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