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         "encoding/json"
  10         "errors"
  11         "flag"
  12         "fmt"
  13         "io"
  14         "io/ioutil"
  15         "log"
  16         "os"
  17         "os/exec"
  18         "os/signal"
  19         "path"
  20         "path/filepath"
  21         "regexp"
  22         "runtime"
  23         "runtime/pprof"
  24         "sort"
  25         "strings"
  26         "sync"
  27         "syscall"
  28         "time"
  29
  30         "git.curoverse.com/arvados.git/lib/crunchstat"
  31         "git.curoverse.com/arvados.git/sdk/go/arvados"
  32         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  33         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  34         "git.curoverse.com/arvados.git/sdk/go/manifest"
  35         "golang.org/x/net/context"
  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         ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) 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 // ContainerRunner is the main stateful struct used for a single execution of a
  86 // container.
  87 type ContainerRunner struct {
  88         Docker    ThinDockerClient
  89         ArvClient IArvadosClient
  90         Kc        IKeepClient
  91         arvados.Container
  92         ContainerConfig dockercontainer.Config
  93         dockercontainer.HostConfig
  94         token       string
  95         ContainerID string
  96         ExitCode    *int
  97         NewLogWriter
  98         loggingDone   chan bool
  99         CrunchLog     *ThrottledLogger
 100         Stdout        io.WriteCloser
 101         Stderr        io.WriteCloser
 102         LogCollection *CollectionWriter
 103         LogsPDH       *string
 104         RunArvMount
 105         MkTempDir
 106         ArvMount       *exec.Cmd
 107         ArvMountPoint  string
 108         HostOutputDir  string
 109         CleanupTempDir []string
 110         Binds          []string
 111         Volumes        map[string]struct{}
 112         OutputPDH      *string
 113         SigChan        chan os.Signal
 114         ArvMountExit   chan error
 115         finalState     string
 116
 117         statLogger   io.WriteCloser
 118         statReporter *crunchstat.Reporter
 119         statInterval time.Duration
 120         cgroupRoot   string
 121         // What we expect the container's cgroup parent to be.
 122         expectCgroupParent string
 123         // What we tell docker to use as the container's cgroup
 124         // parent. Note: Ideally we would use the same field for both
 125         // expectCgroupParent and setCgroupParent, and just make it
 126         // default to "docker". However, when using docker < 1.10 with
 127         // systemd, specifying a non-empty cgroup parent (even the
 128         // default value "docker") hits a docker bug
 129         // (https://github.com/docker/docker/issues/17126). Using two
 130         // separate fields makes it possible to use the "expect cgroup
 131         // parent to be X" feature even on sites where the "specify
 132         // cgroup parent" feature breaks.
 133         setCgroupParent string
 134
 135         cStateLock sync.Mutex
 136         cCancelled bool // StopContainer() invoked
 137
 138         enableNetwork string // one of "default" or "always"
 139         networkMode   string // passed through to HostConfig.NetworkMode
 140         arvMountLog   *ThrottledLogger
 141 }
 142
 143 // setupSignals sets up signal handling to gracefully terminate the underlying
 144 // Docker container and update state when receiving a TERM, INT or QUIT signal.
 145 func (runner *ContainerRunner) setupSignals() {
 146         runner.SigChan = make(chan os.Signal, 1)
 147         signal.Notify(runner.SigChan, syscall.SIGTERM)
 148         signal.Notify(runner.SigChan, syscall.SIGINT)
 149         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 150
 151         go func(sig chan os.Signal) {
 152                 for s := range sig {
 153                         runner.CrunchLog.Printf("caught signal: %v", s)
 154                         runner.stop()
 155                 }
 156         }(runner.SigChan)
 157 }
 158
 159 // stop the underlying Docker container.
 160 func (runner *ContainerRunner) stop() {
 161         runner.cStateLock.Lock()
 162         defer runner.cStateLock.Unlock()
 163         if runner.ContainerID == "" {
 164                 return
 165         }
 166         runner.cCancelled = true
 167         runner.CrunchLog.Printf("removing container")
 168         err := runner.Docker.ContainerRemove(context.TODO(), runner.ContainerID, dockertypes.ContainerRemoveOptions{Force: true})
 169         if err != nil {
 170                 runner.CrunchLog.Printf("error removing container: %s", err)
 171         }
 172 }
 173
 174 func (runner *ContainerRunner) stopSignals() {
 175         if runner.SigChan != nil {
 176                 signal.Stop(runner.SigChan)
 177         }
 178 }
 179
 180 var errorBlacklist = []string{
 181         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 182         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 183 }
 184 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)")
 185
 186 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 187         for _, d := range errorBlacklist {
 188                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 189                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 190                         if *brokenNodeHook == "" {
 191                                 runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
 192                         } else {
 193                                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 194                                 // run killme script
 195                                 c := exec.Command(*brokenNodeHook)
 196                                 c.Stdout = runner.CrunchLog
 197                                 c.Stderr = runner.CrunchLog
 198                                 err := c.Run()
 199                                 if err != nil {
 200                                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 201                                 }
 202                         }
 203                         return true
 204                 }
 205         }
 206         return false
 207 }
 208
 209 // LoadImage determines the docker image id from the container record and
 210 // checks if it is available in the local Docker image store.  If not, it loads
 211 // the image from Keep.
 212 func (runner *ContainerRunner) LoadImage() (err error) {
 213
 214         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 215
 216         var collection arvados.Collection
 217         err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
 218         if err != nil {
 219                 return fmt.Errorf("While getting container image collection: %v", err)
 220         }
 221         manifest := manifest.Manifest{Text: collection.ManifestText}
 222         var img, imageID string
 223         for ms := range manifest.StreamIter() {
 224                 img = ms.FileStreamSegments[0].Name
 225                 if !strings.HasSuffix(img, ".tar") {
 226                         return fmt.Errorf("First file in the container image collection does not end in .tar")
 227                 }
 228                 imageID = img[:len(img)-4]
 229         }
 230
 231         runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
 232
 233         _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
 234         if err != nil {
 235                 runner.CrunchLog.Print("Loading Docker image from keep")
 236
 237                 var readCloser io.ReadCloser
 238                 readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
 239                 if err != nil {
 240                         return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
 241                 }
 242
 243                 response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, true)
 244                 if err != nil {
 245                         return fmt.Errorf("While loading container image into Docker: %v", err)
 246                 }
 247
 248                 defer response.Body.Close()
 249                 rbody, err := ioutil.ReadAll(response.Body)
 250                 if err != nil {
 251                         return fmt.Errorf("Reading response to image load: %v", err)
 252                 }
 253                 runner.CrunchLog.Printf("Docker response: %s", rbody)
 254         } else {
 255                 runner.CrunchLog.Print("Docker image is available")
 256         }
 257
 258         runner.ContainerConfig.Image = imageID
 259
 260         runner.Kc.ClearBlockCache()
 261
 262         return nil
 263 }
 264
 265 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 266         c = exec.Command("arv-mount", arvMountCmd...)
 267
 268         // Copy our environment, but override ARVADOS_API_TOKEN with
 269         // the container auth token.
 270         c.Env = nil
 271         for _, s := range os.Environ() {
 272                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 273                         c.Env = append(c.Env, s)
 274                 }
 275         }
 276         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 277
 278         runner.arvMountLog = NewThrottledLogger(runner.NewLogWriter("arv-mount"))
 279         c.Stdout = runner.arvMountLog
 280         c.Stderr = runner.arvMountLog
 281
 282         runner.CrunchLog.Printf("Running %v", c.Args)
 283
 284         err = c.Start()
 285         if err != nil {
 286                 return nil, err
 287         }
 288
 289         statReadme := make(chan bool)
 290         runner.ArvMountExit = make(chan error)
 291
 292         keepStatting := true
 293         go func() {
 294                 for keepStatting {
 295                         time.Sleep(100 * time.Millisecond)
 296                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 297                         if err == nil {
 298                                 keepStatting = false
 299                                 statReadme <- true
 300                         }
 301                 }
 302                 close(statReadme)
 303         }()
 304
 305         go func() {
 306                 mnterr := c.Wait()
 307                 if mnterr != nil {
 308                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 309                 }
 310                 runner.ArvMountExit <- mnterr
 311                 close(runner.ArvMountExit)
 312         }()
 313
 314         select {
 315         case <-statReadme:
 316                 break
 317         case err := <-runner.ArvMountExit:
 318                 runner.ArvMount = nil
 319                 keepStatting = false
 320                 return nil, err
 321         }
 322
 323         return c, nil
 324 }
 325
 326 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 327         if runner.ArvMountPoint == "" {
 328                 runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
 329         }
 330         return
 331 }
 332
 333 func (runner *ContainerRunner) SetupMounts() (err error) {
 334         err = runner.SetupArvMountPoint("keep")
 335         if err != nil {
 336                 return fmt.Errorf("While creating keep mount temp dir: %v", err)
 337         }
 338
 339         token, err := runner.ContainerToken()
 340         if err != nil {
 341                 return fmt.Errorf("could not get container token: %s", err)
 342         }
 343
 344         pdhOnly := true
 345         tmpcount := 0
 346         arvMountCmd := []string{
 347                 "--foreground",
 348                 "--allow-other",
 349                 "--read-write",
 350                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 351
 352         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 353                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 354         }
 355
 356         collectionPaths := []string{}
 357         runner.Binds = nil
 358         runner.Volumes = make(map[string]struct{})
 359         needCertMount := true
 360
 361         var binds []string
 362         for bind := range runner.Container.Mounts {
 363                 binds = append(binds, bind)
 364         }
 365         sort.Strings(binds)
 366
 367         for _, bind := range binds {
 368                 mnt := runner.Container.Mounts[bind]
 369                 if bind == "stdout" || bind == "stderr" {
 370                         // Is it a "file" mount kind?
 371                         if mnt.Kind != "file" {
 372                                 return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind)
 373                         }
 374
 375                         // Does path start with OutputPath?
 376                         prefix := runner.Container.OutputPath
 377                         if !strings.HasSuffix(prefix, "/") {
 378                                 prefix += "/"
 379                         }
 380                         if !strings.HasPrefix(mnt.Path, prefix) {
 381                                 return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 382                         }
 383                 }
 384
 385                 if bind == "stdin" {
 386                         // Is it a "collection" mount kind?
 387                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 388                                 return fmt.Errorf("Unsupported mount kind '%s' for stdin. Only 'collection' or 'json' are supported.", mnt.Kind)
 389                         }
 390                 }
 391
 392                 if bind == "/etc/arvados/ca-certificates.crt" {
 393                         needCertMount = false
 394                 }
 395
 396                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 397                         if mnt.Kind != "collection" {
 398                                 return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind)
 399                         }
 400                 }
 401
 402                 switch {
 403                 case mnt.Kind == "collection" && bind != "stdin":
 404                         var src string
 405                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 406                                 return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 407                         }
 408                         if mnt.UUID != "" {
 409                                 if mnt.Writable {
 410                                         return fmt.Errorf("Writing to existing collections currently not permitted.")
 411                                 }
 412                                 pdhOnly = false
 413                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 414                         } else if mnt.PortableDataHash != "" {
 415                                 if mnt.Writable {
 416                                         return fmt.Errorf("Can never write to a collection specified by portable data hash")
 417                                 }
 418                                 idx := strings.Index(mnt.PortableDataHash, "/")
 419                                 if idx > 0 {
 420                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 421                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 422                                         runner.Container.Mounts[bind] = mnt
 423                                 }
 424                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 425                                 if mnt.Path != "" && mnt.Path != "." {
 426                                         if strings.HasPrefix(mnt.Path, "./") {
 427                                                 mnt.Path = mnt.Path[2:]
 428                                         } else if strings.HasPrefix(mnt.Path, "/") {
 429                                                 mnt.Path = mnt.Path[1:]
 430                                         }
 431                                         src += "/" + mnt.Path
 432                                 }
 433                         } else {
 434                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 435                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 436                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 437                                 tmpcount += 1
 438                         }
 439                         if mnt.Writable {
 440                                 if bind == runner.Container.OutputPath {
 441                                         runner.HostOutputDir = src
 442                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 443                                         return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind)
 444                                 }
 445                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 446                         } else {
 447                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
 448                         }
 449                         collectionPaths = append(collectionPaths, src)
 450
 451                 case mnt.Kind == "tmp":
 452                         var tmpdir string
 453                         tmpdir, err = runner.MkTempDir("", "")
 454                         if err != nil {
 455                                 return fmt.Errorf("While creating mount temp dir: %v", err)
 456                         }
 457                         st, staterr := os.Stat(tmpdir)
 458                         if staterr != nil {
 459                                 return fmt.Errorf("While Stat on temp dir: %v", staterr)
 460                         }
 461                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 462                         if staterr != nil {
 463                                 return fmt.Errorf("While Chmod temp dir: %v", err)
 464                         }
 465                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 466                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
 467                         if bind == runner.Container.OutputPath {
 468                                 runner.HostOutputDir = tmpdir
 469                         }
 470
 471                 case mnt.Kind == "json":
 472                         jsondata, err := json.Marshal(mnt.Content)
 473                         if err != nil {
 474                                 return fmt.Errorf("encoding json data: %v", err)
 475                         }
 476                         // Create a tempdir with a single file
 477                         // (instead of just a tempfile): this way we
 478                         // can ensure the file is world-readable
 479                         // inside the container, without having to
 480                         // make it world-readable on the docker host.
 481                         tmpdir, err := runner.MkTempDir("", "")
 482                         if err != nil {
 483                                 return fmt.Errorf("creating temp dir: %v", err)
 484                         }
 485                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 486                         tmpfn := filepath.Join(tmpdir, "mountdata.json")
 487                         err = ioutil.WriteFile(tmpfn, jsondata, 0644)
 488                         if err != nil {
 489                                 return fmt.Errorf("writing temp file: %v", err)
 490                         }
 491                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
 492
 493                 case mnt.Kind == "git_tree":
 494                         tmpdir, err := runner.MkTempDir("", "")
 495                         if err != nil {
 496                                 return fmt.Errorf("creating temp dir: %v", err)
 497                         }
 498                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 499                         err = gitMount(mnt).extractTree(runner.ArvClient, tmpdir, token)
 500                         if err != nil {
 501                                 return err
 502                         }
 503                         runner.Binds = append(runner.Binds, tmpdir+":"+bind+":ro")
 504                 }
 505         }
 506
 507         if runner.HostOutputDir == "" {
 508                 return fmt.Errorf("Output path does not correspond to a writable mount point")
 509         }
 510
 511         if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
 512                 for _, certfile := range arvadosclient.CertFiles {
 513                         _, err := os.Stat(certfile)
 514                         if err == nil {
 515                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
 516                                 break
 517                         }
 518                 }
 519         }
 520
 521         if pdhOnly {
 522                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 523         } else {
 524                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 525         }
 526         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 527
 528         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 529         if err != nil {
 530                 return fmt.Errorf("While trying to start arv-mount: %v", err)
 531         }
 532
 533         for _, p := range collectionPaths {
 534                 _, err = os.Stat(p)
 535                 if err != nil {
 536                         return fmt.Errorf("While checking that input files exist: %v", err)
 537                 }
 538         }
 539
 540         return nil
 541 }
 542
 543 func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
 544         // Handle docker log protocol
 545         // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
 546
 547         header := make([]byte, 8)
 548         for {
 549                 _, readerr := io.ReadAtLeast(containerReader, header, 8)
 550
 551                 if readerr == nil {
 552                         readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
 553                         if header[0] == 1 {
 554                                 // stdout
 555                                 _, readerr = io.CopyN(runner.Stdout, containerReader, readsize)
 556                         } else {
 557                                 // stderr
 558                                 _, readerr = io.CopyN(runner.Stderr, containerReader, readsize)
 559                         }
 560                 }
 561
 562                 if readerr != nil {
 563                         if readerr != io.EOF {
 564                                 runner.CrunchLog.Printf("While reading docker logs: %v", readerr)
 565                         }
 566
 567                         closeerr := runner.Stdout.Close()
 568                         if closeerr != nil {
 569                                 runner.CrunchLog.Printf("While closing stdout logs: %v", closeerr)
 570                         }
 571
 572                         closeerr = runner.Stderr.Close()
 573                         if closeerr != nil {
 574                                 runner.CrunchLog.Printf("While closing stderr logs: %v", closeerr)
 575                         }
 576
 577                         if runner.statReporter != nil {
 578                                 runner.statReporter.Stop()
 579                                 closeerr = runner.statLogger.Close()
 580                                 if closeerr != nil {
 581                                         runner.CrunchLog.Printf("While closing crunchstat logs: %v", closeerr)
 582                                 }
 583                         }
 584
 585                         close(runner.loggingDone)
 586                         return
 587                 }
 588         }
 589 }
 590
 591 func (runner *ContainerRunner) StartCrunchstat() {
 592         runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
 593         runner.statReporter = &crunchstat.Reporter{
 594                 CID:          runner.ContainerID,
 595                 Logger:       log.New(runner.statLogger, "", 0),
 596                 CgroupParent: runner.expectCgroupParent,
 597                 CgroupRoot:   runner.cgroupRoot,
 598                 PollPeriod:   runner.statInterval,
 599         }
 600         runner.statReporter.Start()
 601 }
 602
 603 type infoCommand struct {
 604         label string
 605         cmd   []string
 606 }
 607
 608 // LogHostInfo logs info about the current host, for debugging and
 609 // accounting purposes. Although it's logged as "node-info", this is
 610 // about the environment where crunch-run is actually running, which
 611 // might differ from what's described in the node record (see
 612 // LogNodeRecord).
 613 func (runner *ContainerRunner) LogHostInfo() (err error) {
 614         w := runner.NewLogWriter("node-info")
 615
 616         commands := []infoCommand{
 617                 {
 618                         label: "Host Information",
 619                         cmd:   []string{"uname", "-a"},
 620                 },
 621                 {
 622                         label: "CPU Information",
 623                         cmd:   []string{"cat", "/proc/cpuinfo"},
 624                 },
 625                 {
 626                         label: "Memory Information",
 627                         cmd:   []string{"cat", "/proc/meminfo"},
 628                 },
 629                 {
 630                         label: "Disk Space",
 631                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 632                 },
 633                 {
 634                         label: "Disk INodes",
 635                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 636                 },
 637         }
 638
 639         // Run commands with informational output to be logged.
 640         for _, command := range commands {
 641                 fmt.Fprintln(w, command.label)
 642                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 643                 cmd.Stdout = w
 644                 cmd.Stderr = w
 645                 if err := cmd.Run(); err != nil {
 646                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 647                         fmt.Fprintln(w, err)
 648                         return err
 649                 }
 650                 fmt.Fprintln(w, "")
 651         }
 652
 653         err = w.Close()
 654         if err != nil {
 655                 return fmt.Errorf("While closing node-info logs: %v", err)
 656         }
 657         return nil
 658 }
 659
 660 // LogContainerRecord gets and saves the raw JSON container record from the API server
 661 func (runner *ContainerRunner) LogContainerRecord() error {
 662         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 663         if !logged && err == nil {
 664                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 665         }
 666         return err
 667 }
 668
 669 // LogNodeRecord logs arvados#node record corresponding to the current host.
 670 func (runner *ContainerRunner) LogNodeRecord() error {
 671         hostname := os.Getenv("SLURMD_NODENAME")
 672         if hostname == "" {
 673                 hostname, _ = os.Hostname()
 674         }
 675         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 676                 // The "info" field has admin-only info when obtained
 677                 // with a privileged token, and should not be logged.
 678                 node, ok := resp.(map[string]interface{})
 679                 if ok {
 680                         delete(node, "info")
 681                 }
 682         })
 683         return err
 684 }
 685
 686 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 687         w := &ArvLogWriter{
 688                 ArvClient:     runner.ArvClient,
 689                 UUID:          runner.Container.UUID,
 690                 loggingStream: label,
 691                 writeCloser:   runner.LogCollection.Open(label + ".json"),
 692         }
 693
 694         reader, err := runner.ArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 695         if err != nil {
 696                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 697         }
 698         defer reader.Close()
 699
 700         dec := json.NewDecoder(reader)
 701         dec.UseNumber()
 702         var resp map[string]interface{}
 703         if err = dec.Decode(&resp); err != nil {
 704                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 705         }
 706         items, ok := resp["items"].([]interface{})
 707         if !ok {
 708                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 709         } else if len(items) < 1 {
 710                 return false, nil
 711         }
 712         if munge != nil {
 713                 munge(items[0])
 714         }
 715         // Re-encode it using indentation to improve readability
 716         enc := json.NewEncoder(w)
 717         enc.SetIndent("", "    ")
 718         if err = enc.Encode(items[0]); err != nil {
 719                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 720         }
 721         err = w.Close()
 722         if err != nil {
 723                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 724         }
 725         return true, nil
 726 }
 727
 728 // AttachStreams connects the docker container stdin, stdout and stderr logs
 729 // to the Arvados logger which logs to Keep and the API server logs table.
 730 func (runner *ContainerRunner) AttachStreams() (err error) {
 731
 732         runner.CrunchLog.Print("Attaching container streams")
 733
 734         // If stdin mount is provided, attach it to the docker container
 735         var stdinRdr arvados.File
 736         var stdinJson []byte
 737         if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
 738                 if stdinMnt.Kind == "collection" {
 739                         var stdinColl arvados.Collection
 740                         collId := stdinMnt.UUID
 741                         if collId == "" {
 742                                 collId = stdinMnt.PortableDataHash
 743                         }
 744                         err = runner.ArvClient.Get("collections", collId, nil, &stdinColl)
 745                         if err != nil {
 746                                 return fmt.Errorf("While getting stding collection: %v", err)
 747                         }
 748
 749                         stdinRdr, err = runner.Kc.ManifestFileReader(manifest.Manifest{Text: stdinColl.ManifestText}, stdinMnt.Path)
 750                         if os.IsNotExist(err) {
 751                                 return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
 752                         } else if err != nil {
 753                                 return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
 754                         }
 755                 } else if stdinMnt.Kind == "json" {
 756                         stdinJson, err = json.Marshal(stdinMnt.Content)
 757                         if err != nil {
 758                                 return fmt.Errorf("While encoding stdin json data: %v", err)
 759                         }
 760                 }
 761         }
 762
 763         stdinUsed := stdinRdr != nil || len(stdinJson) != 0
 764         response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
 765                 dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, Stdout: true, Stderr: true})
 766         if err != nil {
 767                 return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
 768         }
 769
 770         runner.loggingDone = make(chan bool)
 771
 772         if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
 773                 stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
 774                 if err != nil {
 775                         return err
 776                 }
 777                 runner.Stdout = stdoutFile
 778         } else {
 779                 runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
 780         }
 781
 782         if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
 783                 stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
 784                 if err != nil {
 785                         return err
 786                 }
 787                 runner.Stderr = stderrFile
 788         } else {
 789                 runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
 790         }
 791
 792         if stdinRdr != nil {
 793                 go func() {
 794                         _, err := io.Copy(response.Conn, stdinRdr)
 795                         if err != nil {
 796                                 runner.CrunchLog.Print("While writing stdin collection to docker container %q", err)
 797                                 runner.stop()
 798                         }
 799                         stdinRdr.Close()
 800                         response.CloseWrite()
 801                 }()
 802         } else if len(stdinJson) != 0 {
 803                 go func() {
 804                         _, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
 805                         if err != nil {
 806                                 runner.CrunchLog.Print("While writing stdin json to docker container %q", err)
 807                                 runner.stop()
 808                         }
 809                         response.CloseWrite()
 810                 }()
 811         }
 812
 813         go runner.ProcessDockerAttach(response.Reader)
 814
 815         return nil
 816 }
 817
 818 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 819         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 820         index := strings.LastIndex(stdoutPath, "/")
 821         if index > 0 {
 822                 subdirs := stdoutPath[:index]
 823                 if subdirs != "" {
 824                         st, err := os.Stat(runner.HostOutputDir)
 825                         if err != nil {
 826                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 827                         }
 828                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 829                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 830                         if err != nil {
 831                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 832                         }
 833                 }
 834         }
 835         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 836         if err != nil {
 837                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 838         }
 839
 840         return stdoutFile, nil
 841 }
 842
 843 // CreateContainer creates the docker container.
 844 func (runner *ContainerRunner) CreateContainer() error {
 845         runner.CrunchLog.Print("Creating Docker container")
 846
 847         runner.ContainerConfig.Cmd = runner.Container.Command
 848         if runner.Container.Cwd != "." {
 849                 runner.ContainerConfig.WorkingDir = runner.Container.Cwd
 850         }
 851
 852         for k, v := range runner.Container.Environment {
 853                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
 854         }
 855
 856         runner.ContainerConfig.Volumes = runner.Volumes
 857
 858         runner.HostConfig = dockercontainer.HostConfig{
 859                 Binds: runner.Binds,
 860                 LogConfig: dockercontainer.LogConfig{
 861                         Type: "none",
 862                 },
 863                 Resources: dockercontainer.Resources{
 864                         CgroupParent: runner.setCgroupParent,
 865                 },
 866         }
 867
 868         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
 869                 tok, err := runner.ContainerToken()
 870                 if err != nil {
 871                         return err
 872                 }
 873                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
 874                         "ARVADOS_API_TOKEN="+tok,
 875                         "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
 876                         "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
 877                 )
 878                 runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 879         } else {
 880                 if runner.enableNetwork == "always" {
 881                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 882                 } else {
 883                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
 884                 }
 885         }
 886
 887         _, stdinUsed := runner.Container.Mounts["stdin"]
 888         runner.ContainerConfig.OpenStdin = stdinUsed
 889         runner.ContainerConfig.StdinOnce = stdinUsed
 890         runner.ContainerConfig.AttachStdin = stdinUsed
 891         runner.ContainerConfig.AttachStdout = true
 892         runner.ContainerConfig.AttachStderr = true
 893
 894         createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
 895         if err != nil {
 896                 return fmt.Errorf("While creating container: %v", err)
 897         }
 898
 899         runner.ContainerID = createdBody.ID
 900
 901         return runner.AttachStreams()
 902 }
 903
 904 // StartContainer starts the docker container created by CreateContainer.
 905 func (runner *ContainerRunner) StartContainer() error {
 906         runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
 907         runner.cStateLock.Lock()
 908         defer runner.cStateLock.Unlock()
 909         if runner.cCancelled {
 910                 return ErrCancelled
 911         }
 912         err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
 913                 dockertypes.ContainerStartOptions{})
 914         if err != nil {
 915                 var advice string
 916                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
 917                         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])
 918                 }
 919                 return fmt.Errorf("could not start container: %v%s", err, advice)
 920         }
 921         return nil
 922 }
 923
 924 // WaitFinish waits for the container to terminate, capture the exit code, and
 925 // close the stdout/stderr logging.
 926 func (runner *ContainerRunner) WaitFinish() error {
 927         runner.CrunchLog.Print("Waiting for container to finish")
 928
 929         waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning)
 930         arvMountExit := runner.ArvMountExit
 931         for {
 932                 select {
 933                 case waitBody := <-waitOk:
 934                         runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode)
 935                         code := int(waitBody.StatusCode)
 936                         runner.ExitCode = &code
 937
 938                         // wait for stdout/stderr to complete
 939                         <-runner.loggingDone
 940                         return nil
 941
 942                 case err := <-waitErr:
 943                         return fmt.Errorf("container wait: %v", err)
 944
 945                 case <-arvMountExit:
 946                         runner.CrunchLog.Printf("arv-mount exited while container is still running.  Stopping container.")
 947                         runner.stop()
 948                         // arvMountExit will always be ready now that
 949                         // it's closed, but that doesn't interest us.
 950                         arvMountExit = nil
 951                 }
 952         }
 953 }
 954
 955 var ErrNotInOutputDir = fmt.Errorf("Must point to path within the output directory")
 956
 957 func (runner *ContainerRunner) derefOutputSymlink(path string, startinfo os.FileInfo) (tgt string, readlinktgt string, info os.FileInfo, err error) {
 958         // Follow symlinks if necessary
 959         info = startinfo
 960         tgt = path
 961         readlinktgt = ""
 962         nextlink := path
 963         for followed := 0; info.Mode()&os.ModeSymlink != 0; followed++ {
 964                 if followed >= limitFollowSymlinks {
 965                         // Got stuck in a loop or just a pathological number of links, give up.
 966                         err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
 967                         return
 968                 }
 969
 970                 readlinktgt, err = os.Readlink(nextlink)
 971                 if err != nil {
 972                         return
 973                 }
 974
 975                 tgt = readlinktgt
 976                 if !strings.HasPrefix(tgt, "/") {
 977                         // Relative symlink, resolve it to host path
 978                         tgt = filepath.Join(filepath.Dir(path), tgt)
 979                 }
 980                 if strings.HasPrefix(tgt, runner.Container.OutputPath+"/") && !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
 981                         // Absolute symlink to container output path, adjust it to host output path.
 982                         tgt = filepath.Join(runner.HostOutputDir, tgt[len(runner.Container.OutputPath):])
 983                 }
 984                 if !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
 985                         // After dereferencing, symlink target must either be
 986                         // within output directory, or must point to a
 987                         // collection mount.
 988                         err = ErrNotInOutputDir
 989                         return
 990                 }
 991
 992                 info, err = os.Lstat(tgt)
 993                 if err != nil {
 994                         // tgt
 995                         err = fmt.Errorf("Symlink in output %q points to invalid location %q: %v",
 996                                 path[len(runner.HostOutputDir):], readlinktgt, err)
 997                         return
 998                 }
 999
1000                 nextlink = tgt
1001         }
1002
1003         return
1004 }
1005
1006 var limitFollowSymlinks = 10
1007
1008 // UploadFile uploads files within the output directory, with special handling
1009 // for symlinks. If the symlink leads to a keep mount, copy the manifest text
1010 // from the keep mount into the output manifestText.  Ensure that whether
1011 // symlinks are relative or absolute, every symlink target (even targets that
1012 // are symlinks themselves) must point to a path in either the output directory
1013 // or a collection mount.
1014 //
1015 // Assumes initial value of "path" is absolute, and located within runner.HostOutputDir.
1016 func (runner *ContainerRunner) UploadOutputFile(
1017         path string,
1018         info os.FileInfo,
1019         infoerr error,
1020         binds []string,
1021         walkUpload *WalkUpload,
1022         relocateFrom string,
1023         relocateTo string,
1024         followed int) (manifestText string, err error) {
1025
1026         if infoerr != nil {
1027                 return "", infoerr
1028         }
1029
1030         if info.Mode().IsDir() {
1031                 // if empty, need to create a .keep file
1032                 dir, direrr := os.Open(path)
1033                 if direrr != nil {
1034                         return "", direrr
1035                 }
1036                 defer dir.Close()
1037                 names, eof := dir.Readdirnames(1)
1038                 if len(names) == 0 && eof == io.EOF && path != runner.HostOutputDir {
1039                         containerPath := runner.OutputPath + path[len(runner.HostOutputDir):]
1040                         for _, bind := range binds {
1041                                 mnt := runner.Container.Mounts[bind]
1042                                 // Check if there is a bind for this
1043                                 // directory, in which case assume we don't need .keep
1044                                 if (containerPath == bind || strings.HasPrefix(containerPath, bind+"/")) && mnt.PortableDataHash != "d41d8cd98f00b204e9800998ecf8427e+0" {
1045                                         return
1046                                 }
1047                         }
1048                         outputSuffix := path[len(runner.HostOutputDir)+1:]
1049                         return fmt.Sprintf("./%v d41d8cd98f00b204e9800998ecf8427e+0 0:0:.keep\n", outputSuffix), nil
1050                 }
1051                 return
1052         }
1053
1054         if followed >= limitFollowSymlinks {
1055                 // Got stuck in a loop or just a pathological number of
1056                 // directory links, give up.
1057                 err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
1058                 return
1059         }
1060
1061         // "path" is the actual path we are visiting
1062         // "tgt" is the target of "path" (a non-symlink) after following symlinks
1063         // "relocated" is the path in the output manifest where the file should be placed,
1064         // but has HostOutputDir as a prefix.
1065
1066         // The destination path in the output manifest may need to be
1067         // logically relocated to some other path in order to appear
1068         // in the correct location as a result of following a symlink.
1069         // Remove the relocateFrom prefix and replace it with
1070         // relocateTo.
1071         relocated := relocateTo + path[len(relocateFrom):]
1072
1073         tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info)
1074         if derefErr != nil && derefErr != ErrNotInOutputDir {
1075                 return "", derefErr
1076         }
1077
1078         // go through mounts and try reverse map to collection reference
1079         for _, bind := range binds {
1080                 mnt := runner.Container.Mounts[bind]
1081                 if tgt == bind || strings.HasPrefix(tgt, bind+"/") {
1082                         // get path relative to bind
1083                         targetSuffix := tgt[len(bind):]
1084
1085                         // Copy mount and adjust the path to add path relative to the bind
1086                         adjustedMount := mnt
1087                         adjustedMount.Path = filepath.Join(adjustedMount.Path, targetSuffix)
1088
1089                         // Terminates in this keep mount, so add the
1090                         // manifest text at appropriate location.
1091                         outputSuffix := relocated[len(runner.HostOutputDir):]
1092                         manifestText, err = runner.getCollectionManifestForPath(adjustedMount, outputSuffix)
1093                         return
1094                 }
1095         }
1096
1097         // If target is not a collection mount, it must be located within the
1098         // output directory, otherwise it is an error.
1099         if derefErr == ErrNotInOutputDir {
1100                 err = fmt.Errorf("Symlink in output %q points to invalid location %q, must point to path within the output directory.",
1101                         path[len(runner.HostOutputDir):], readlinktgt)
1102                 return
1103         }
1104
1105         if info.Mode().IsRegular() {
1106                 return "", walkUpload.UploadFile(relocated, tgt)
1107         }
1108
1109         if info.Mode().IsDir() {
1110                 // Symlink leads to directory.  Walk() doesn't follow
1111                 // directory symlinks, so we walk the target directory
1112                 // instead.  Within the walk, file paths are relocated
1113                 // so they appear under the original symlink path.
1114                 err = filepath.Walk(tgt, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
1115                         var m string
1116                         m, walkerr = runner.UploadOutputFile(walkpath, walkinfo, walkerr,
1117                                 binds, walkUpload, tgt, relocated, followed+1)
1118                         if walkerr == nil {
1119                                 manifestText = manifestText + m
1120                         }
1121                         return walkerr
1122                 })
1123                 return
1124         }
1125
1126         return
1127 }
1128
1129 // HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
1130 func (runner *ContainerRunner) CaptureOutput() error {
1131         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
1132                 // Output may have been set directly by the container, so
1133                 // refresh the container record to check.
1134                 err := runner.ArvClient.Get("containers", runner.Container.UUID,
1135                         nil, &runner.Container)
1136                 if err != nil {
1137                         return err
1138                 }
1139                 if runner.Container.Output != "" {
1140                         // Container output is already set.
1141                         runner.OutputPDH = &runner.Container.Output
1142                         return nil
1143                 }
1144         }
1145
1146         if runner.HostOutputDir == "" {
1147                 return nil
1148         }
1149
1150         _, err := os.Stat(runner.HostOutputDir)
1151         if err != nil {
1152                 return fmt.Errorf("While checking host output path: %v", err)
1153         }
1154
1155         // Pre-populate output from the configured mount points
1156         var binds []string
1157         for bind, mnt := range runner.Container.Mounts {
1158                 if mnt.Kind == "collection" {
1159                         binds = append(binds, bind)
1160                 }
1161         }
1162         sort.Strings(binds)
1163
1164         var manifestText string
1165
1166         collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
1167         _, err = os.Stat(collectionMetafile)
1168         if err != nil {
1169                 // Regular directory
1170
1171                 cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
1172                 walkUpload := cw.BeginUpload(runner.HostOutputDir, runner.CrunchLog.Logger)
1173
1174                 var m string
1175                 err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error {
1176                         m, err = runner.UploadOutputFile(path, info, err, binds, walkUpload, "", "", 0)
1177                         if err == nil {
1178                                 manifestText = manifestText + m
1179                         }
1180                         return err
1181                 })
1182
1183                 cw.EndUpload(walkUpload)
1184
1185                 if err != nil {
1186                         return fmt.Errorf("While uploading output files: %v", err)
1187                 }
1188
1189                 m, err = cw.ManifestText()
1190                 manifestText = manifestText + m
1191                 if err != nil {
1192                         return fmt.Errorf("While uploading output files: %v", err)
1193                 }
1194         } else {
1195                 // FUSE mount directory
1196                 file, openerr := os.Open(collectionMetafile)
1197                 if openerr != nil {
1198                         return fmt.Errorf("While opening FUSE metafile: %v", err)
1199                 }
1200                 defer file.Close()
1201
1202                 var rec arvados.Collection
1203                 err = json.NewDecoder(file).Decode(&rec)
1204                 if err != nil {
1205                         return fmt.Errorf("While reading FUSE metafile: %v", err)
1206                 }
1207                 manifestText = rec.ManifestText
1208         }
1209
1210         for _, bind := range binds {
1211                 mnt := runner.Container.Mounts[bind]
1212
1213                 bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
1214
1215                 if bindSuffix == bind || len(bindSuffix) <= 0 {
1216                         // either does not start with OutputPath or is OutputPath itself
1217                         continue
1218                 }
1219
1220                 if mnt.ExcludeFromOutput == true {
1221                         continue
1222                 }
1223
1224                 // append to manifest_text
1225                 m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
1226                 if err != nil {
1227                         return err
1228                 }
1229
1230                 manifestText = manifestText + m
1231         }
1232
1233         // Save output
1234         var response arvados.Collection
1235         manifest := manifest.Manifest{Text: manifestText}
1236         manifestText = manifest.Extract(".", ".").Text
1237         err = runner.ArvClient.Create("collections",
1238                 arvadosclient.Dict{
1239                         "ensure_unique_name": true,
1240                         "collection": arvadosclient.Dict{
1241                                 "is_trashed":    true,
1242                                 "name":          "output for " + runner.Container.UUID,
1243                                 "manifest_text": manifestText}},
1244                 &response)
1245         if err != nil {
1246                 return fmt.Errorf("While creating output collection: %v", err)
1247         }
1248         runner.OutputPDH = &response.PortableDataHash
1249         return nil
1250 }
1251
1252 var outputCollections = make(map[string]arvados.Collection)
1253
1254 // Fetch the collection for the mnt.PortableDataHash
1255 // Return the manifest_text fragment corresponding to the specified mnt.Path
1256 //  after making any required updates.
1257 //  Ex:
1258 //    If mnt.Path is not specified,
1259 //      return the entire manifest_text after replacing any "." with bindSuffix
1260 //    If mnt.Path corresponds to one stream,
1261 //      return the manifest_text for that stream after replacing that stream name with bindSuffix
1262 //    Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
1263 //      for that stream after replacing stream name with bindSuffix minus the last word
1264 //      and the file name with last word of the bindSuffix
1265 //  Allowed path examples:
1266 //    "path":"/"
1267 //    "path":"/subdir1"
1268 //    "path":"/subdir1/subdir2"
1269 //    "path":"/subdir/filename" etc
1270 func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
1271         collection := outputCollections[mnt.PortableDataHash]
1272         if collection.PortableDataHash == "" {
1273                 err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
1274                 if err != nil {
1275                         return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
1276                 }
1277                 outputCollections[mnt.PortableDataHash] = collection
1278         }
1279
1280         if collection.ManifestText == "" {
1281                 runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
1282                 return "", nil
1283         }
1284
1285         mft := manifest.Manifest{Text: collection.ManifestText}
1286         extracted := mft.Extract(mnt.Path, bindSuffix)
1287         if extracted.Err != nil {
1288                 return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
1289         }
1290         return extracted.Text, nil
1291 }
1292
1293 func (runner *ContainerRunner) CleanupDirs() {
1294         if runner.ArvMount != nil {
1295                 var delay int64 = 8
1296                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1297                 umount.Stdout = runner.CrunchLog
1298                 umount.Stderr = runner.CrunchLog
1299                 runner.CrunchLog.Printf("Running %v", umount.Args)
1300                 umnterr := umount.Start()
1301
1302                 if umnterr != nil {
1303                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1304                 } else {
1305                         // If arv-mount --unmount gets stuck for any reason, we
1306                         // don't want to wait for it forever.  Do Wait() in a goroutine
1307                         // so it doesn't block crunch-run.
1308                         umountExit := make(chan error)
1309                         go func() {
1310                                 mnterr := umount.Wait()
1311                                 if mnterr != nil {
1312                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1313                                 }
1314                                 umountExit <- mnterr
1315                         }()
1316
1317                         for again := true; again; {
1318                                 again = false
1319                                 select {
1320                                 case <-umountExit:
1321                                         umount = nil
1322                                         again = true
1323                                 case <-runner.ArvMountExit:
1324                                         break
1325                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1326                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1327                                         if umount != nil {
1328                                                 umount.Process.Kill()
1329                                         }
1330                                         runner.ArvMount.Process.Kill()
1331                                 }
1332                         }
1333                 }
1334         }
1335
1336         if runner.ArvMountPoint != "" {
1337                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1338                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1339                 }
1340         }
1341
1342         for _, tmpdir := range runner.CleanupTempDir {
1343                 if rmerr := os.RemoveAll(tmpdir); rmerr != nil {
1344                         runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", tmpdir, rmerr)
1345                 }
1346         }
1347 }
1348
1349 // CommitLogs posts the collection containing the final container logs.
1350 func (runner *ContainerRunner) CommitLogs() error {
1351         runner.CrunchLog.Print(runner.finalState)
1352
1353         if runner.arvMountLog != nil {
1354                 runner.arvMountLog.Close()
1355         }
1356         runner.CrunchLog.Close()
1357
1358         // Closing CrunchLog above allows them to be committed to Keep at this
1359         // point, but re-open crunch log with ArvClient in case there are any
1360         // other further errors (such as failing to write the log to Keep!)
1361         // while shutting down
1362         runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient,
1363                 UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: nil})
1364         runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1365
1366         if runner.LogsPDH != nil {
1367                 // If we have already assigned something to LogsPDH,
1368                 // we must be closing the re-opened log, which won't
1369                 // end up getting attached to the container record and
1370                 // therefore doesn't need to be saved as a collection
1371                 // -- it exists only to send logs to other channels.
1372                 return nil
1373         }
1374
1375         mt, err := runner.LogCollection.ManifestText()
1376         if err != nil {
1377                 return fmt.Errorf("While creating log manifest: %v", err)
1378         }
1379
1380         var response arvados.Collection
1381         err = runner.ArvClient.Create("collections",
1382                 arvadosclient.Dict{
1383                         "ensure_unique_name": true,
1384                         "collection": arvadosclient.Dict{
1385                                 "is_trashed":    true,
1386                                 "name":          "logs for " + runner.Container.UUID,
1387                                 "manifest_text": mt}},
1388                 &response)
1389         if err != nil {
1390                 return fmt.Errorf("While creating log collection: %v", err)
1391         }
1392         runner.LogsPDH = &response.PortableDataHash
1393         return nil
1394 }
1395
1396 // UpdateContainerRunning updates the container state to "Running"
1397 func (runner *ContainerRunner) UpdateContainerRunning() error {
1398         runner.cStateLock.Lock()
1399         defer runner.cStateLock.Unlock()
1400         if runner.cCancelled {
1401                 return ErrCancelled
1402         }
1403         return runner.ArvClient.Update("containers", runner.Container.UUID,
1404                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
1405 }
1406
1407 // ContainerToken returns the api_token the container (and any
1408 // arv-mount processes) are allowed to use.
1409 func (runner *ContainerRunner) ContainerToken() (string, error) {
1410         if runner.token != "" {
1411                 return runner.token, nil
1412         }
1413
1414         var auth arvados.APIClientAuthorization
1415         err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1416         if err != nil {
1417                 return "", err
1418         }
1419         runner.token = auth.APIToken
1420         return runner.token, nil
1421 }
1422
1423 // UpdateContainerComplete updates the container record state on API
1424 // server to "Complete" or "Cancelled"
1425 func (runner *ContainerRunner) UpdateContainerFinal() error {
1426         update := arvadosclient.Dict{}
1427         update["state"] = runner.finalState
1428         if runner.LogsPDH != nil {
1429                 update["log"] = *runner.LogsPDH
1430         }
1431         if runner.finalState == "Complete" {
1432                 if runner.ExitCode != nil {
1433                         update["exit_code"] = *runner.ExitCode
1434                 }
1435                 if runner.OutputPDH != nil {
1436                         update["output"] = *runner.OutputPDH
1437                 }
1438         }
1439         return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1440 }
1441
1442 // IsCancelled returns the value of Cancelled, with goroutine safety.
1443 func (runner *ContainerRunner) IsCancelled() bool {
1444         runner.cStateLock.Lock()
1445         defer runner.cStateLock.Unlock()
1446         return runner.cCancelled
1447 }
1448
1449 // NewArvLogWriter creates an ArvLogWriter
1450 func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser {
1451         return &ArvLogWriter{
1452                 ArvClient:     runner.ArvClient,
1453                 UUID:          runner.Container.UUID,
1454                 loggingStream: name,
1455                 writeCloser:   runner.LogCollection.Open(name + ".txt")}
1456 }
1457
1458 // Run the full container lifecycle.
1459 func (runner *ContainerRunner) Run() (err error) {
1460         runner.CrunchLog.Printf("crunch-run %s started", version)
1461         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1462
1463         hostname, hosterr := os.Hostname()
1464         if hosterr != nil {
1465                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1466         } else {
1467                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1468         }
1469
1470         runner.finalState = "Queued"
1471
1472         defer func() {
1473                 runner.stopSignals()
1474                 runner.CleanupDirs()
1475
1476                 runner.CrunchLog.Printf("crunch-run finished")
1477                 runner.CrunchLog.Close()
1478         }()
1479
1480         defer func() {
1481                 // checkErr prints e (unless it's nil) and sets err to
1482                 // e (unless err is already non-nil). Thus, if err
1483                 // hasn't already been assigned when Run() returns,
1484                 // this cleanup func will cause Run() to return the
1485                 // first non-nil error that is passed to checkErr().
1486                 checkErr := func(e error) {
1487                         if e == nil {
1488                                 return
1489                         }
1490                         runner.CrunchLog.Print(e)
1491                         if err == nil {
1492                                 err = e
1493                         }
1494                         if runner.finalState == "Complete" {
1495                                 // There was an error in the finalization.
1496                                 runner.finalState = "Cancelled"
1497                         }
1498                 }
1499
1500                 // Log the error encountered in Run(), if any
1501                 checkErr(err)
1502
1503                 if runner.finalState == "Queued" {
1504                         runner.UpdateContainerFinal()
1505                         return
1506                 }
1507
1508                 if runner.IsCancelled() {
1509                         runner.finalState = "Cancelled"
1510                         // but don't return yet -- we still want to
1511                         // capture partial output and write logs
1512                 }
1513
1514                 checkErr(runner.CaptureOutput())
1515                 checkErr(runner.CommitLogs())
1516                 checkErr(runner.UpdateContainerFinal())
1517         }()
1518
1519         err = runner.fetchContainerRecord()
1520         if err != nil {
1521                 return
1522         }
1523
1524         // setup signal handling
1525         runner.setupSignals()
1526
1527         // check for and/or load image
1528         err = runner.LoadImage()
1529         if err != nil {
1530                 if !runner.checkBrokenNode(err) {
1531                         // Failed to load image but not due to a "broken node"
1532                         // condition, probably user error.
1533                         runner.finalState = "Cancelled"
1534                 }
1535                 err = fmt.Errorf("While loading container image: %v", err)
1536                 return
1537         }
1538
1539         // set up FUSE mount and binds
1540         err = runner.SetupMounts()
1541         if err != nil {
1542                 runner.finalState = "Cancelled"
1543                 err = fmt.Errorf("While setting up mounts: %v", err)
1544                 return
1545         }
1546
1547         err = runner.CreateContainer()
1548         if err != nil {
1549                 return
1550         }
1551         err = runner.LogHostInfo()
1552         if err != nil {
1553                 return
1554         }
1555         err = runner.LogNodeRecord()
1556         if err != nil {
1557                 return
1558         }
1559         err = runner.LogContainerRecord()
1560         if err != nil {
1561                 return
1562         }
1563
1564         if runner.IsCancelled() {
1565                 return
1566         }
1567
1568         err = runner.UpdateContainerRunning()
1569         if err != nil {
1570                 return
1571         }
1572         runner.finalState = "Cancelled"
1573
1574         runner.StartCrunchstat()
1575
1576         err = runner.StartContainer()
1577         if err != nil {
1578                 runner.checkBrokenNode(err)
1579                 return
1580         }
1581
1582         err = runner.WaitFinish()
1583         if err == nil && !runner.IsCancelled() {
1584                 runner.finalState = "Complete"
1585         }
1586         return
1587 }
1588
1589 // Fetch the current container record (uuid = runner.Container.UUID)
1590 // into runner.Container.
1591 func (runner *ContainerRunner) fetchContainerRecord() error {
1592         reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1593         if err != nil {
1594                 return fmt.Errorf("error fetching container record: %v", err)
1595         }
1596         defer reader.Close()
1597
1598         dec := json.NewDecoder(reader)
1599         dec.UseNumber()
1600         err = dec.Decode(&runner.Container)
1601         if err != nil {
1602                 return fmt.Errorf("error decoding container record: %v", err)
1603         }
1604         return nil
1605 }
1606
1607 // NewContainerRunner creates a new container runner.
1608 func NewContainerRunner(api IArvadosClient,
1609         kc IKeepClient,
1610         docker ThinDockerClient,
1611         containerUUID string) *ContainerRunner {
1612
1613         cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
1614         cr.NewLogWriter = cr.NewArvLogWriter
1615         cr.RunArvMount = cr.ArvMountCmd
1616         cr.MkTempDir = ioutil.TempDir
1617         cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
1618         cr.Container.UUID = containerUUID
1619         cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
1620         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1621
1622         loadLogThrottleParams(api)
1623
1624         return cr
1625 }
1626
1627 func main() {
1628         statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1629         cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1630         cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1631         cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1632         caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
1633         enableNetwork := flag.String("container-enable-networking", "default",
1634                 `Specify if networking should be enabled for container.  One of 'default', 'always':
1635         default: only enable networking if container requests it.
1636         always:  containers always have networking enabled
1637         `)
1638         networkMode := flag.String("container-network-mode", "default",
1639                 `Set networking mode for container.  Corresponds to Docker network mode (--net).
1640         `)
1641         memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container")
1642         getVersion := flag.Bool("version", false, "Print version information and exit.")
1643         flag.Parse()
1644
1645         // Print version information if requested
1646         if *getVersion {
1647                 fmt.Printf("crunch-run %s\n", version)
1648                 return
1649         }
1650
1651         log.Printf("crunch-run %s started", version)
1652
1653         containerId := flag.Arg(0)
1654
1655         if *caCertsPath != "" {
1656                 arvadosclient.CertFiles = []string{*caCertsPath}
1657         }
1658
1659         api, err := arvadosclient.MakeArvadosClient()
1660         if err != nil {
1661                 log.Fatalf("%s: %v", containerId, err)
1662         }
1663         api.Retries = 8
1664
1665         kc, kcerr := keepclient.MakeKeepClient(api)
1666         if kcerr != nil {
1667                 log.Fatalf("%s: %v", containerId, kcerr)
1668         }
1669         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1670         kc.Retries = 4
1671
1672         // API version 1.21 corresponds to Docker 1.9, which is currently the
1673         // minimum version we want to support.
1674         docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
1675
1676         cr := NewContainerRunner(api, kc, docker, containerId)
1677         if dockererr != nil {
1678                 cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
1679                 cr.checkBrokenNode(dockererr)
1680                 cr.CrunchLog.Close()
1681                 os.Exit(1)
1682         }
1683
1684         cr.statInterval = *statInterval
1685         cr.cgroupRoot = *cgroupRoot
1686         cr.expectCgroupParent = *cgroupParent
1687         cr.enableNetwork = *enableNetwork
1688         cr.networkMode = *networkMode
1689         if *cgroupParentSubsystem != "" {
1690                 p := findCgroup(*cgroupParentSubsystem)
1691                 cr.setCgroupParent = p
1692                 cr.expectCgroupParent = p
1693         }
1694
1695         runerr := cr.Run()
1696
1697         if *memprofile != "" {
1698                 f, err := os.Create(*memprofile)
1699                 if err != nil {
1700                         log.Printf("could not create memory profile: ", err)
1701                 }
1702                 runtime.GC() // get up-to-date statistics
1703                 if err := pprof.WriteHeapProfile(f); err != nil {
1704                         log.Printf("could not write memory profile: ", err)
1705                 }
1706                 closeerr := f.Close()
1707                 if closeerr != nil {
1708                         log.Printf("closing memprofile file: ", err)
1709                 }
1710         }
1711
1712         if runerr != nil {
1713                 log.Fatalf("%s: %v", containerId, runerr)
1714         }
1715 }