lib/crunchrun/crunchrun.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package crunchrun
   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.arvados.org/arvados.git/lib/cmd"
  31         "git.arvados.org/arvados.git/lib/crunchstat"
  32         "git.arvados.org/arvados.git/sdk/go/arvados"
  33         "git.arvados.org/arvados.git/sdk/go/arvadosclient"
  34         "git.arvados.org/arvados.git/sdk/go/keepclient"
  35         "git.arvados.org/arvados.git/sdk/go/manifest"
  36         "golang.org/x/net/context"
  37 )
  38
  39 type command struct{}
  40
  41 var Command = command{}
  42
  43 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  44 type IArvadosClient interface {
  45         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  46         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  47         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  48         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  49         CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
  50         Discovery(key string) (interface{}, error)
  51 }
  52
  53 // ErrCancelled is the error returned when the container is cancelled.
  54 var ErrCancelled = errors.New("Cancelled")
  55
  56 // IKeepClient is the minimal Keep API methods used by crunch-run.
  57 type IKeepClient interface {
  58         PutB(buf []byte) (string, int, error)
  59         ReadAt(locator string, p []byte, off int) (int, error)
  60         ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
  61         LocalLocator(locator string) (string, 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, error)
  67
  68 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  69
  70 type MkTempDir func(string, string) (string, error)
  71
  72 type PsProcess interface {
  73         CmdlineSlice() ([]string, error)
  74 }
  75
  76 // ContainerRunner is the main stateful struct used for a single execution of a
  77 // container.
  78 type ContainerRunner struct {
  79         executor containerExecutor
  80
  81         // Dispatcher client is initialized with the Dispatcher token.
  82         // This is a privileged token used to manage container status
  83         // and logs.
  84         //
  85         // We have both dispatcherClient and DispatcherArvClient
  86         // because there are two different incompatible Arvados Go
  87         // SDKs and we have to use both (hopefully this gets fixed in
  88         // #14467)
  89         dispatcherClient     *arvados.Client
  90         DispatcherArvClient  IArvadosClient
  91         DispatcherKeepClient IKeepClient
  92
  93         // Container client is initialized with the Container token
  94         // This token controls the permissions of the container, and
  95         // must be used for operations such as reading collections.
  96         //
  97         // Same comment as above applies to
  98         // containerClient/ContainerArvClient.
  99         containerClient     *arvados.Client
 100         ContainerArvClient  IArvadosClient
 101         ContainerKeepClient IKeepClient
 102
 103         Container     arvados.Container
 104         token         string
 105         ExitCode      *int
 106         NewLogWriter  NewLogWriter
 107         CrunchLog     *ThrottledLogger
 108         Stdout        io.WriteCloser
 109         Stderr        io.WriteCloser
 110         logUUID       string
 111         logMtx        sync.Mutex
 112         LogCollection arvados.CollectionFileSystem
 113         LogsPDH       *string
 114         RunArvMount   RunArvMount
 115         MkTempDir     MkTempDir
 116         ArvMount      *exec.Cmd
 117         ArvMountPoint string
 118         HostOutputDir string
 119         Volumes       map[string]struct{}
 120         OutputPDH     *string
 121         SigChan       chan os.Signal
 122         ArvMountExit  chan error
 123         SecretMounts  map[string]arvados.Mount
 124         MkArvClient   func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
 125         finalState    string
 126         parentTemp    string
 127
 128         statLogger       io.WriteCloser
 129         statReporter     *crunchstat.Reporter
 130         hoststatLogger   io.WriteCloser
 131         hoststatReporter *crunchstat.Reporter
 132         statInterval     time.Duration
 133         cgroupRoot       string
 134         // What we expect the container's cgroup parent to be.
 135         expectCgroupParent string
 136         // What we tell docker to use as the container's cgroup
 137         // parent. Note: Ideally we would use the same field for both
 138         // expectCgroupParent and setCgroupParent, and just make it
 139         // default to "docker". However, when using docker < 1.10 with
 140         // systemd, specifying a non-empty cgroup parent (even the
 141         // default value "docker") hits a docker bug
 142         // (https://github.com/docker/docker/issues/17126). Using two
 143         // separate fields makes it possible to use the "expect cgroup
 144         // parent to be X" feature even on sites where the "specify
 145         // cgroup parent" feature breaks.
 146         setCgroupParent string
 147
 148         cStateLock sync.Mutex
 149         cCancelled bool // StopContainer() invoked
 150
 151         enableNetwork string // one of "default" or "always"
 152         networkMode   string // "none", "host", or "" -- passed through to executor
 153         arvMountLog   *ThrottledLogger
 154
 155         containerWatchdogInterval time.Duration
 156
 157         gateway Gateway
 158 }
 159
 160 // setupSignals sets up signal handling to gracefully terminate the
 161 // underlying container and update state when receiving a TERM, INT or
 162 // QUIT signal.
 163 func (runner *ContainerRunner) setupSignals() {
 164         runner.SigChan = make(chan os.Signal, 1)
 165         signal.Notify(runner.SigChan, syscall.SIGTERM)
 166         signal.Notify(runner.SigChan, syscall.SIGINT)
 167         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 168
 169         go func(sig chan os.Signal) {
 170                 for s := range sig {
 171                         runner.stop(s)
 172                 }
 173         }(runner.SigChan)
 174 }
 175
 176 // stop the underlying container.
 177 func (runner *ContainerRunner) stop(sig os.Signal) {
 178         runner.cStateLock.Lock()
 179         defer runner.cStateLock.Unlock()
 180         if sig != nil {
 181                 runner.CrunchLog.Printf("caught signal: %v", sig)
 182         }
 183         runner.cCancelled = true
 184         runner.CrunchLog.Printf("stopping container")
 185         err := runner.executor.Stop()
 186         if err != nil {
 187                 runner.CrunchLog.Printf("error stopping container: %s", err)
 188         }
 189 }
 190
 191 var errorBlacklist = []string{
 192         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 193         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 194         "(?ms).*grpc: the connection is unavailable.*",
 195 }
 196 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)")
 197
 198 func (runner *ContainerRunner) runBrokenNodeHook() {
 199         if *brokenNodeHook == "" {
 200                 path := filepath.Join(lockdir, brokenfile)
 201                 runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
 202                 f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
 203                 if err != nil {
 204                         runner.CrunchLog.Printf("Error writing %s: %s", path, err)
 205                         return
 206                 }
 207                 f.Close()
 208         } else {
 209                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 210                 // run killme script
 211                 c := exec.Command(*brokenNodeHook)
 212                 c.Stdout = runner.CrunchLog
 213                 c.Stderr = runner.CrunchLog
 214                 err := c.Run()
 215                 if err != nil {
 216                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 217                 }
 218         }
 219 }
 220
 221 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 222         for _, d := range errorBlacklist {
 223                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 224                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 225                         runner.runBrokenNodeHook()
 226                         return true
 227                 }
 228         }
 229         return false
 230 }
 231
 232 // LoadImage determines the docker image id from the container record and
 233 // checks if it is available in the local Docker image store.  If not, it loads
 234 // the image from Keep.
 235 func (runner *ContainerRunner) LoadImage() (string, error) {
 236         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 237
 238         d, err := os.Open(runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage)
 239         if err != nil {
 240                 return "", err
 241         }
 242         defer d.Close()
 243         allfiles, err := d.Readdirnames(-1)
 244         if err != nil {
 245                 return "", err
 246         }
 247         var tarfiles []string
 248         for _, fnm := range allfiles {
 249                 if strings.HasSuffix(fnm, ".tar") {
 250                         tarfiles = append(tarfiles, fnm)
 251                 }
 252         }
 253         if len(tarfiles) == 0 {
 254                 return "", fmt.Errorf("image collection does not include a .tar image file")
 255         }
 256         if len(tarfiles) > 1 {
 257                 return "", fmt.Errorf("cannot choose from multiple tar files in image collection: %v", tarfiles)
 258         }
 259         imageID := tarfiles[0][:len(tarfiles[0])-4]
 260         imageFile := runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage + "/" + tarfiles[0]
 261         runner.CrunchLog.Printf("Using Docker image id %q", imageID)
 262
 263         if !runner.executor.ImageLoaded(imageID) {
 264                 runner.CrunchLog.Print("Loading Docker image from keep")
 265                 err = runner.executor.LoadImage(imageFile)
 266                 if err != nil {
 267                         return "", err
 268                 }
 269         } else {
 270                 runner.CrunchLog.Print("Docker image is available")
 271         }
 272         return imageID, nil
 273 }
 274
 275 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 276         c = exec.Command("arv-mount", arvMountCmd...)
 277
 278         // Copy our environment, but override ARVADOS_API_TOKEN with
 279         // the container auth token.
 280         c.Env = nil
 281         for _, s := range os.Environ() {
 282                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 283                         c.Env = append(c.Env, s)
 284                 }
 285         }
 286         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 287
 288         w, err := runner.NewLogWriter("arv-mount")
 289         if err != nil {
 290                 return nil, err
 291         }
 292         runner.arvMountLog = NewThrottledLogger(w)
 293         c.Stdout = runner.arvMountLog
 294         c.Stderr = runner.arvMountLog
 295
 296         runner.CrunchLog.Printf("Running %v", c.Args)
 297
 298         err = c.Start()
 299         if err != nil {
 300                 return nil, err
 301         }
 302
 303         statReadme := make(chan bool)
 304         runner.ArvMountExit = make(chan error)
 305
 306         keepStatting := true
 307         go func() {
 308                 for keepStatting {
 309                         time.Sleep(100 * time.Millisecond)
 310                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 311                         if err == nil {
 312                                 keepStatting = false
 313                                 statReadme <- true
 314                         }
 315                 }
 316                 close(statReadme)
 317         }()
 318
 319         go func() {
 320                 mnterr := c.Wait()
 321                 if mnterr != nil {
 322                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 323                 }
 324                 runner.ArvMountExit <- mnterr
 325                 close(runner.ArvMountExit)
 326         }()
 327
 328         select {
 329         case <-statReadme:
 330                 break
 331         case err := <-runner.ArvMountExit:
 332                 runner.ArvMount = nil
 333                 keepStatting = false
 334                 return nil, err
 335         }
 336
 337         return c, nil
 338 }
 339
 340 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 341         if runner.ArvMountPoint == "" {
 342                 runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
 343         }
 344         return
 345 }
 346
 347 func copyfile(src string, dst string) (err error) {
 348         srcfile, err := os.Open(src)
 349         if err != nil {
 350                 return
 351         }
 352
 353         os.MkdirAll(path.Dir(dst), 0777)
 354
 355         dstfile, err := os.Create(dst)
 356         if err != nil {
 357                 return
 358         }
 359         _, err = io.Copy(dstfile, srcfile)
 360         if err != nil {
 361                 return
 362         }
 363
 364         err = srcfile.Close()
 365         err2 := dstfile.Close()
 366
 367         if err != nil {
 368                 return
 369         }
 370
 371         if err2 != nil {
 372                 return err2
 373         }
 374
 375         return nil
 376 }
 377
 378 func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
 379         bindmounts := map[string]bindmount{}
 380         err := runner.SetupArvMountPoint("keep")
 381         if err != nil {
 382                 return nil, fmt.Errorf("While creating keep mount temp dir: %v", err)
 383         }
 384
 385         token, err := runner.ContainerToken()
 386         if err != nil {
 387                 return nil, fmt.Errorf("could not get container token: %s", err)
 388         }
 389
 390         pdhOnly := true
 391         tmpcount := 0
 392         arvMountCmd := []string{
 393                 "--foreground",
 394                 "--allow-other",
 395                 "--read-write",
 396                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 397
 398         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 399                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 400         }
 401
 402         collectionPaths := []string{}
 403         needCertMount := true
 404         type copyFile struct {
 405                 src  string
 406                 bind string
 407         }
 408         var copyFiles []copyFile
 409
 410         var binds []string
 411         for bind := range runner.Container.Mounts {
 412                 binds = append(binds, bind)
 413         }
 414         for bind := range runner.SecretMounts {
 415                 if _, ok := runner.Container.Mounts[bind]; ok {
 416                         return nil, fmt.Errorf("secret mount %q conflicts with regular mount", bind)
 417                 }
 418                 if runner.SecretMounts[bind].Kind != "json" &&
 419                         runner.SecretMounts[bind].Kind != "text" {
 420                         return nil, fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
 421                                 bind, runner.SecretMounts[bind].Kind)
 422                 }
 423                 binds = append(binds, bind)
 424         }
 425         sort.Strings(binds)
 426
 427         for _, bind := range binds {
 428                 mnt, ok := runner.Container.Mounts[bind]
 429                 if !ok {
 430                         mnt = runner.SecretMounts[bind]
 431                 }
 432                 if bind == "stdout" || bind == "stderr" {
 433                         // Is it a "file" mount kind?
 434                         if mnt.Kind != "file" {
 435                                 return nil, fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
 436                         }
 437
 438                         // Does path start with OutputPath?
 439                         prefix := runner.Container.OutputPath
 440                         if !strings.HasSuffix(prefix, "/") {
 441                                 prefix += "/"
 442                         }
 443                         if !strings.HasPrefix(mnt.Path, prefix) {
 444                                 return nil, fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 445                         }
 446                 }
 447
 448                 if bind == "stdin" {
 449                         // Is it a "collection" mount kind?
 450                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 451                                 return nil, fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
 452                         }
 453                 }
 454
 455                 if bind == "/etc/arvados/ca-certificates.crt" {
 456                         needCertMount = false
 457                 }
 458
 459                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 460                         if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
 461                                 return nil, fmt.Errorf("only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
 462                         }
 463                 }
 464
 465                 switch {
 466                 case mnt.Kind == "collection" && bind != "stdin":
 467                         var src string
 468                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 469                                 return nil, fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 470                         }
 471                         if mnt.UUID != "" {
 472                                 if mnt.Writable {
 473                                         return nil, fmt.Errorf("writing to existing collections currently not permitted")
 474                                 }
 475                                 pdhOnly = false
 476                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 477                         } else if mnt.PortableDataHash != "" {
 478                                 if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 479                                         return nil, fmt.Errorf("can never write to a collection specified by portable data hash")
 480                                 }
 481                                 idx := strings.Index(mnt.PortableDataHash, "/")
 482                                 if idx > 0 {
 483                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 484                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 485                                         runner.Container.Mounts[bind] = mnt
 486                                 }
 487                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 488                                 if mnt.Path != "" && mnt.Path != "." {
 489                                         if strings.HasPrefix(mnt.Path, "./") {
 490                                                 mnt.Path = mnt.Path[2:]
 491                                         } else if strings.HasPrefix(mnt.Path, "/") {
 492                                                 mnt.Path = mnt.Path[1:]
 493                                         }
 494                                         src += "/" + mnt.Path
 495                                 }
 496                         } else {
 497                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 498                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 499                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 500                                 tmpcount++
 501                         }
 502                         if mnt.Writable {
 503                                 if bind == runner.Container.OutputPath {
 504                                         runner.HostOutputDir = src
 505                                         bindmounts[bind] = bindmount{HostPath: src}
 506                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 507                                         copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 508                                 } else {
 509                                         bindmounts[bind] = bindmount{HostPath: src}
 510                                 }
 511                         } else {
 512                                 bindmounts[bind] = bindmount{HostPath: src, ReadOnly: true}
 513                         }
 514                         collectionPaths = append(collectionPaths, src)
 515
 516                 case mnt.Kind == "tmp":
 517                         var tmpdir string
 518                         tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
 519                         if err != nil {
 520                                 return nil, fmt.Errorf("while creating mount temp dir: %v", err)
 521                         }
 522                         st, staterr := os.Stat(tmpdir)
 523                         if staterr != nil {
 524                                 return nil, fmt.Errorf("while Stat on temp dir: %v", staterr)
 525                         }
 526                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 527                         if staterr != nil {
 528                                 return nil, fmt.Errorf("while Chmod temp dir: %v", err)
 529                         }
 530                         bindmounts[bind] = bindmount{HostPath: tmpdir}
 531                         if bind == runner.Container.OutputPath {
 532                                 runner.HostOutputDir = tmpdir
 533                         }
 534
 535                 case mnt.Kind == "json" || mnt.Kind == "text":
 536                         var filedata []byte
 537                         if mnt.Kind == "json" {
 538                                 filedata, err = json.Marshal(mnt.Content)
 539                                 if err != nil {
 540                                         return nil, fmt.Errorf("encoding json data: %v", err)
 541                                 }
 542                         } else {
 543                                 text, ok := mnt.Content.(string)
 544                                 if !ok {
 545                                         return nil, fmt.Errorf("content for mount %q must be a string", bind)
 546                                 }
 547                                 filedata = []byte(text)
 548                         }
 549
 550                         tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
 551                         if err != nil {
 552                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 553                         }
 554                         tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
 555                         err = ioutil.WriteFile(tmpfn, filedata, 0444)
 556                         if err != nil {
 557                                 return nil, fmt.Errorf("writing temp file: %v", err)
 558                         }
 559                         if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 560                                 copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 561                         } else {
 562                                 bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
 563                         }
 564
 565                 case mnt.Kind == "git_tree":
 566                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
 567                         if err != nil {
 568                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 569                         }
 570                         err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
 571                         if err != nil {
 572                                 return nil, err
 573                         }
 574                         bindmounts[bind] = bindmount{HostPath: tmpdir, ReadOnly: true}
 575                 }
 576         }
 577
 578         if runner.HostOutputDir == "" {
 579                 return nil, fmt.Errorf("output path does not correspond to a writable mount point")
 580         }
 581
 582         if needCertMount && runner.Container.RuntimeConstraints.API {
 583                 for _, certfile := range arvadosclient.CertFiles {
 584                         _, err := os.Stat(certfile)
 585                         if err == nil {
 586                                 bindmounts["/etc/arvados/ca-certificates.crt"] = bindmount{HostPath: certfile, ReadOnly: true}
 587                                 break
 588                         }
 589                 }
 590         }
 591
 592         if pdhOnly {
 593                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 594         } else {
 595                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 596         }
 597         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 598
 599         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 600         if err != nil {
 601                 return nil, fmt.Errorf("while trying to start arv-mount: %v", err)
 602         }
 603
 604         for _, p := range collectionPaths {
 605                 _, err = os.Stat(p)
 606                 if err != nil {
 607                         return nil, fmt.Errorf("while checking that input files exist: %v", err)
 608                 }
 609         }
 610
 611         for _, cp := range copyFiles {
 612                 st, err := os.Stat(cp.src)
 613                 if err != nil {
 614                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 615                 }
 616                 if st.IsDir() {
 617                         err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
 618                                 if walkerr != nil {
 619                                         return walkerr
 620                                 }
 621                                 target := path.Join(cp.bind, walkpath[len(cp.src):])
 622                                 if walkinfo.Mode().IsRegular() {
 623                                         copyerr := copyfile(walkpath, target)
 624                                         if copyerr != nil {
 625                                                 return copyerr
 626                                         }
 627                                         return os.Chmod(target, walkinfo.Mode()|0777)
 628                                 } else if walkinfo.Mode().IsDir() {
 629                                         mkerr := os.MkdirAll(target, 0777)
 630                                         if mkerr != nil {
 631                                                 return mkerr
 632                                         }
 633                                         return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 634                                 } else {
 635                                         return fmt.Errorf("source %q is not a regular file or directory", cp.src)
 636                                 }
 637                         })
 638                 } else if st.Mode().IsRegular() {
 639                         err = copyfile(cp.src, cp.bind)
 640                         if err == nil {
 641                                 err = os.Chmod(cp.bind, st.Mode()|0777)
 642                         }
 643                 }
 644                 if err != nil {
 645                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 646                 }
 647         }
 648
 649         return bindmounts, nil
 650 }
 651
 652 func (runner *ContainerRunner) stopHoststat() error {
 653         if runner.hoststatReporter == nil {
 654                 return nil
 655         }
 656         runner.hoststatReporter.Stop()
 657         err := runner.hoststatLogger.Close()
 658         if err != nil {
 659                 return fmt.Errorf("error closing hoststat logs: %v", err)
 660         }
 661         return nil
 662 }
 663
 664 func (runner *ContainerRunner) startHoststat() error {
 665         w, err := runner.NewLogWriter("hoststat")
 666         if err != nil {
 667                 return err
 668         }
 669         runner.hoststatLogger = NewThrottledLogger(w)
 670         runner.hoststatReporter = &crunchstat.Reporter{
 671                 Logger:     log.New(runner.hoststatLogger, "", 0),
 672                 CgroupRoot: runner.cgroupRoot,
 673                 PollPeriod: runner.statInterval,
 674         }
 675         runner.hoststatReporter.Start()
 676         return nil
 677 }
 678
 679 func (runner *ContainerRunner) startCrunchstat() error {
 680         w, err := runner.NewLogWriter("crunchstat")
 681         if err != nil {
 682                 return err
 683         }
 684         runner.statLogger = NewThrottledLogger(w)
 685         runner.statReporter = &crunchstat.Reporter{
 686                 CID:          runner.executor.CgroupID(),
 687                 Logger:       log.New(runner.statLogger, "", 0),
 688                 CgroupParent: runner.expectCgroupParent,
 689                 CgroupRoot:   runner.cgroupRoot,
 690                 PollPeriod:   runner.statInterval,
 691                 TempDir:      runner.parentTemp,
 692         }
 693         runner.statReporter.Start()
 694         return nil
 695 }
 696
 697 type infoCommand struct {
 698         label string
 699         cmd   []string
 700 }
 701
 702 // LogHostInfo logs info about the current host, for debugging and
 703 // accounting purposes. Although it's logged as "node-info", this is
 704 // about the environment where crunch-run is actually running, which
 705 // might differ from what's described in the node record (see
 706 // LogNodeRecord).
 707 func (runner *ContainerRunner) LogHostInfo() (err error) {
 708         w, err := runner.NewLogWriter("node-info")
 709         if err != nil {
 710                 return
 711         }
 712
 713         commands := []infoCommand{
 714                 {
 715                         label: "Host Information",
 716                         cmd:   []string{"uname", "-a"},
 717                 },
 718                 {
 719                         label: "CPU Information",
 720                         cmd:   []string{"cat", "/proc/cpuinfo"},
 721                 },
 722                 {
 723                         label: "Memory Information",
 724                         cmd:   []string{"cat", "/proc/meminfo"},
 725                 },
 726                 {
 727                         label: "Disk Space",
 728                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 729                 },
 730                 {
 731                         label: "Disk INodes",
 732                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 733                 },
 734         }
 735
 736         // Run commands with informational output to be logged.
 737         for _, command := range commands {
 738                 fmt.Fprintln(w, command.label)
 739                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 740                 cmd.Stdout = w
 741                 cmd.Stderr = w
 742                 if err := cmd.Run(); err != nil {
 743                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 744                         fmt.Fprintln(w, err)
 745                         return err
 746                 }
 747                 fmt.Fprintln(w, "")
 748         }
 749
 750         err = w.Close()
 751         if err != nil {
 752                 return fmt.Errorf("While closing node-info logs: %v", err)
 753         }
 754         return nil
 755 }
 756
 757 // LogContainerRecord gets and saves the raw JSON container record from the API server
 758 func (runner *ContainerRunner) LogContainerRecord() error {
 759         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 760         if !logged && err == nil {
 761                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 762         }
 763         return err
 764 }
 765
 766 // LogNodeRecord logs the current host's InstanceType config entry (or
 767 // the arvados#node record, if running via crunch-dispatch-slurm).
 768 func (runner *ContainerRunner) LogNodeRecord() error {
 769         if it := os.Getenv("InstanceType"); it != "" {
 770                 // Dispatched via arvados-dispatch-cloud. Save
 771                 // InstanceType config fragment received from
 772                 // dispatcher on stdin.
 773                 w, err := runner.LogCollection.OpenFile("node.json", os.O_CREATE|os.O_WRONLY, 0666)
 774                 if err != nil {
 775                         return err
 776                 }
 777                 defer w.Close()
 778                 _, err = io.WriteString(w, it)
 779                 if err != nil {
 780                         return err
 781                 }
 782                 return w.Close()
 783         }
 784         // Dispatched via crunch-dispatch-slurm. Look up
 785         // apiserver's node record corresponding to
 786         // $SLURMD_NODENAME.
 787         hostname := os.Getenv("SLURMD_NODENAME")
 788         if hostname == "" {
 789                 hostname, _ = os.Hostname()
 790         }
 791         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 792                 // The "info" field has admin-only info when
 793                 // obtained with a privileged token, and
 794                 // should not be logged.
 795                 node, ok := resp.(map[string]interface{})
 796                 if ok {
 797                         delete(node, "info")
 798                 }
 799         })
 800         return err
 801 }
 802
 803 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 804         writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
 805         if err != nil {
 806                 return false, err
 807         }
 808         w := &ArvLogWriter{
 809                 ArvClient:     runner.DispatcherArvClient,
 810                 UUID:          runner.Container.UUID,
 811                 loggingStream: label,
 812                 writeCloser:   writer,
 813         }
 814
 815         reader, err := runner.DispatcherArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 816         if err != nil {
 817                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 818         }
 819         defer reader.Close()
 820
 821         dec := json.NewDecoder(reader)
 822         dec.UseNumber()
 823         var resp map[string]interface{}
 824         if err = dec.Decode(&resp); err != nil {
 825                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 826         }
 827         items, ok := resp["items"].([]interface{})
 828         if !ok {
 829                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 830         } else if len(items) < 1 {
 831                 return false, nil
 832         }
 833         if munge != nil {
 834                 munge(items[0])
 835         }
 836         // Re-encode it using indentation to improve readability
 837         enc := json.NewEncoder(w)
 838         enc.SetIndent("", "    ")
 839         if err = enc.Encode(items[0]); err != nil {
 840                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 841         }
 842         err = w.Close()
 843         if err != nil {
 844                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 845         }
 846         return true, nil
 847 }
 848
 849 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 850         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 851         index := strings.LastIndex(stdoutPath, "/")
 852         if index > 0 {
 853                 subdirs := stdoutPath[:index]
 854                 if subdirs != "" {
 855                         st, err := os.Stat(runner.HostOutputDir)
 856                         if err != nil {
 857                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 858                         }
 859                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 860                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 861                         if err != nil {
 862                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 863                         }
 864                 }
 865         }
 866         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 867         if err != nil {
 868                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 869         }
 870
 871         return stdoutFile, nil
 872 }
 873
 874 // CreateContainer creates the docker container.
 875 func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[string]bindmount) error {
 876         var stdin io.ReadCloser
 877         if mnt, ok := runner.Container.Mounts["stdin"]; ok {
 878                 switch mnt.Kind {
 879                 case "collection":
 880                         var collID string
 881                         if mnt.UUID != "" {
 882                                 collID = mnt.UUID
 883                         } else {
 884                                 collID = mnt.PortableDataHash
 885                         }
 886                         path := runner.ArvMountPoint + "/by_id/" + collID + "/" + mnt.Path
 887                         f, err := os.Open(path)
 888                         if err != nil {
 889                                 return err
 890                         }
 891                         stdin = f
 892                 case "json":
 893                         j, err := json.Marshal(mnt.Content)
 894                         if err != nil {
 895                                 return fmt.Errorf("error encoding stdin json data: %v", err)
 896                         }
 897                         stdin = ioutil.NopCloser(bytes.NewReader(j))
 898                 default:
 899                         return fmt.Errorf("stdin mount has unsupported kind %q", mnt.Kind)
 900                 }
 901         }
 902
 903         var stdout, stderr io.WriteCloser
 904         if mnt, ok := runner.Container.Mounts["stdout"]; ok {
 905                 f, err := runner.getStdoutFile(mnt.Path)
 906                 if err != nil {
 907                         return err
 908                 }
 909                 stdout = f
 910         } else if w, err := runner.NewLogWriter("stdout"); err != nil {
 911                 return err
 912         } else {
 913                 stdout = NewThrottledLogger(w)
 914         }
 915
 916         if mnt, ok := runner.Container.Mounts["stderr"]; ok {
 917                 f, err := runner.getStdoutFile(mnt.Path)
 918                 if err != nil {
 919                         return err
 920                 }
 921                 stderr = f
 922         } else if w, err := runner.NewLogWriter("stderr"); err != nil {
 923                 return err
 924         } else {
 925                 stderr = NewThrottledLogger(w)
 926         }
 927
 928         env := runner.Container.Environment
 929         enableNetwork := runner.enableNetwork == "always"
 930         if runner.Container.RuntimeConstraints.API {
 931                 enableNetwork = true
 932                 tok, err := runner.ContainerToken()
 933                 if err != nil {
 934                         return err
 935                 }
 936                 env = map[string]string{}
 937                 for k, v := range runner.Container.Environment {
 938                         env[k] = v
 939                 }
 940                 env["ARVADOS_API_TOKEN"] = tok
 941                 env["ARVADOS_API_HOST"] = os.Getenv("ARVADOS_API_HOST")
 942                 env["ARVADOS_API_HOST_INSECURE"] = os.Getenv("ARVADOS_API_HOST_INSECURE")
 943         }
 944         workdir := runner.Container.Cwd
 945         if workdir == "." {
 946                 // both "" and "." mean default
 947                 workdir = ""
 948         }
 949
 950         return runner.executor.Create(containerSpec{
 951                 Image:         imageID,
 952                 VCPUs:         runner.Container.RuntimeConstraints.VCPUs,
 953                 RAM:           runner.Container.RuntimeConstraints.RAM,
 954                 WorkingDir:    workdir,
 955                 Env:           env,
 956                 BindMounts:    bindmounts,
 957                 Command:       runner.Container.Command,
 958                 EnableNetwork: enableNetwork,
 959                 NetworkMode:   runner.networkMode,
 960                 CgroupParent:  runner.setCgroupParent,
 961                 Stdin:         stdin,
 962                 Stdout:        stdout,
 963                 Stderr:        stderr,
 964         })
 965 }
 966
 967 // StartContainer starts the docker container created by CreateContainer.
 968 func (runner *ContainerRunner) StartContainer() error {
 969         runner.CrunchLog.Printf("Starting container")
 970         runner.cStateLock.Lock()
 971         defer runner.cStateLock.Unlock()
 972         if runner.cCancelled {
 973                 return ErrCancelled
 974         }
 975         err := runner.executor.Start()
 976         if err != nil {
 977                 var advice string
 978                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
 979                         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])
 980                 }
 981                 return fmt.Errorf("could not start container: %v%s", err, advice)
 982         }
 983         return nil
 984 }
 985
 986 // WaitFinish waits for the container to terminate, capture the exit code, and
 987 // close the stdout/stderr logging.
 988 func (runner *ContainerRunner) WaitFinish() error {
 989         runner.CrunchLog.Print("Waiting for container to finish")
 990         var timeout <-chan time.Time
 991         if s := runner.Container.SchedulingParameters.MaxRunTime; s > 0 {
 992                 timeout = time.After(time.Duration(s) * time.Second)
 993         }
 994         ctx, cancel := context.WithCancel(context.Background())
 995         defer cancel()
 996         go func() {
 997                 select {
 998                 case <-timeout:
 999                         runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
1000                         runner.stop(nil)
1001                 case <-runner.ArvMountExit:
1002                         runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
1003                         runner.stop(nil)
1004                 case <-ctx.Done():
1005                 }
1006         }()
1007         exitcode, err := runner.executor.Wait(ctx)
1008         if err != nil {
1009                 runner.checkBrokenNode(err)
1010                 return err
1011         }
1012         runner.ExitCode = &exitcode
1013
1014         if runner.statReporter != nil {
1015                 runner.statReporter.Stop()
1016                 err = runner.statLogger.Close()
1017                 if err != nil {
1018                         runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
1019                 }
1020         }
1021         return nil
1022 }
1023
1024 func (runner *ContainerRunner) updateLogs() {
1025         ticker := time.NewTicker(crunchLogUpdatePeriod / 360)
1026         defer ticker.Stop()
1027
1028         sigusr1 := make(chan os.Signal, 1)
1029         signal.Notify(sigusr1, syscall.SIGUSR1)
1030         defer signal.Stop(sigusr1)
1031
1032         saveAtTime := time.Now().Add(crunchLogUpdatePeriod)
1033         saveAtSize := crunchLogUpdateSize
1034         var savedSize int64
1035         for {
1036                 select {
1037                 case <-ticker.C:
1038                 case <-sigusr1:
1039                         saveAtTime = time.Now()
1040                 }
1041                 runner.logMtx.Lock()
1042                 done := runner.LogsPDH != nil
1043                 runner.logMtx.Unlock()
1044                 if done {
1045                         return
1046                 }
1047                 size := runner.LogCollection.Size()
1048                 if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) {
1049                         continue
1050                 }
1051                 saveAtTime = time.Now().Add(crunchLogUpdatePeriod)
1052                 saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize
1053                 saved, err := runner.saveLogCollection(false)
1054                 if err != nil {
1055                         runner.CrunchLog.Printf("error updating log collection: %s", err)
1056                         continue
1057                 }
1058
1059                 var updated arvados.Container
1060                 err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
1061                         "container": arvadosclient.Dict{"log": saved.PortableDataHash},
1062                 }, &updated)
1063                 if err != nil {
1064                         runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
1065                         continue
1066                 }
1067
1068                 savedSize = size
1069         }
1070 }
1071
1072 // CaptureOutput saves data from the container's output directory if
1073 // needed, and updates the container output accordingly.
1074 func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) error {
1075         if runner.Container.RuntimeConstraints.API {
1076                 // Output may have been set directly by the container, so
1077                 // refresh the container record to check.
1078                 err := runner.DispatcherArvClient.Get("containers", runner.Container.UUID,
1079                         nil, &runner.Container)
1080                 if err != nil {
1081                         return err
1082                 }
1083                 if runner.Container.Output != "" {
1084                         // Container output is already set.
1085                         runner.OutputPDH = &runner.Container.Output
1086                         return nil
1087                 }
1088         }
1089
1090         txt, err := (&copier{
1091                 client:        runner.containerClient,
1092                 arvClient:     runner.ContainerArvClient,
1093                 keepClient:    runner.ContainerKeepClient,
1094                 hostOutputDir: runner.HostOutputDir,
1095                 ctrOutputDir:  runner.Container.OutputPath,
1096                 bindmounts:    bindmounts,
1097                 mounts:        runner.Container.Mounts,
1098                 secretMounts:  runner.SecretMounts,
1099                 logger:        runner.CrunchLog,
1100         }).Copy()
1101         if err != nil {
1102                 return err
1103         }
1104         if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 {
1105                 runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n)
1106                 fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.containerClient, runner.ContainerKeepClient)
1107                 if err != nil {
1108                         return err
1109                 }
1110                 txt, err = fs.MarshalManifest(".")
1111                 if err != nil {
1112                         return err
1113                 }
1114         }
1115         var resp arvados.Collection
1116         err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
1117                 "ensure_unique_name": true,
1118                 "collection": arvadosclient.Dict{
1119                         "is_trashed":    true,
1120                         "name":          "output for " + runner.Container.UUID,
1121                         "manifest_text": txt,
1122                 },
1123         }, &resp)
1124         if err != nil {
1125                 return fmt.Errorf("error creating output collection: %v", err)
1126         }
1127         runner.OutputPDH = &resp.PortableDataHash
1128         return nil
1129 }
1130
1131 func (runner *ContainerRunner) CleanupDirs() {
1132         if runner.ArvMount != nil {
1133                 var delay int64 = 8
1134                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1135                 umount.Stdout = runner.CrunchLog
1136                 umount.Stderr = runner.CrunchLog
1137                 runner.CrunchLog.Printf("Running %v", umount.Args)
1138                 umnterr := umount.Start()
1139
1140                 if umnterr != nil {
1141                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1142                 } else {
1143                         // If arv-mount --unmount gets stuck for any reason, we
1144                         // don't want to wait for it forever.  Do Wait() in a goroutine
1145                         // so it doesn't block crunch-run.
1146                         umountExit := make(chan error)
1147                         go func() {
1148                                 mnterr := umount.Wait()
1149                                 if mnterr != nil {
1150                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1151                                 }
1152                                 umountExit <- mnterr
1153                         }()
1154
1155                         for again := true; again; {
1156                                 again = false
1157                                 select {
1158                                 case <-umountExit:
1159                                         umount = nil
1160                                         again = true
1161                                 case <-runner.ArvMountExit:
1162                                         break
1163                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1164                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1165                                         if umount != nil {
1166                                                 umount.Process.Kill()
1167                                         }
1168                                         runner.ArvMount.Process.Kill()
1169                                 }
1170                         }
1171                 }
1172         }
1173
1174         if runner.ArvMountPoint != "" {
1175                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1176                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1177                 }
1178         }
1179
1180         if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
1181                 runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
1182         }
1183 }
1184
1185 // CommitLogs posts the collection containing the final container logs.
1186 func (runner *ContainerRunner) CommitLogs() error {
1187         func() {
1188                 // Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
1189                 runner.cStateLock.Lock()
1190                 defer runner.cStateLock.Unlock()
1191
1192                 runner.CrunchLog.Print(runner.finalState)
1193
1194                 if runner.arvMountLog != nil {
1195                         runner.arvMountLog.Close()
1196                 }
1197                 runner.CrunchLog.Close()
1198
1199                 // Closing CrunchLog above allows them to be committed to Keep at this
1200                 // point, but re-open crunch log with ArvClient in case there are any
1201                 // other further errors (such as failing to write the log to Keep!)
1202                 // while shutting down
1203                 runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
1204                         ArvClient:     runner.DispatcherArvClient,
1205                         UUID:          runner.Container.UUID,
1206                         loggingStream: "crunch-run",
1207                         writeCloser:   nil,
1208                 })
1209                 runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1210         }()
1211
1212         if runner.LogsPDH != nil {
1213                 // If we have already assigned something to LogsPDH,
1214                 // we must be closing the re-opened log, which won't
1215                 // end up getting attached to the container record and
1216                 // therefore doesn't need to be saved as a collection
1217                 // -- it exists only to send logs to other channels.
1218                 return nil
1219         }
1220         saved, err := runner.saveLogCollection(true)
1221         if err != nil {
1222                 return fmt.Errorf("error saving log collection: %s", err)
1223         }
1224         runner.logMtx.Lock()
1225         defer runner.logMtx.Unlock()
1226         runner.LogsPDH = &saved.PortableDataHash
1227         return nil
1228 }
1229
1230 func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
1231         runner.logMtx.Lock()
1232         defer runner.logMtx.Unlock()
1233         if runner.LogsPDH != nil {
1234                 // Already finalized.
1235                 return
1236         }
1237         updates := arvadosclient.Dict{
1238                 "name": "logs for " + runner.Container.UUID,
1239         }
1240         mt, err1 := runner.LogCollection.MarshalManifest(".")
1241         if err1 == nil {
1242                 // Only send updated manifest text if there was no
1243                 // error.
1244                 updates["manifest_text"] = mt
1245         }
1246
1247         // Even if flushing the manifest had an error, we still want
1248         // to update the log record, if possible, to push the trash_at
1249         // and delete_at times into the future.  Details on bug
1250         // #17293.
1251         if final {
1252                 updates["is_trashed"] = true
1253         } else {
1254                 exp := time.Now().Add(crunchLogUpdatePeriod * 24)
1255                 updates["trash_at"] = exp
1256                 updates["delete_at"] = exp
1257         }
1258         reqBody := arvadosclient.Dict{"collection": updates}
1259         var err2 error
1260         if runner.logUUID == "" {
1261                 reqBody["ensure_unique_name"] = true
1262                 err2 = runner.DispatcherArvClient.Create("collections", reqBody, &response)
1263         } else {
1264                 err2 = runner.DispatcherArvClient.Update("collections", runner.logUUID, reqBody, &response)
1265         }
1266         if err2 == nil {
1267                 runner.logUUID = response.UUID
1268         }
1269
1270         if err1 != nil || err2 != nil {
1271                 err = fmt.Errorf("error recording logs: %q, %q", err1, err2)
1272         }
1273         return
1274 }
1275
1276 // UpdateContainerRunning updates the container state to "Running"
1277 func (runner *ContainerRunner) UpdateContainerRunning() error {
1278         runner.cStateLock.Lock()
1279         defer runner.cStateLock.Unlock()
1280         if runner.cCancelled {
1281                 return ErrCancelled
1282         }
1283         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID,
1284                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running", "gateway_address": runner.gateway.Address}}, nil)
1285 }
1286
1287 // ContainerToken returns the api_token the container (and any
1288 // arv-mount processes) are allowed to use.
1289 func (runner *ContainerRunner) ContainerToken() (string, error) {
1290         if runner.token != "" {
1291                 return runner.token, nil
1292         }
1293
1294         var auth arvados.APIClientAuthorization
1295         err := runner.DispatcherArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1296         if err != nil {
1297                 return "", err
1298         }
1299         runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID)
1300         return runner.token, nil
1301 }
1302
1303 // UpdateContainerFinal updates the container record state on API
1304 // server to "Complete" or "Cancelled"
1305 func (runner *ContainerRunner) UpdateContainerFinal() error {
1306         update := arvadosclient.Dict{}
1307         update["state"] = runner.finalState
1308         if runner.LogsPDH != nil {
1309                 update["log"] = *runner.LogsPDH
1310         }
1311         if runner.finalState == "Complete" {
1312                 if runner.ExitCode != nil {
1313                         update["exit_code"] = *runner.ExitCode
1314                 }
1315                 if runner.OutputPDH != nil {
1316                         update["output"] = *runner.OutputPDH
1317                 }
1318         }
1319         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1320 }
1321
1322 // IsCancelled returns the value of Cancelled, with goroutine safety.
1323 func (runner *ContainerRunner) IsCancelled() bool {
1324         runner.cStateLock.Lock()
1325         defer runner.cStateLock.Unlock()
1326         return runner.cCancelled
1327 }
1328
1329 // NewArvLogWriter creates an ArvLogWriter
1330 func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) {
1331         writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
1332         if err != nil {
1333                 return nil, err
1334         }
1335         return &ArvLogWriter{
1336                 ArvClient:     runner.DispatcherArvClient,
1337                 UUID:          runner.Container.UUID,
1338                 loggingStream: name,
1339                 writeCloser:   writer,
1340         }, nil
1341 }
1342
1343 // Run the full container lifecycle.
1344 func (runner *ContainerRunner) Run() (err error) {
1345         runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
1346         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1347
1348         hostname, hosterr := os.Hostname()
1349         if hosterr != nil {
1350                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1351         } else {
1352                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1353         }
1354
1355         runner.finalState = "Queued"
1356
1357         defer func() {
1358                 runner.CleanupDirs()
1359
1360                 runner.CrunchLog.Printf("crunch-run finished")
1361                 runner.CrunchLog.Close()
1362         }()
1363
1364         err = runner.fetchContainerRecord()
1365         if err != nil {
1366                 return
1367         }
1368         if runner.Container.State != "Locked" {
1369                 return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
1370         }
1371
1372         var bindmounts map[string]bindmount
1373         defer func() {
1374                 // checkErr prints e (unless it's nil) and sets err to
1375                 // e (unless err is already non-nil). Thus, if err
1376                 // hasn't already been assigned when Run() returns,
1377                 // this cleanup func will cause Run() to return the
1378                 // first non-nil error that is passed to checkErr().
1379                 checkErr := func(errorIn string, e error) {
1380                         if e == nil {
1381                                 return
1382                         }
1383                         runner.CrunchLog.Printf("error in %s: %v", errorIn, e)
1384                         if err == nil {
1385                                 err = e
1386                         }
1387                         if runner.finalState == "Complete" {
1388                                 // There was an error in the finalization.
1389                                 runner.finalState = "Cancelled"
1390                         }
1391                 }
1392
1393                 // Log the error encountered in Run(), if any
1394                 checkErr("Run", err)
1395
1396                 if runner.finalState == "Queued" {
1397                         runner.UpdateContainerFinal()
1398                         return
1399                 }
1400
1401                 if runner.IsCancelled() {
1402                         runner.finalState = "Cancelled"
1403                         // but don't return yet -- we still want to
1404                         // capture partial output and write logs
1405                 }
1406
1407                 if bindmounts != nil {
1408                         checkErr("CaptureOutput", runner.CaptureOutput(bindmounts))
1409                 }
1410                 checkErr("stopHoststat", runner.stopHoststat())
1411                 checkErr("CommitLogs", runner.CommitLogs())
1412                 checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
1413         }()
1414
1415         runner.setupSignals()
1416         err = runner.startHoststat()
1417         if err != nil {
1418                 return
1419         }
1420
1421         // set up FUSE mount and binds
1422         bindmounts, err = runner.SetupMounts()
1423         if err != nil {
1424                 runner.finalState = "Cancelled"
1425                 err = fmt.Errorf("While setting up mounts: %v", err)
1426                 return
1427         }
1428
1429         // check for and/or load image
1430         imageID, err := runner.LoadImage()
1431         if err != nil {
1432                 if !runner.checkBrokenNode(err) {
1433                         // Failed to load image but not due to a "broken node"
1434                         // condition, probably user error.
1435                         runner.finalState = "Cancelled"
1436                 }
1437                 err = fmt.Errorf("While loading container image: %v", err)
1438                 return
1439         }
1440
1441         err = runner.CreateContainer(imageID, bindmounts)
1442         if err != nil {
1443                 return
1444         }
1445         err = runner.LogHostInfo()
1446         if err != nil {
1447                 return
1448         }
1449         err = runner.LogNodeRecord()
1450         if err != nil {
1451                 return
1452         }
1453         err = runner.LogContainerRecord()
1454         if err != nil {
1455                 return
1456         }
1457
1458         if runner.IsCancelled() {
1459                 return
1460         }
1461
1462         err = runner.UpdateContainerRunning()
1463         if err != nil {
1464                 return
1465         }
1466         runner.finalState = "Cancelled"
1467
1468         err = runner.startCrunchstat()
1469         if err != nil {
1470                 return
1471         }
1472
1473         err = runner.StartContainer()
1474         if err != nil {
1475                 runner.checkBrokenNode(err)
1476                 return
1477         }
1478
1479         err = runner.WaitFinish()
1480         if err == nil && !runner.IsCancelled() {
1481                 runner.finalState = "Complete"
1482         }
1483         return
1484 }
1485
1486 // Fetch the current container record (uuid = runner.Container.UUID)
1487 // into runner.Container.
1488 func (runner *ContainerRunner) fetchContainerRecord() error {
1489         reader, err := runner.DispatcherArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1490         if err != nil {
1491                 return fmt.Errorf("error fetching container record: %v", err)
1492         }
1493         defer reader.Close()
1494
1495         dec := json.NewDecoder(reader)
1496         dec.UseNumber()
1497         err = dec.Decode(&runner.Container)
1498         if err != nil {
1499                 return fmt.Errorf("error decoding container record: %v", err)
1500         }
1501
1502         var sm struct {
1503                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
1504         }
1505
1506         containerToken, err := runner.ContainerToken()
1507         if err != nil {
1508                 return fmt.Errorf("error getting container token: %v", err)
1509         }
1510
1511         runner.ContainerArvClient, runner.ContainerKeepClient,
1512                 runner.containerClient, err = runner.MkArvClient(containerToken)
1513         if err != nil {
1514                 return fmt.Errorf("error creating container API client: %v", err)
1515         }
1516
1517         err = runner.ContainerArvClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
1518         if err != nil {
1519                 if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
1520                         return fmt.Errorf("error fetching secret_mounts: %v", err)
1521                 }
1522                 // ok && apierr.HttpStatusCode == 404, which means
1523                 // secret_mounts isn't supported by this API server.
1524         }
1525         runner.SecretMounts = sm.SecretMounts
1526
1527         return nil
1528 }
1529
1530 // NewContainerRunner creates a new container runner.
1531 func NewContainerRunner(dispatcherClient *arvados.Client,
1532         dispatcherArvClient IArvadosClient,
1533         dispatcherKeepClient IKeepClient,
1534         containerUUID string) (*ContainerRunner, error) {
1535
1536         cr := &ContainerRunner{
1537                 dispatcherClient:     dispatcherClient,
1538                 DispatcherArvClient:  dispatcherArvClient,
1539                 DispatcherKeepClient: dispatcherKeepClient,
1540         }
1541         cr.NewLogWriter = cr.NewArvLogWriter
1542         cr.RunArvMount = cr.ArvMountCmd
1543         cr.MkTempDir = ioutil.TempDir
1544         cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
1545                 cl, err := arvadosclient.MakeArvadosClient()
1546                 if err != nil {
1547                         return nil, nil, nil, err
1548                 }
1549                 cl.ApiToken = token
1550                 kc, err := keepclient.MakeKeepClient(cl)
1551                 if err != nil {
1552                         return nil, nil, nil, err
1553                 }
1554                 c2 := arvados.NewClientFromEnv()
1555                 c2.AuthToken = token
1556                 return cl, kc, c2, nil
1557         }
1558         var err error
1559         cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.dispatcherClient, cr.DispatcherKeepClient)
1560         if err != nil {
1561                 return nil, err
1562         }
1563         cr.Container.UUID = containerUUID
1564         w, err := cr.NewLogWriter("crunch-run")
1565         if err != nil {
1566                 return nil, err
1567         }
1568         cr.CrunchLog = NewThrottledLogger(w)
1569         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1570
1571         loadLogThrottleParams(dispatcherArvClient)
1572         go cr.updateLogs()
1573
1574         return cr, nil
1575 }
1576
1577 func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
1578         flags := flag.NewFlagSet(prog, flag.ContinueOnError)
1579         statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1580         cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1581         cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1582         cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1583         caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
1584         detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
1585         stdinEnv := flags.Bool("stdin-env", false, "Load environment variables from JSON message on stdin")
1586         sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
1587         kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
1588         list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
1589         enableNetwork := flags.String("container-enable-networking", "default", "enable networking \"always\" (for all containers) or \"default\" (for containers that request it)")
1590         networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
1591         memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
1592         runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
1593         flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
1594
1595         ignoreDetachFlag := false
1596         if len(args) > 0 && args[0] == "-no-detach" {
1597                 // This process was invoked by a parent process, which
1598                 // has passed along its own arguments, including
1599                 // -detach, after the leading -no-detach flag.  Strip
1600                 // the leading -no-detach flag (it's not recognized by
1601                 // flags.Parse()) and ignore the -detach flag that
1602                 // comes later.
1603                 args = args[1:]
1604                 ignoreDetachFlag = true
1605         }
1606
1607         if err := flags.Parse(args); err == flag.ErrHelp {
1608                 return 0
1609         } else if err != nil {
1610                 log.Print(err)
1611                 return 1
1612         }
1613
1614         if *stdinEnv && !ignoreDetachFlag {
1615                 // Load env vars on stdin if asked (but not in a
1616                 // detached child process, in which case stdin is
1617                 // /dev/null).
1618                 err := loadEnv(os.Stdin)
1619                 if err != nil {
1620                         log.Print(err)
1621                         return 1
1622                 }
1623         }
1624
1625         containerUUID := flags.Arg(0)
1626
1627         switch {
1628         case *detach && !ignoreDetachFlag:
1629                 return Detach(containerUUID, prog, args, os.Stdout, os.Stderr)
1630         case *kill >= 0:
1631                 return KillProcess(containerUUID, syscall.Signal(*kill), os.Stdout, os.Stderr)
1632         case *list:
1633                 return ListProcesses(os.Stdout, os.Stderr)
1634         }
1635
1636         if containerUUID == "" {
1637                 log.Printf("usage: %s [options] UUID", prog)
1638                 return 1
1639         }
1640
1641         log.Printf("crunch-run %s started", cmd.Version.String())
1642         time.Sleep(*sleep)
1643
1644         if *caCertsPath != "" {
1645                 arvadosclient.CertFiles = []string{*caCertsPath}
1646         }
1647
1648         api, err := arvadosclient.MakeArvadosClient()
1649         if err != nil {
1650                 log.Printf("%s: %v", containerUUID, err)
1651                 return 1
1652         }
1653         api.Retries = 8
1654
1655         kc, kcerr := keepclient.MakeKeepClient(api)
1656         if kcerr != nil {
1657                 log.Printf("%s: %v", containerUUID, kcerr)
1658                 return 1
1659         }
1660         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1661         kc.Retries = 4
1662
1663         cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, containerUUID)
1664         if err != nil {
1665                 log.Print(err)
1666                 return 1
1667         }
1668
1669         switch *runtimeEngine {
1670         case "docker":
1671                 cr.executor, err = newDockerExecutor(containerUUID, cr.CrunchLog.Printf, cr.containerWatchdogInterval)
1672         case "singularity":
1673                 cr.executor, err = newSingularityExecutor(cr.CrunchLog.Printf)
1674         default:
1675                 cr.CrunchLog.Printf("%s: unsupported RuntimeEngine %q", containerUUID, *runtimeEngine)
1676                 cr.CrunchLog.Close()
1677                 return 1
1678         }
1679         if err != nil {
1680                 cr.CrunchLog.Printf("%s: %v", containerUUID, err)
1681                 cr.checkBrokenNode(err)
1682                 cr.CrunchLog.Close()
1683                 return 1
1684         }
1685         defer cr.executor.Close()
1686
1687         gwAuthSecret := os.Getenv("GatewayAuthSecret")
1688         os.Unsetenv("GatewayAuthSecret")
1689         if gwAuthSecret == "" {
1690                 // not safe to run a gateway service without an auth
1691                 // secret
1692         } else if gwListen := os.Getenv("GatewayAddress"); gwListen == "" {
1693                 // dispatcher did not tell us which external IP
1694                 // address to advertise --> no gateway service
1695         } else if de, ok := cr.executor.(*dockerExecutor); ok {
1696                 cr.gateway = Gateway{
1697                         Address:            gwListen,
1698                         AuthSecret:         gwAuthSecret,
1699                         ContainerUUID:      containerUUID,
1700                         DockerContainerID:  &de.containerID,
1701                         Log:                cr.CrunchLog,
1702                         ContainerIPAddress: dockerContainerIPAddress(&de.containerID),
1703                 }
1704                 err = cr.gateway.Start()
1705                 if err != nil {
1706                         log.Printf("error starting gateway server: %s", err)
1707                         return 1
1708                 }
1709         }
1710
1711         parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerUUID+".")
1712         if tmperr != nil {
1713                 log.Printf("%s: %v", containerUUID, tmperr)
1714                 return 1
1715         }
1716
1717         cr.parentTemp = parentTemp
1718         cr.statInterval = *statInterval
1719         cr.cgroupRoot = *cgroupRoot
1720         cr.expectCgroupParent = *cgroupParent
1721         cr.enableNetwork = *enableNetwork
1722         cr.networkMode = *networkMode
1723         if *cgroupParentSubsystem != "" {
1724                 p := findCgroup(*cgroupParentSubsystem)
1725                 cr.setCgroupParent = p
1726                 cr.expectCgroupParent = p
1727         }
1728
1729         runerr := cr.Run()
1730
1731         if *memprofile != "" {
1732                 f, err := os.Create(*memprofile)
1733                 if err != nil {
1734                         log.Printf("could not create memory profile: %s", err)
1735                 }
1736                 runtime.GC() // get up-to-date statistics
1737                 if err := pprof.WriteHeapProfile(f); err != nil {
1738                         log.Printf("could not write memory profile: %s", err)
1739                 }
1740                 closeerr := f.Close()
1741                 if closeerr != nil {
1742                         log.Printf("closing memprofile file: %s", err)
1743                 }
1744         }
1745
1746         if runerr != nil {
1747                 log.Printf("%s: %v", containerUUID, runerr)
1748                 return 1
1749         }
1750         return 0
1751 }
1752
1753 func loadEnv(rdr io.Reader) error {
1754         buf, err := ioutil.ReadAll(rdr)
1755         if err != nil {
1756                 return fmt.Errorf("read stdin: %s", err)
1757         }
1758         var env map[string]string
1759         err = json.Unmarshal(buf, &env)
1760         if err != nil {
1761                 return fmt.Errorf("decode stdin: %s", err)
1762         }
1763         for k, v := range env {
1764                 err = os.Setenv(k, v)
1765                 if err != nil {
1766                         return fmt.Errorf("setenv(%q): %s", k, err)
1767                 }
1768         }
1769         return nil
1770 }