, err := os.Create(*memprofile)
1709                 if err != nil {
1710                         log.Printf("could not create memory profile: ", err)
1711                 }
1712                 runtime.GC() // get up-to-date statistics
1713                 if err := pprof.WriteHeapProfile(f); err != nil {
1714                         log.Printf("could not write memory profile: ", err)
1715                 }
1716                 closeerr := f.Close()
1717                 if closeerr != nil {
1718                         log.Printf("closing memprofile file: ", err)
1719                 }
1720         }
1721
1722         if runerr != nil {
1723                 log.Fatalf("%s: %v", containerId, runerr)
1724         }
1725 }