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         BlockWrite(context.Context, arvados.BlockWriteOptions) (arvados.BlockWriteResponse, 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         SetStorageClasses(sc []string)
  64 }
  65
  66 // NewLogWriter is a factory function to create a new log writer.
  67 type NewLogWriter func(name string) (io.WriteCloser, error)
  68
  69 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  70
  71 type MkTempDir func(string, string) (string, error)
  72
  73 type PsProcess interface {
  74         CmdlineSlice() ([]string, error)
  75 }
  76
  77 // ContainerRunner is the main stateful struct used for a single execution of a
  78 // container.
  79 type ContainerRunner struct {
  80         executor       containerExecutor
  81         executorStdin  io.Closer
  82         executorStdout io.Closer
  83         executorStderr io.Closer
  84
  85         // Dispatcher client is initialized with the Dispatcher token.
  86         // This is a privileged token used to manage container status
  87         // and logs.
  88         //
  89         // We have both dispatcherClient and DispatcherArvClient
  90         // because there are two different incompatible Arvados Go
  91         // SDKs and we have to use both (hopefully this gets fixed in
  92         // #14467)
  93         dispatcherClient     *arvados.Client
  94         DispatcherArvClient  IArvadosClient
  95         DispatcherKeepClient IKeepClient
  96
  97         // Container client is initialized with the Container token
  98         // This token controls the permissions of the container, and
  99         // must be used for operations such as reading collections.
 100         //
 101         // Same comment as above applies to
 102         // containerClient/ContainerArvClient.
 103         containerClient     *arvados.Client
 104         ContainerArvClient  IArvadosClient
 105         ContainerKeepClient IKeepClient
 106
 107         Container     arvados.Container
 108         token         string
 109         ExitCode      *int
 110         NewLogWriter  NewLogWriter
 111         CrunchLog     *ThrottledLogger
 112         logUUID       string
 113         logMtx        sync.Mutex
 114         LogCollection arvados.CollectionFileSystem
 115         LogsPDH       *string
 116         RunArvMount   RunArvMount
 117         MkTempDir     MkTempDir
 118         ArvMount      *exec.Cmd
 119         ArvMountPoint string
 120         HostOutputDir string
 121         Volumes       map[string]struct{}
 122         OutputPDH     *string
 123         SigChan       chan os.Signal
 124         ArvMountExit  chan error
 125         SecretMounts  map[string]arvados.Mount
 126         MkArvClient   func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
 127         finalState    string
 128         parentTemp    string
 129
 130         statLogger       io.WriteCloser
 131         statReporter     *crunchstat.Reporter
 132         hoststatLogger   io.WriteCloser
 133         hoststatReporter *crunchstat.Reporter
 134         statInterval     time.Duration
 135         cgroupRoot       string
 136         // What we expect the container's cgroup parent to be.
 137         expectCgroupParent string
 138         // What we tell docker to use as the container's cgroup
 139         // parent. Note: Ideally we would use the same field for both
 140         // expectCgroupParent and setCgroupParent, and just make it
 141         // default to "docker". However, when using docker < 1.10 with
 142         // systemd, specifying a non-empty cgroup parent (even the
 143         // default value "docker") hits a docker bug
 144         // (https://github.com/docker/docker/issues/17126). Using two
 145         // separate fields makes it possible to use the "expect cgroup
 146         // parent to be X" feature even on sites where the "specify
 147         // cgroup parent" feature breaks.
 148         setCgroupParent string
 149
 150         cStateLock sync.Mutex
 151         cCancelled bool // StopContainer() invoked
 152
 153         enableMemoryLimit bool
 154         enableNetwork     string // one of "default" or "always"
 155         networkMode       string // "none", "host", or "" -- passed through to executor
 156         arvMountLog       *ThrottledLogger
 157
 158         containerWatchdogInterval time.Duration
 159
 160         gateway Gateway
 161 }
 162
 163 // setupSignals sets up signal handling to gracefully terminate the
 164 // underlying container and update state when receiving a TERM, INT or
 165 // QUIT signal.
 166 func (runner *ContainerRunner) setupSignals() {
 167         runner.SigChan = make(chan os.Signal, 1)
 168         signal.Notify(runner.SigChan, syscall.SIGTERM)
 169         signal.Notify(runner.SigChan, syscall.SIGINT)
 170         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 171
 172         go func(sig chan os.Signal) {
 173                 for s := range sig {
 174                         runner.stop(s)
 175                 }
 176         }(runner.SigChan)
 177 }
 178
 179 // stop the underlying container.
 180 func (runner *ContainerRunner) stop(sig os.Signal) {
 181         runner.cStateLock.Lock()
 182         defer runner.cStateLock.Unlock()
 183         if sig != nil {
 184                 runner.CrunchLog.Printf("caught signal: %v", sig)
 185         }
 186         runner.cCancelled = true
 187         runner.CrunchLog.Printf("stopping container")
 188         err := runner.executor.Stop()
 189         if err != nil {
 190                 runner.CrunchLog.Printf("error stopping container: %s", err)
 191         }
 192 }
 193
 194 var errorBlacklist = []string{
 195         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 196         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 197         "(?ms).*grpc: the connection is unavailable.*",
 198 }
 199 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)")
 200
 201 func (runner *ContainerRunner) runBrokenNodeHook() {
 202         if *brokenNodeHook == "" {
 203                 path := filepath.Join(lockdir, brokenfile)
 204                 runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
 205                 f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
 206                 if err != nil {
 207                         runner.CrunchLog.Printf("Error writing %s: %s", path, err)
 208                         return
 209                 }
 210                 f.Close()
 211         } else {
 212                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 213                 // run killme script
 214                 c := exec.Command(*brokenNodeHook)
 215                 c.Stdout = runner.CrunchLog
 216                 c.Stderr = runner.CrunchLog
 217                 err := c.Run()
 218                 if err != nil {
 219                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 220                 }
 221         }
 222 }
 223
 224 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 225         for _, d := range errorBlacklist {
 226                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 227                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 228                         runner.runBrokenNodeHook()
 229                         return true
 230                 }
 231         }
 232         return false
 233 }
 234
 235 // LoadImage determines the docker image id from the container record and
 236 // checks if it is available in the local Docker image store.  If not, it loads
 237 // the image from Keep.
 238 func (runner *ContainerRunner) LoadImage() (string, error) {
 239         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 240
 241         d, err := os.Open(runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage)
 242         if err != nil {
 243                 return "", err
 244         }
 245         defer d.Close()
 246         allfiles, err := d.Readdirnames(-1)
 247         if err != nil {
 248                 return "", err
 249         }
 250         var tarfiles []string
 251         for _, fnm := range allfiles {
 252                 if strings.HasSuffix(fnm, ".tar") {
 253                         tarfiles = append(tarfiles, fnm)
 254                 }
 255         }
 256         if len(tarfiles) == 0 {
 257                 return "", fmt.Errorf("image collection does not include a .tar image file")
 258         }
 259         if len(tarfiles) > 1 {
 260                 return "", fmt.Errorf("cannot choose from multiple tar files in image collection: %v", tarfiles)
 261         }
 262         imageID := tarfiles[0][:len(tarfiles[0])-4]
 263         imageFile := runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage + "/" + tarfiles[0]
 264         runner.CrunchLog.Printf("Using Docker image id %q", imageID)
 265
 266         if !runner.executor.ImageLoaded(imageID) {
 267                 runner.CrunchLog.Print("Loading Docker image from keep")
 268                 err = runner.executor.LoadImage(imageFile)
 269                 if err != nil {
 270                         return "", err
 271                 }
 272         } else {
 273                 runner.CrunchLog.Print("Docker image is available")
 274         }
 275         return imageID, nil
 276 }
 277
 278 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 279         c = exec.Command("arv-mount", arvMountCmd...)
 280
 281         // Copy our environment, but override ARVADOS_API_TOKEN with
 282         // the container auth token.
 283         c.Env = nil
 284         for _, s := range os.Environ() {
 285                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 286                         c.Env = append(c.Env, s)
 287                 }
 288         }
 289         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 290
 291         w, err := runner.NewLogWriter("arv-mount")
 292         if err != nil {
 293                 return nil, err
 294         }
 295         runner.arvMountLog = NewThrottledLogger(w)
 296         c.Stdout = runner.arvMountLog
 297         c.Stderr = io.MultiWriter(runner.arvMountLog, os.Stderr)
 298
 299         runner.CrunchLog.Printf("Running %v", c.Args)
 300
 301         err = c.Start()
 302         if err != nil {
 303                 return nil, err
 304         }
 305
 306         statReadme := make(chan bool)
 307         runner.ArvMountExit = make(chan error)
 308
 309         keepStatting := true
 310         go func() {
 311                 for keepStatting {
 312                         time.Sleep(100 * time.Millisecond)
 313                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 314                         if err == nil {
 315                                 keepStatting = false
 316                                 statReadme <- true
 317                         }
 318                 }
 319                 close(statReadme)
 320         }()
 321
 322         go func() {
 323                 mnterr := c.Wait()
 324                 if mnterr != nil {
 325                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 326                 }
 327                 runner.ArvMountExit <- mnterr
 328                 close(runner.ArvMountExit)
 329         }()
 330
 331         select {
 332         case <-statReadme:
 333                 break
 334         case err := <-runner.ArvMountExit:
 335                 runner.ArvMount = nil
 336                 keepStatting = false
 337                 return nil, err
 338         }
 339
 340         return c, nil
 341 }
 342
 343 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 344         if runner.ArvMountPoint == "" {
 345                 runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
 346         }
 347         return
 348 }
 349
 350 func copyfile(src string, dst string) (err error) {
 351         srcfile, err := os.Open(src)
 352         if err != nil {
 353                 return
 354         }
 355
 356         os.MkdirAll(path.Dir(dst), 0777)
 357
 358         dstfile, err := os.Create(dst)
 359         if err != nil {
 360                 return
 361         }
 362         _, err = io.Copy(dstfile, srcfile)
 363         if err != nil {
 364                 return
 365         }
 366
 367         err = srcfile.Close()
 368         err2 := dstfile.Close()
 369
 370         if err != nil {
 371                 return
 372         }
 373
 374         if err2 != nil {
 375                 return err2
 376         }
 377
 378         return nil
 379 }
 380
 381 func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
 382         bindmounts := map[string]bindmount{}
 383         err := runner.SetupArvMountPoint("keep")
 384         if err != nil {
 385                 return nil, fmt.Errorf("While creating keep mount temp dir: %v", err)
 386         }
 387
 388         token, err := runner.ContainerToken()
 389         if err != nil {
 390                 return nil, fmt.Errorf("could not get container token: %s", err)
 391         }
 392         runner.CrunchLog.Printf("container token %q", token)
 393
 394         pdhOnly := true
 395         tmpcount := 0
 396         arvMountCmd := []string{
 397                 "--foreground",
 398                 "--allow-other",
 399                 "--read-write",
 400                 "--storage-classes", strings.Join(runner.Container.OutputStorageClasses, ","),
 401                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 402
 403         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 404                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 405         }
 406
 407         collectionPaths := []string{}
 408         needCertMount := true
 409         type copyFile struct {
 410                 src  string
 411                 bind string
 412         }
 413         var copyFiles []copyFile
 414
 415         var binds []string
 416         for bind := range runner.Container.Mounts {
 417                 binds = append(binds, bind)
 418         }
 419         for bind := range runner.SecretMounts {
 420                 if _, ok := runner.Container.Mounts[bind]; ok {
 421                         return nil, fmt.Errorf("secret mount %q conflicts with regular mount", bind)
 422                 }
 423                 if runner.SecretMounts[bind].Kind != "json" &&
 424                         runner.SecretMounts[bind].Kind != "text" {
 425                         return nil, fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
 426                                 bind, runner.SecretMounts[bind].Kind)
 427                 }
 428                 binds = append(binds, bind)
 429         }
 430         sort.Strings(binds)
 431
 432         for _, bind := range binds {
 433                 mnt, ok := runner.Container.Mounts[bind]
 434                 if !ok {
 435                         mnt = runner.SecretMounts[bind]
 436                 }
 437                 if bind == "stdout" || bind == "stderr" {
 438                         // Is it a "file" mount kind?
 439                         if mnt.Kind != "file" {
 440                                 return nil, fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
 441                         }
 442
 443                         // Does path start with OutputPath?
 444                         prefix := runner.Container.OutputPath
 445                         if !strings.HasSuffix(prefix, "/") {
 446                                 prefix += "/"
 447                         }
 448                         if !strings.HasPrefix(mnt.Path, prefix) {
 449                                 return nil, fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 450                         }
 451                 }
 452
 453                 if bind == "stdin" {
 454                         // Is it a "collection" mount kind?
 455                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 456                                 return nil, fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
 457                         }
 458                 }
 459
 460                 if bind == "/etc/arvados/ca-certificates.crt" {
 461                         needCertMount = false
 462                 }
 463
 464                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 465                         if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
 466                                 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)
 467                         }
 468                 }
 469
 470                 switch {
 471                 case mnt.Kind == "collection" && bind != "stdin":
 472                         var src string
 473                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 474                                 return nil, fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 475                         }
 476                         if mnt.UUID != "" {
 477                                 if mnt.Writable {
 478                                         return nil, fmt.Errorf("writing to existing collections currently not permitted")
 479                                 }
 480                                 pdhOnly = false
 481                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 482                         } else if mnt.PortableDataHash != "" {
 483                                 if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 484                                         return nil, fmt.Errorf("can never write to a collection specified by portable data hash")
 485                                 }
 486                                 idx := strings.Index(mnt.PortableDataHash, "/")
 487                                 if idx > 0 {
 488                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 489                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 490                                         runner.Container.Mounts[bind] = mnt
 491                                 }
 492                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 493                                 if mnt.Path != "" && mnt.Path != "." {
 494                                         if strings.HasPrefix(mnt.Path, "./") {
 495                                                 mnt.Path = mnt.Path[2:]
 496                                         } else if strings.HasPrefix(mnt.Path, "/") {
 497                                                 mnt.Path = mnt.Path[1:]
 498                                         }
 499                                         src += "/" + mnt.Path
 500                                 }
 501                         } else {
 502                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 503                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 504                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 505                                 tmpcount++
 506                         }
 507                         if mnt.Writable {
 508                                 if bind == runner.Container.OutputPath {
 509                                         runner.HostOutputDir = src
 510                                         bindmounts[bind] = bindmount{HostPath: src}
 511                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 512                                         copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 513                                 } else {
 514                                         bindmounts[bind] = bindmount{HostPath: src}
 515                                 }
 516                         } else {
 517                                 bindmounts[bind] = bindmount{HostPath: src, ReadOnly: true}
 518                         }
 519                         collectionPaths = append(collectionPaths, src)
 520
 521                 case mnt.Kind == "tmp":
 522                         var tmpdir string
 523                         tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
 524                         if err != nil {
 525                                 return nil, fmt.Errorf("while creating mount temp dir: %v", err)
 526                         }
 527                         st, staterr := os.Stat(tmpdir)
 528                         if staterr != nil {
 529                                 return nil, fmt.Errorf("while Stat on temp dir: %v", staterr)
 530                         }
 531                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 532                         if staterr != nil {
 533                                 return nil, fmt.Errorf("while Chmod temp dir: %v", err)
 534                         }
 535                         bindmounts[bind] = bindmount{HostPath: tmpdir}
 536                         if bind == runner.Container.OutputPath {
 537                                 runner.HostOutputDir = tmpdir
 538                         }
 539
 540                 case mnt.Kind == "json" || mnt.Kind == "text":
 541                         var filedata []byte
 542                         if mnt.Kind == "json" {
 543                                 filedata, err = json.Marshal(mnt.Content)
 544                                 if err != nil {
 545                                         return nil, fmt.Errorf("encoding json data: %v", err)
 546                                 }
 547                         } else {
 548                                 text, ok := mnt.Content.(string)
 549                                 if !ok {
 550                                         return nil, fmt.Errorf("content for mount %q must be a string", bind)
 551                                 }
 552                                 filedata = []byte(text)
 553                         }
 554
 555                         tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
 556                         if err != nil {
 557                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 558                         }
 559                         tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
 560                         err = ioutil.WriteFile(tmpfn, filedata, 0444)
 561                         if err != nil {
 562                                 return nil, fmt.Errorf("writing temp file: %v", err)
 563                         }
 564                         if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 565                                 copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 566                         } else {
 567                                 bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
 568                         }
 569
 570                 case mnt.Kind == "git_tree":
 571                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
 572                         if err != nil {
 573                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 574                         }
 575                         err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
 576                         if err != nil {
 577                                 return nil, err
 578                         }
 579                         bindmounts[bind] = bindmount{HostPath: tmpdir, ReadOnly: true}
 580                 }
 581         }
 582
 583         if runner.HostOutputDir == "" {
 584                 return nil, fmt.Errorf("output path does not correspond to a writable mount point")
 585         }
 586
 587         if needCertMount && runner.Container.RuntimeConstraints.API {
 588                 for _, certfile := range arvadosclient.CertFiles {
 589                         _, err := os.Stat(certfile)
 590                         if err == nil {
 591                                 bindmounts["/etc/arvados/ca-certificates.crt"] = bindmount{HostPath: certfile, ReadOnly: true}
 592                                 break
 593                         }
 594                 }
 595         }
 596
 597         if pdhOnly {
 598                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 599         } else {
 600                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 601         }
 602         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 603
 604         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 605         if err != nil {
 606                 return nil, fmt.Errorf("while trying to start arv-mount: %v", err)
 607         }
 608
 609         for _, p := range collectionPaths {
 610                 _, err = os.Stat(p)
 611                 if err != nil {
 612                         return nil, fmt.Errorf("while checking that input files exist: %v", err)
 613                 }
 614         }
 615
 616         for _, cp := range copyFiles {
 617                 st, err := os.Stat(cp.src)
 618                 if err != nil {
 619                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 620                 }
 621                 if st.IsDir() {
 622                         err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
 623                                 if walkerr != nil {
 624                                         return walkerr
 625                                 }
 626                                 target := path.Join(cp.bind, walkpath[len(cp.src):])
 627                                 if walkinfo.Mode().IsRegular() {
 628                                         copyerr := copyfile(walkpath, target)
 629                                         if copyerr != nil {
 630                                                 return copyerr
 631                                         }
 632                                         return os.Chmod(target, walkinfo.Mode()|0777)
 633                                 } else if walkinfo.Mode().IsDir() {
 634                                         mkerr := os.MkdirAll(target, 0777)
 635                                         if mkerr != nil {
 636                                                 return mkerr
 637                                         }
 638                                         return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 639                                 } else {
 640                                         return fmt.Errorf("source %q is not a regular file or directory", cp.src)
 641                                 }
 642                         })
 643                 } else if st.Mode().IsRegular() {
 644                         err = copyfile(cp.src, cp.bind)
 645                         if err == nil {
 646                                 err = os.Chmod(cp.bind, st.Mode()|0777)
 647                         }
 648                 }
 649                 if err != nil {
 650                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 651                 }
 652         }
 653
 654         return bindmounts, nil
 655 }
 656
 657 func (runner *ContainerRunner) stopHoststat() error {
 658         if runner.hoststatReporter == nil {
 659                 return nil
 660         }
 661         runner.hoststatReporter.Stop()
 662         err := runner.hoststatLogger.Close()
 663         if err != nil {
 664                 return fmt.Errorf("error closing hoststat logs: %v", err)
 665         }
 666         return nil
 667 }
 668
 669 func (runner *ContainerRunner) startHoststat() error {
 670         w, err := runner.NewLogWriter("hoststat")
 671         if err != nil {
 672                 return err
 673         }
 674         runner.hoststatLogger = NewThrottledLogger(w)
 675         runner.hoststatReporter = &crunchstat.Reporter{
 676                 Logger:     log.New(runner.hoststatLogger, "", 0),
 677                 CgroupRoot: runner.cgroupRoot,
 678                 PollPeriod: runner.statInterval,
 679         }
 680         runner.hoststatReporter.Start()
 681         return nil
 682 }
 683
 684 func (runner *ContainerRunner) startCrunchstat() error {
 685         w, err := runner.NewLogWriter("crunchstat")
 686         if err != nil {
 687                 return err
 688         }
 689         runner.statLogger = NewThrottledLogger(w)
 690         runner.statReporter = &crunchstat.Reporter{
 691                 CID:          runner.executor.CgroupID(),
 692                 Logger:       log.New(runner.statLogger, "", 0),
 693                 CgroupParent: runner.expectCgroupParent,
 694                 CgroupRoot:   runner.cgroupRoot,
 695                 PollPeriod:   runner.statInterval,
 696                 TempDir:      runner.parentTemp,
 697         }
 698         runner.statReporter.Start()
 699         return nil
 700 }
 701
 702 type infoCommand struct {
 703         label string
 704         cmd   []string
 705 }
 706
 707 // LogHostInfo logs info about the current host, for debugging and
 708 // accounting purposes. Although it's logged as "node-info", this is
 709 // about the environment where crunch-run is actually running, which
 710 // might differ from what's described in the node record (see
 711 // LogNodeRecord).
 712 func (runner *ContainerRunner) LogHostInfo() (err error) {
 713         w, err := runner.NewLogWriter("node-info")
 714         if err != nil {
 715                 return
 716         }
 717
 718         commands := []infoCommand{
 719                 {
 720                         label: "Host Information",
 721                         cmd:   []string{"uname", "-a"},
 722                 },
 723                 {
 724                         label: "CPU Information",
 725                         cmd:   []string{"cat", "/proc/cpuinfo"},
 726                 },
 727                 {
 728                         label: "Memory Information",
 729                         cmd:   []string{"cat", "/proc/meminfo"},
 730                 },
 731                 {
 732                         label: "Disk Space",
 733                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 734                 },
 735                 {
 736                         label: "Disk INodes",
 737                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 738                 },
 739         }
 740
 741         // Run commands with informational output to be logged.
 742         for _, command := range commands {
 743                 fmt.Fprintln(w, command.label)
 744                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 745                 cmd.Stdout = w
 746                 cmd.Stderr = w
 747                 if err := cmd.Run(); err != nil {
 748                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 749                         fmt.Fprintln(w, err)
 750                         return err
 751                 }
 752                 fmt.Fprintln(w, "")
 753         }
 754
 755         err = w.Close()
 756         if err != nil {
 757                 return fmt.Errorf("While closing node-info logs: %v", err)
 758         }
 759         return nil
 760 }
 761
 762 // LogContainerRecord gets and saves the raw JSON container record from the API server
 763 func (runner *ContainerRunner) LogContainerRecord() error {
 764         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 765         if !logged && err == nil {
 766                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 767         }
 768         return err
 769 }
 770
 771 // LogNodeRecord logs the current host's InstanceType config entry (or
 772 // the arvados#node record, if running via crunch-dispatch-slurm).
 773 func (runner *ContainerRunner) LogNodeRecord() error {
 774         if it := os.Getenv("InstanceType"); it != "" {
 775                 // Dispatched via arvados-dispatch-cloud. Save
 776                 // InstanceType config fragment received from
 777                 // dispatcher on stdin.
 778                 w, err := runner.LogCollection.OpenFile("node.json", os.O_CREATE|os.O_WRONLY, 0666)
 779                 if err != nil {
 780                         return err
 781                 }
 782                 defer w.Close()
 783                 _, err = io.WriteString(w, it)
 784                 if err != nil {
 785                         return err
 786                 }
 787                 return w.Close()
 788         }
 789         // Dispatched via crunch-dispatch-slurm. Look up
 790         // apiserver's node record corresponding to
 791         // $SLURMD_NODENAME.
 792         hostname := os.Getenv("SLURMD_NODENAME")
 793         if hostname == "" {
 794                 hostname, _ = os.Hostname()
 795         }
 796         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 797                 // The "info" field has admin-only info when
 798                 // obtained with a privileged token, and
 799                 // should not be logged.
 800                 node, ok := resp.(map[string]interface{})
 801                 if ok {
 802                         delete(node, "info")
 803                 }
 804         })
 805         return err
 806 }
 807
 808 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 809         writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
 810         if err != nil {
 811                 return false, err
 812         }
 813         w := &ArvLogWriter{
 814                 ArvClient:     runner.DispatcherArvClient,
 815                 UUID:          runner.Container.UUID,
 816                 loggingStream: label,
 817                 writeCloser:   writer,
 818         }
 819
 820         reader, err := runner.DispatcherArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 821         if err != nil {
 822                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 823         }
 824         defer reader.Close()
 825
 826         dec := json.NewDecoder(reader)
 827         dec.UseNumber()
 828         var resp map[string]interface{}
 829         if err = dec.Decode(&resp); err != nil {
 830                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 831         }
 832         items, ok := resp["items"].([]interface{})
 833         if !ok {
 834                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 835         } else if len(items) < 1 {
 836                 return false, nil
 837         }
 838         if munge != nil {
 839                 munge(items[0])
 840         }
 841         // Re-encode it using indentation to improve readability
 842         enc := json.NewEncoder(w)
 843         enc.SetIndent("", "    ")
 844         if err = enc.Encode(items[0]); err != nil {
 845                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 846         }
 847         err = w.Close()
 848         if err != nil {
 849                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 850         }
 851         return true, nil
 852 }
 853
 854 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 855         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 856         index := strings.LastIndex(stdoutPath, "/")
 857         if index > 0 {
 858                 subdirs := stdoutPath[:index]
 859                 if subdirs != "" {
 860                         st, err := os.Stat(runner.HostOutputDir)
 861                         if err != nil {
 862                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 863                         }
 864                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 865                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 866                         if err != nil {
 867                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 868                         }
 869                 }
 870         }
 871         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 872         if err != nil {
 873                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 874         }
 875
 876         return stdoutFile, nil
 877 }
 878
 879 // CreateContainer creates the docker container.
 880 func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[string]bindmount) error {
 881         var stdin io.ReadCloser = ioutil.NopCloser(bytes.NewReader(nil))
 882         if mnt, ok := runner.Container.Mounts["stdin"]; ok {
 883                 switch mnt.Kind {
 884                 case "collection":
 885                         var collID string
 886                         if mnt.UUID != "" {
 887                                 collID = mnt.UUID
 888                         } else {
 889                                 collID = mnt.PortableDataHash
 890                         }
 891                         path := runner.ArvMountPoint + "/by_id/" + collID + "/" + mnt.Path
 892                         f, err := os.Open(path)
 893                         if err != nil {
 894                                 return err
 895                         }
 896                         stdin = f
 897                 case "json":
 898                         j, err := json.Marshal(mnt.Content)
 899                         if err != nil {
 900                                 return fmt.Errorf("error encoding stdin json data: %v", err)
 901                         }
 902                         stdin = ioutil.NopCloser(bytes.NewReader(j))
 903                 default:
 904                         return fmt.Errorf("stdin mount has unsupported kind %q", mnt.Kind)
 905                 }
 906         }
 907
 908         var stdout, stderr io.WriteCloser
 909         if mnt, ok := runner.Container.Mounts["stdout"]; ok {
 910                 f, err := runner.getStdoutFile(mnt.Path)
 911                 if err != nil {
 912                         return err
 913                 }
 914                 stdout = f
 915         } else if w, err := runner.NewLogWriter("stdout"); err != nil {
 916                 return err
 917         } else {
 918                 stdout = NewThrottledLogger(w)
 919         }
 920
 921         if mnt, ok := runner.Container.Mounts["stderr"]; ok {
 922                 f, err := runner.getStdoutFile(mnt.Path)
 923                 if err != nil {
 924                         return err
 925                 }
 926                 stderr = f
 927         } else if w, err := runner.NewLogWriter("stderr"); err != nil {
 928                 return err
 929         } else {
 930                 stderr = NewThrottledLogger(w)
 931         }
 932
 933         env := runner.Container.Environment
 934         enableNetwork := runner.enableNetwork == "always"
 935         if runner.Container.RuntimeConstraints.API {
 936                 enableNetwork = true
 937                 tok, err := runner.ContainerToken()
 938                 if err != nil {
 939                         return err
 940                 }
 941                 env = map[string]string{}
 942                 for k, v := range runner.Container.Environment {
 943                         env[k] = v
 944                 }
 945                 env["ARVADOS_API_TOKEN"] = tok
 946                 env["ARVADOS_API_HOST"] = os.Getenv("ARVADOS_API_HOST")
 947                 env["ARVADOS_API_HOST_INSECURE"] = os.Getenv("ARVADOS_API_HOST_INSECURE")
 948         }
 949         workdir := runner.Container.Cwd
 950         if workdir == "." {
 951                 // both "" and "." mean default
 952                 workdir = ""
 953         }
 954         ram := runner.Container.RuntimeConstraints.RAM
 955         if !runner.enableMemoryLimit {
 956                 ram = 0
 957         }
 958         runner.executorStdin = stdin
 959         runner.executorStdout = stdout
 960         runner.executorStderr = stderr
 961         return runner.executor.Create(containerSpec{
 962                 Image:         imageID,
 963                 VCPUs:         runner.Container.RuntimeConstraints.VCPUs,
 964                 RAM:           ram,
 965                 WorkingDir:    workdir,
 966                 Env:           env,
 967                 BindMounts:    bindmounts,
 968                 Command:       runner.Container.Command,
 969                 EnableNetwork: enableNetwork,
 970                 NetworkMode:   runner.networkMode,
 971                 CgroupParent:  runner.setCgroupParent,
 972                 Stdin:         stdin,
 973                 Stdout:        stdout,
 974                 Stderr:        stderr,
 975         })
 976 }
 977
 978 // StartContainer starts the docker container created by CreateContainer.
 979 func (runner *ContainerRunner) StartContainer() error {
 980         runner.CrunchLog.Printf("Starting container")
 981         runner.cStateLock.Lock()
 982         defer runner.cStateLock.Unlock()
 983         if runner.cCancelled {
 984                 return ErrCancelled
 985         }
 986         err := runner.executor.Start()
 987         if err != nil {
 988                 var advice string
 989                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
 990                         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])
 991                 }
 992                 return fmt.Errorf("could not start container: %v%s", err, advice)
 993         }
 994         return nil
 995 }
 996
 997 // WaitFinish waits for the container to terminate, capture the exit code, and
 998 // close the stdout/stderr logging.
 999 func (runner *ContainerRunner) WaitFinish() error {
1000         runner.CrunchLog.Print("Waiting for container to finish")
1001         var timeout <-chan time.Time
1002         if s := runner.Container.SchedulingParameters.MaxRunTime; s > 0 {
1003                 timeout = time.After(time.Duration(s) * time.Second)
1004         }
1005         ctx, cancel := context.WithCancel(context.Background())
1006         defer cancel()
1007         go func() {
1008                 select {
1009                 case <-timeout:
1010                         runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
1011                         runner.stop(nil)
1012                 case <-runner.ArvMountExit:
1013                         runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
1014                         runner.stop(nil)
1015                 case <-ctx.Done():
1016                 }
1017         }()
1018         exitcode, err := runner.executor.Wait(ctx)
1019         if err != nil {
1020                 runner.checkBrokenNode(err)
1021                 return err
1022         }
1023         runner.ExitCode = &exitcode
1024
1025         var returnErr error
1026         if err = runner.executorStdin.Close(); err != nil {
1027                 err = fmt.Errorf("error closing container stdin: %s", err)
1028                 runner.CrunchLog.Printf("%s", err)
1029                 returnErr = err
1030         }
1031         if err = runner.executorStdout.Close(); err != nil {
1032                 err = fmt.Errorf("error closing container stdout: %s", err)
1033                 runner.CrunchLog.Printf("%s", err)
1034                 if returnErr == nil {
1035                         returnErr = err
1036                 }
1037         }
1038         if err = runner.executorStderr.Close(); err != nil {
1039                 err = fmt.Errorf("error closing container stderr: %s", err)
1040                 runner.CrunchLog.Printf("%s", err)
1041                 if returnErr == nil {
1042                         returnErr = err
1043                 }
1044         }
1045
1046         if runner.statReporter != nil {
1047                 runner.statReporter.Stop()
1048                 err = runner.statLogger.Close()
1049                 if err != nil {
1050                         runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
1051                 }
1052         }
1053         return returnErr
1054 }
1055
1056 func (runner *ContainerRunner) updateLogs() {
1057         ticker := time.NewTicker(crunchLogUpdatePeriod / 360)
1058         defer ticker.Stop()
1059
1060         sigusr1 := make(chan os.Signal, 1)
1061         signal.Notify(sigusr1, syscall.SIGUSR1)
1062         defer signal.Stop(sigusr1)
1063
1064         saveAtTime := time.Now().Add(crunchLogUpdatePeriod)
1065         saveAtSize := crunchLogUpdateSize
1066         var savedSize int64
1067         for {
1068                 select {
1069                 case <-ticker.C:
1070                 case <-sigusr1:
1071                         saveAtTime = time.Now()
1072                 }
1073                 runner.logMtx.Lock()
1074                 done := runner.LogsPDH != nil
1075                 runner.logMtx.Unlock()
1076                 if done {
1077                         return
1078                 }
1079                 size := runner.LogCollection.Size()
1080                 if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) {
1081                         continue
1082                 }
1083                 saveAtTime = time.Now().Add(crunchLogUpdatePeriod)
1084                 saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize
1085                 saved, err := runner.saveLogCollection(false)
1086                 if err != nil {
1087                         runner.CrunchLog.Printf("error updating log collection: %s", err)
1088                         continue
1089                 }
1090
1091                 var updated arvados.Container
1092                 err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
1093                         "container": arvadosclient.Dict{"log": saved.PortableDataHash},
1094                 }, &updated)
1095                 if err != nil {
1096                         runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
1097                         continue
1098                 }
1099
1100                 savedSize = size
1101         }
1102 }
1103
1104 // CaptureOutput saves data from the container's output directory if
1105 // needed, and updates the container output accordingly.
1106 func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) error {
1107         if runner.Container.RuntimeConstraints.API {
1108                 // Output may have been set directly by the container, so
1109                 // refresh the container record to check.
1110                 err := runner.DispatcherArvClient.Get("containers", runner.Container.UUID,
1111                         nil, &runner.Container)
1112                 if err != nil {
1113                         return err
1114                 }
1115                 if runner.Container.Output != "" {
1116                         // Container output is already set.
1117                         runner.OutputPDH = &runner.Container.Output
1118                         return nil
1119                 }
1120         }
1121
1122         txt, err := (&copier{
1123                 client:        runner.containerClient,
1124                 arvClient:     runner.ContainerArvClient,
1125                 keepClient:    runner.ContainerKeepClient,
1126                 hostOutputDir: runner.HostOutputDir,
1127                 ctrOutputDir:  runner.Container.OutputPath,
1128                 bindmounts:    bindmounts,
1129                 mounts:        runner.Container.Mounts,
1130                 secretMounts:  runner.SecretMounts,
1131                 logger:        runner.CrunchLog,
1132         }).Copy()
1133         if err != nil {
1134                 return err
1135         }
1136         if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 {
1137                 runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n)
1138                 fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.containerClient, runner.ContainerKeepClient)
1139                 if err != nil {
1140                         return err
1141                 }
1142                 txt, err = fs.MarshalManifest(".")
1143                 if err != nil {
1144                         return err
1145                 }
1146         }
1147         var resp arvados.Collection
1148         err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
1149                 "ensure_unique_name": true,
1150                 "collection": arvadosclient.Dict{
1151                         "is_trashed":    true,
1152                         "name":          "output for " + runner.Container.UUID,
1153                         "manifest_text": txt,
1154                 },
1155         }, &resp)
1156         if err != nil {
1157                 return fmt.Errorf("error creating output collection: %v", err)
1158         }
1159         runner.OutputPDH = &resp.PortableDataHash
1160         return nil
1161 }
1162
1163 func (runner *ContainerRunner) CleanupDirs() {
1164         if runner.ArvMount != nil {
1165                 var delay int64 = 8
1166                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1167                 umount.Stdout = runner.CrunchLog
1168                 umount.Stderr = runner.CrunchLog
1169                 runner.CrunchLog.Printf("Running %v", umount.Args)
1170                 umnterr := umount.Start()
1171
1172                 if umnterr != nil {
1173                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1174                 } else {
1175                         // If arv-mount --unmount gets stuck for any reason, we
1176                         // don't want to wait for it forever.  Do Wait() in a goroutine
1177                         // so it doesn't block crunch-run.
1178                         umountExit := make(chan error)
1179                         go func() {
1180                                 mnterr := umount.Wait()
1181                                 if mnterr != nil {
1182                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1183                                 }
1184                                 umountExit <- mnterr
1185                         }()
1186
1187                         for again := true; again; {
1188                                 again = false
1189                                 select {
1190                                 case <-umountExit:
1191                                         umount = nil
1192                                         again = true
1193                                 case <-runner.ArvMountExit:
1194                                         break
1195                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1196                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1197                                         if umount != nil {
1198                                                 umount.Process.Kill()
1199                                         }
1200                                         runner.ArvMount.Process.Kill()
1201                                 }
1202                         }
1203                 }
1204         }
1205
1206         if runner.ArvMountPoint != "" {
1207                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1208                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1209                 }
1210         }
1211
1212         if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
1213                 runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
1214         }
1215 }
1216
1217 // CommitLogs posts the collection containing the final container logs.
1218 func (runner *ContainerRunner) CommitLogs() error {
1219         func() {
1220                 // Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
1221                 runner.cStateLock.Lock()
1222                 defer runner.cStateLock.Unlock()
1223
1224                 runner.CrunchLog.Print(runner.finalState)
1225
1226                 if runner.arvMountLog != nil {
1227                         runner.arvMountLog.Close()
1228                 }
1229                 runner.CrunchLog.Close()
1230
1231                 // Closing CrunchLog above allows them to be committed to Keep at this
1232                 // point, but re-open crunch log with ArvClient in case there are any
1233                 // other further errors (such as failing to write the log to Keep!)
1234                 // while shutting down
1235                 runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
1236                         ArvClient:     runner.DispatcherArvClient,
1237                         UUID:          runner.Container.UUID,
1238                         loggingStream: "crunch-run",
1239                         writeCloser:   nil,
1240                 })
1241                 runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1242         }()
1243
1244         if runner.LogsPDH != nil {
1245                 // If we have already assigned something to LogsPDH,
1246                 // we must be closing the re-opened log, which won't
1247                 // end up getting attached to the container record and
1248                 // therefore doesn't need to be saved as a collection
1249                 // -- it exists only to send logs to other channels.
1250                 return nil
1251         }
1252         saved, err := runner.saveLogCollection(true)
1253         if err != nil {
1254                 return fmt.Errorf("error saving log collection: %s", err)
1255         }
1256         runner.logMtx.Lock()
1257         defer runner.logMtx.Unlock()
1258         runner.LogsPDH = &saved.PortableDataHash
1259         return nil
1260 }
1261
1262 func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
1263         runner.logMtx.Lock()
1264         defer runner.logMtx.Unlock()
1265         if runner.LogsPDH != nil {
1266                 // Already finalized.
1267                 return
1268         }
1269         updates := arvadosclient.Dict{
1270                 "name": "logs for " + runner.Container.UUID,
1271         }
1272         mt, err1 := runner.LogCollection.MarshalManifest(".")
1273         if err1 == nil {
1274                 // Only send updated manifest text if there was no
1275                 // error.
1276                 updates["manifest_text"] = mt
1277         }
1278
1279         // Even if flushing the manifest had an error, we still want
1280         // to update the log record, if possible, to push the trash_at
1281         // and delete_at times into the future.  Details on bug
1282         // #17293.
1283         if final {
1284                 updates["is_trashed"] = true
1285         } else {
1286                 exp := time.Now().Add(crunchLogUpdatePeriod * 24)
1287                 updates["trash_at"] = exp
1288                 updates["delete_at"] = exp
1289         }
1290         reqBody := arvadosclient.Dict{"collection": updates}
1291         var err2 error
1292         if runner.logUUID == "" {
1293                 reqBody["ensure_unique_name"] = true
1294                 err2 = runner.DispatcherArvClient.Create("collections", reqBody, &response)
1295         } else {
1296                 err2 = runner.DispatcherArvClient.Update("collections", runner.logUUID, reqBody, &response)
1297         }
1298         if err2 == nil {
1299                 runner.logUUID = response.UUID
1300         }
1301
1302         if err1 != nil || err2 != nil {
1303                 err = fmt.Errorf("error recording logs: %q, %q", err1, err2)
1304         }
1305         return
1306 }
1307
1308 // UpdateContainerRunning updates the container state to "Running"
1309 func (runner *ContainerRunner) UpdateContainerRunning() error {
1310         runner.cStateLock.Lock()
1311         defer runner.cStateLock.Unlock()
1312         if runner.cCancelled {
1313                 return ErrCancelled
1314         }
1315         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID,
1316                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running", "gateway_address": runner.gateway.Address}}, nil)
1317 }
1318
1319 // ContainerToken returns the api_token the container (and any
1320 // arv-mount processes) are allowed to use.
1321 func (runner *ContainerRunner) ContainerToken() (string, error) {
1322         if runner.token != "" {
1323                 return runner.token, nil
1324         }
1325
1326         var auth arvados.APIClientAuthorization
1327         err := runner.DispatcherArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1328         if err != nil {
1329                 return "", err
1330         }
1331         runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID)
1332         return runner.token, nil
1333 }
1334
1335 // UpdateContainerFinal updates the container record state on API
1336 // server to "Complete" or "Cancelled"
1337 func (runner *ContainerRunner) UpdateContainerFinal() error {
1338         update := arvadosclient.Dict{}
1339         update["state"] = runner.finalState
1340         if runner.LogsPDH != nil {
1341                 update["log"] = *runner.LogsPDH
1342         }
1343         if runner.finalState == "Complete" {
1344                 if runner.ExitCode != nil {
1345                         update["exit_code"] = *runner.ExitCode
1346                 }
1347                 if runner.OutputPDH != nil {
1348                         update["output"] = *runner.OutputPDH
1349                 }
1350         }
1351         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1352 }
1353
1354 // IsCancelled returns the value of Cancelled, with goroutine safety.
1355 func (runner *ContainerRunner) IsCancelled() bool {
1356         runner.cStateLock.Lock()
1357         defer runner.cStateLock.Unlock()
1358         return runner.cCancelled
1359 }
1360
1361 // NewArvLogWriter creates an ArvLogWriter
1362 func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) {
1363         writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
1364         if err != nil {
1365                 return nil, err
1366         }
1367         return &ArvLogWriter{
1368                 ArvClient:     runner.DispatcherArvClient,
1369                 UUID:          runner.Container.UUID,
1370                 loggingStream: name,
1371                 writeCloser:   writer,
1372         }, nil
1373 }
1374
1375 // Run the full container lifecycle.
1376 func (runner *ContainerRunner) Run() (err error) {
1377         runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
1378         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1379
1380         hostname, hosterr := os.Hostname()
1381         if hosterr != nil {
1382                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1383         } else {
1384                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1385         }
1386
1387         runner.finalState = "Queued"
1388
1389         defer func() {
1390                 runner.CleanupDirs()
1391
1392                 runner.CrunchLog.Printf("crunch-run finished")
1393                 runner.CrunchLog.Close()
1394         }()
1395
1396         err = runner.fetchContainerRecord()
1397         if err != nil {
1398                 return
1399         }
1400         if runner.Container.State != "Locked" {
1401                 return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
1402         }
1403
1404         var bindmounts map[string]bindmount
1405         defer func() {
1406                 // checkErr prints e (unless it's nil) and sets err to
1407                 // e (unless err is already non-nil). Thus, if err
1408                 // hasn't already been assigned when Run() returns,
1409                 // this cleanup func will cause Run() to return the
1410                 // first non-nil error that is passed to checkErr().
1411                 checkErr := func(errorIn string, e error) {
1412                         if e == nil {
1413                                 return
1414                         }
1415                         runner.CrunchLog.Printf("error in %s: %v", errorIn, e)
1416                         if err == nil {
1417                                 err = e
1418                         }
1419                         if runner.finalState == "Complete" {
1420                                 // There was an error in the finalization.
1421                                 runner.finalState = "Cancelled"
1422                         }
1423                 }
1424
1425                 // Log the error encountered in Run(), if any
1426                 checkErr("Run", err)
1427
1428                 if runner.finalState == "Queued" {
1429                         runner.UpdateContainerFinal()
1430                         return
1431                 }
1432
1433                 if runner.IsCancelled() {
1434                         runner.finalState = "Cancelled"
1435                         // but don't return yet -- we still want to
1436                         // capture partial output and write logs
1437                 }
1438
1439                 if bindmounts != nil {
1440                         checkErr("CaptureOutput", runner.CaptureOutput(bindmounts))
1441                 }
1442                 checkErr("stopHoststat", runner.stopHoststat())
1443                 checkErr("CommitLogs", runner.CommitLogs())
1444                 checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
1445         }()
1446
1447         runner.setupSignals()
1448         err = runner.startHoststat()
1449         if err != nil {
1450                 return
1451         }
1452
1453         // set up FUSE mount and binds
1454         bindmounts, err = runner.SetupMounts()
1455         if err != nil {
1456                 runner.finalState = "Cancelled"
1457                 err = fmt.Errorf("While setting up mounts: %v", err)
1458                 return
1459         }
1460
1461         // check for and/or load image
1462         imageID, err := runner.LoadImage()
1463         if err != nil {
1464                 if !runner.checkBrokenNode(err) {
1465                         // Failed to load image but not due to a "broken node"
1466                         // condition, probably user error.
1467                         runner.finalState = "Cancelled"
1468                 }
1469                 err = fmt.Errorf("While loading container image: %v", err)
1470                 return
1471         }
1472
1473         err = runner.CreateContainer(imageID, bindmounts)
1474         if err != nil {
1475                 return
1476         }
1477         err = runner.LogHostInfo()
1478         if err != nil {
1479                 return
1480         }
1481         err = runner.LogNodeRecord()
1482         if err != nil {
1483                 return
1484         }
1485         err = runner.LogContainerRecord()
1486         if err != nil {
1487                 return
1488         }
1489
1490         if runner.IsCancelled() {
1491                 return
1492         }
1493
1494         err = runner.UpdateContainerRunning()
1495         if err != nil {
1496                 return
1497         }
1498         runner.finalState = "Cancelled"
1499
1500         err = runner.startCrunchstat()
1501         if err != nil {
1502                 return
1503         }
1504
1505         err = runner.StartContainer()
1506         if err != nil {
1507                 runner.checkBrokenNode(err)
1508                 return
1509         }
1510
1511         err = runner.WaitFinish()
1512         if err == nil && !runner.IsCancelled() {
1513                 runner.finalState = "Complete"
1514         }
1515         return
1516 }
1517
1518 // Fetch the current container record (uuid = runner.Container.UUID)
1519 // into runner.Container.
1520 func (runner *ContainerRunner) fetchContainerRecord() error {
1521         reader, err := runner.DispatcherArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1522         if err != nil {
1523                 return fmt.Errorf("error fetching container record: %v", err)
1524         }
1525         defer reader.Close()
1526
1527         dec := json.NewDecoder(reader)
1528         dec.UseNumber()
1529         err = dec.Decode(&runner.Container)
1530         if err != nil {
1531                 return fmt.Errorf("error decoding container record: %v", err)
1532         }
1533
1534         var sm struct {
1535                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
1536         }
1537
1538         containerToken, err := runner.ContainerToken()
1539         if err != nil {
1540                 return fmt.Errorf("error getting container token: %v", err)
1541         }
1542
1543         runner.ContainerArvClient, runner.ContainerKeepClient,
1544                 runner.containerClient, err = runner.MkArvClient(containerToken)
1545         if err != nil {
1546                 return fmt.Errorf("error creating container API client: %v", err)
1547         }
1548
1549         runner.ContainerKeepClient.SetStorageClasses(runner.Container.OutputStorageClasses)
1550         runner.DispatcherKeepClient.SetStorageClasses(runner.Container.OutputStorageClasses)
1551
1552         err = runner.ContainerArvClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
1553         if err != nil {
1554                 if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
1555                         return fmt.Errorf("error fetching secret_mounts: %v", err)
1556                 }
1557                 // ok && apierr.HttpStatusCode == 404, which means
1558                 // secret_mounts isn't supported by this API server.
1559         }
1560         runner.SecretMounts = sm.SecretMounts
1561
1562         return nil
1563 }
1564
1565 // NewContainerRunner creates a new container runner.
1566 func NewContainerRunner(dispatcherClient *arvados.Client,
1567         dispatcherArvClient IArvadosClient,
1568         dispatcherKeepClient IKeepClient,
1569         containerUUID string) (*ContainerRunner, error) {
1570
1571         cr := &ContainerRunner{
1572                 dispatcherClient:     dispatcherClient,
1573                 DispatcherArvClient:  dispatcherArvClient,
1574                 DispatcherKeepClient: dispatcherKeepClient,
1575         }
1576         cr.NewLogWriter = cr.NewArvLogWriter
1577         cr.RunArvMount = cr.ArvMountCmd
1578         cr.MkTempDir = ioutil.TempDir
1579         cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
1580                 cl, err := arvadosclient.MakeArvadosClient()
1581                 if err != nil {
1582                         return nil, nil, nil, err
1583                 }
1584                 cl.ApiToken = token
1585                 kc, err := keepclient.MakeKeepClient(cl)
1586                 if err != nil {
1587                         return nil, nil, nil, err
1588                 }
1589                 c2 := arvados.NewClientFromEnv()
1590                 c2.AuthToken = token
1591                 return cl, kc, c2, nil
1592         }
1593         var err error
1594         cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.dispatcherClient, cr.DispatcherKeepClient)
1595         if err != nil {
1596                 return nil, err
1597         }
1598         cr.Container.UUID = containerUUID
1599         w, err := cr.NewLogWriter("crunch-run")
1600         if err != nil {
1601                 return nil, err
1602         }
1603         cr.CrunchLog = NewThrottledLogger(w)
1604         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1605
1606         loadLogThrottleParams(dispatcherArvClient)
1607         go cr.updateLogs()
1608
1609         return cr, nil
1610 }
1611
1612 func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
1613         flags := flag.NewFlagSet(prog, flag.ContinueOnError)
1614         statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1615         cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1616         cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1617         cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1618         caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
1619         detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
1620         stdinEnv := flags.Bool("stdin-env", false, "Load environment variables from JSON message on stdin")
1621         sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
1622         kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
1623         list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
1624         enableMemoryLimit := flags.Bool("enable-memory-limit", true, "tell container runtime to limit container's memory usage")
1625         enableNetwork := flags.String("container-enable-networking", "default", "enable networking \"always\" (for all containers) or \"default\" (for containers that request it)")
1626         networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
1627         memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
1628         runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
1629         flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
1630
1631         ignoreDetachFlag := false
1632         if len(args) > 0 && args[0] == "-no-detach" {
1633                 // This process was invoked by a parent process, which
1634                 // has passed along its own arguments, including
1635                 // -detach, after the leading -no-detach flag.  Strip
1636                 // the leading -no-detach flag (it's not recognized by
1637                 // flags.Parse()) and ignore the -detach flag that
1638                 // comes later.
1639                 args = args[1:]
1640                 ignoreDetachFlag = true
1641         }
1642
1643         if err := flags.Parse(args); err == flag.ErrHelp {
1644                 return 0
1645         } else if err != nil {
1646                 log.Print(err)
1647                 return 1
1648         }
1649
1650         if *stdinEnv && !ignoreDetachFlag {
1651                 // Load env vars on stdin if asked (but not in a
1652                 // detached child process, in which case stdin is
1653                 // /dev/null).
1654                 err := loadEnv(os.Stdin)
1655                 if err != nil {
1656                         log.Print(err)
1657                         return 1
1658                 }
1659         }
1660
1661         containerUUID := flags.Arg(0)
1662
1663         switch {
1664         case *detach && !ignoreDetachFlag:
1665                 return Detach(containerUUID, prog, args, os.Stdout, os.Stderr)
1666         case *kill >= 0:
1667                 return KillProcess(containerUUID, syscall.Signal(*kill), os.Stdout, os.Stderr)
1668         case *list:
1669                 return ListProcesses(os.Stdout, os.Stderr)
1670         }
1671
1672         if containerUUID == "" {
1673                 log.Printf("usage: %s [options] UUID", prog)
1674                 return 1
1675         }
1676
1677         log.Printf("crunch-run %s started", cmd.Version.String())
1678         time.Sleep(*sleep)
1679
1680         if *caCertsPath != "" {
1681                 arvadosclient.CertFiles = []string{*caCertsPath}
1682         }
1683
1684         api, err := arvadosclient.MakeArvadosClient()
1685         if err != nil {
1686                 log.Printf("%s: %v", containerUUID, err)
1687                 return 1
1688         }
1689         api.Retries = 8
1690
1691         kc, kcerr := keepclient.MakeKeepClient(api)
1692         if kcerr != nil {
1693                 log.Printf("%s: %v", containerUUID, kcerr)
1694                 return 1
1695         }
1696         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1697         kc.Retries = 4
1698
1699         cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, containerUUID)
1700         if err != nil {
1701                 log.Print(err)
1702                 return 1
1703         }
1704
1705         switch *runtimeEngine {
1706         case "docker":
1707                 cr.executor, err = newDockerExecutor(containerUUID, cr.CrunchLog.Printf, cr.containerWatchdogInterval)
1708         case "singularity":
1709                 cr.executor, err = newSingularityExecutor(cr.CrunchLog.Printf)
1710         default:
1711                 cr.CrunchLog.Printf("%s: unsupported RuntimeEngine %q", containerUUID, *runtimeEngine)
1712                 cr.CrunchLog.Close()
1713                 return 1
1714         }
1715         if err != nil {
1716                 cr.CrunchLog.Printf("%s: %v", containerUUID, err)
1717                 cr.checkBrokenNode(err)
1718                 cr.CrunchLog.Close()
1719                 return 1
1720         }
1721         defer cr.executor.Close()
1722
1723         gwAuthSecret := os.Getenv("GatewayAuthSecret")
1724         os.Unsetenv("GatewayAuthSecret")
1725         if gwAuthSecret == "" {
1726                 // not safe to run a gateway service without an auth
1727                 // secret
1728                 cr.CrunchLog.Printf("Not starting a gateway server (GatewayAuthSecret was not provided by dispatcher)")
1729         } else if gwListen := os.Getenv("GatewayAddress"); gwListen == "" {
1730                 // dispatcher did not tell us which external IP
1731                 // address to advertise --> no gateway service
1732                 cr.CrunchLog.Printf("Not starting a gateway server (GatewayAddress was not provided by dispatcher)")
1733         } else if de, ok := cr.executor.(*dockerExecutor); ok {
1734                 cr.gateway = Gateway{
1735                         Address:            gwListen,
1736                         AuthSecret:         gwAuthSecret,
1737                         ContainerUUID:      containerUUID,
1738                         DockerContainerID:  &de.containerID,
1739                         Log:                cr.CrunchLog,
1740                         ContainerIPAddress: dockerContainerIPAddress(&de.containerID),
1741                 }
1742                 err = cr.gateway.Start()
1743                 if err != nil {
1744                         log.Printf("error starting gateway server: %s", err)
1745                         return 1
1746                 }
1747         }
1748
1749         parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerUUID+".")
1750         if tmperr != nil {
1751                 log.Printf("%s: %v", containerUUID, tmperr)
1752                 return 1
1753         }
1754
1755         cr.parentTemp = parentTemp
1756         cr.statInterval = *statInterval
1757         cr.cgroupRoot = *cgroupRoot
1758         cr.expectCgroupParent = *cgroupParent
1759         cr.enableMemoryLimit = *enableMemoryLimit
1760         cr.enableNetwork = *enableNetwork
1761         cr.networkMode = *networkMode
1762         if *cgroupParentSubsystem != "" {
1763                 p := findCgroup(*cgroupParentSubsystem)
1764                 cr.setCgroupParent = p
1765                 cr.expectCgroupParent = p
1766         }
1767
1768         runerr := cr.Run()
1769
1770         if *memprofile != "" {
1771                 f, err := os.Create(*memprofile)
1772                 if err != nil {
1773                         log.Printf("could not create memory profile: %s", err)
1774                 }
1775                 runtime.GC() // get up-to-date statistics
1776                 if err := pprof.WriteHeapProfile(f); err != nil {
1777                         log.Printf("could not write memory profile: %s", err)
1778                 }
1779                 closeerr := f.Close()
1780                 if closeerr != nil {
1781                         log.Printf("closing memprofile file: %s", err)
1782                 }
1783         }
1784
1785         if runerr != nil {
1786                 log.Printf("%s: %v", containerUUID, runerr)
1787                 return 1
1788         }
1789         return 0
1790 }
1791
1792 func loadEnv(rdr io.Reader) error {
1793         buf, err := ioutil.ReadAll(rdr)
1794         if err != nil {
1795                 return fmt.Errorf("read stdin: %s", err)
1796         }
1797         var env map[string]string
1798         err = json.Unmarshal(buf, &env)
1799         if err != nil {
1800                 return fmt.Errorf("decode stdin: %s", err)
1801         }
1802         for k, v := range env {
1803                 err = os.Setenv(k, v)
1804                 if err != nil {
1805                         return fmt.Errorf("setenv(%q): %s", k, err)
1806                 }
1807         }
1808         return nil
1809 }