lib/crunchrun/crunchrun.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package crunchrun
   6
   7 import (
   8         "bytes"
   9         "encoding/json"
  10         "errors"
  11         "flag"
  12         "fmt"
  13         "io"
  14         "io/ioutil"
  15         "log"
  16         "os"
  17         "os/exec"
  18         "os/signal"
  19         "path"
  20         "path/filepath"
  21         "regexp"
  22         "runtime"
  23         "runtime/pprof"
  24         "sort"
  25         "strings"
  26         "sync"
  27         "syscall"
  28         "time"
  29
  30         "git.arvados.org/arvados.git/lib/cmd"
  31         "git.arvados.org/arvados.git/lib/crunchstat"
  32         "git.arvados.org/arvados.git/sdk/go/arvados"
  33         "git.arvados.org/arvados.git/sdk/go/arvadosclient"
  34         "git.arvados.org/arvados.git/sdk/go/keepclient"
  35         "git.arvados.org/arvados.git/sdk/go/manifest"
  36         "golang.org/x/net/context"
  37 )
  38
  39 type command struct{}
  40
  41 var Command = command{}
  42
  43 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  44 type IArvadosClient interface {
  45         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  46         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  47         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  48         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  49         CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
  50         Discovery(key string) (interface{}, error)
  51 }
  52
  53 // ErrCancelled is the error returned when the container is cancelled.
  54 var ErrCancelled = errors.New("Cancelled")
  55
  56 // IKeepClient is the minimal Keep API methods used by crunch-run.
  57 type IKeepClient interface {
  58         PutB(buf []byte) (string, int, error)
  59         ReadAt(locator string, p []byte, off int) (int, error)
  60         ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
  61         LocalLocator(locator string) (string, error)
  62         ClearBlockCache()
  63 }
  64
  65 // NewLogWriter is a factory function to create a new log writer.
  66 type NewLogWriter func(name string) (io.WriteCloser, error)
  67
  68 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  69
  70 type MkTempDir func(string, string) (string, error)
  71
  72 type PsProcess interface {
  73         CmdlineSlice() ([]string, error)
  74 }
  75
  76 // ContainerRunner is the main stateful struct used for a single execution of a
  77 // container.
  78 type ContainerRunner struct {
  79         executor containerExecutor
  80
  81         // Dispatcher client is initialized with the Dispatcher token.
  82         // This is a privileged token used to manage container status
  83         // and logs.
  84         //
  85         // We have both dispatcherClient and DispatcherArvClient
  86         // because there are two different incompatible Arvados Go
  87         // SDKs and we have to use both (hopefully this gets fixed in
  88         // #14467)
  89         dispatcherClient     *arvados.Client
  90         DispatcherArvClient  IArvadosClient
  91         DispatcherKeepClient IKeepClient
  92
  93         // Container client is initialized with the Container token
  94         // This token controls the permissions of the container, and
  95         // must be used for operations such as reading collections.
  96         //
  97         // Same comment as above applies to
  98         // containerClient/ContainerArvClient.
  99         containerClient     *arvados.Client
 100         ContainerArvClient  IArvadosClient
 101         ContainerKeepClient IKeepClient
 102
 103         Container     arvados.Container
 104         token         string
 105         ExitCode      *int
 106         NewLogWriter  NewLogWriter
 107         CrunchLog     *ThrottledLogger
 108         Stdout        io.WriteCloser
 109         Stderr        io.WriteCloser
 110         logUUID       string
 111         logMtx        sync.Mutex
 112         LogCollection arvados.CollectionFileSystem
 113         LogsPDH       *string
 114         RunArvMount   RunArvMount
 115         MkTempDir     MkTempDir
 116         ArvMount      *exec.Cmd
 117         ArvMountPoint string
 118         HostOutputDir string
 119         Volumes       map[string]struct{}
 120         OutputPDH     *string
 121         SigChan       chan os.Signal
 122         ArvMountExit  chan error
 123         SecretMounts  map[string]arvados.Mount
 124         MkArvClient   func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
 125         finalState    string
 126         parentTemp    string
 127
 128         statLogger       io.WriteCloser
 129         statReporter     *crunchstat.Reporter
 130         hoststatLogger   io.WriteCloser
 131         hoststatReporter *crunchstat.Reporter
 132         statInterval     time.Duration
 133         cgroupRoot       string
 134         // What we expect the container's cgroup parent to be.
 135         expectCgroupParent string
 136         // What we tell docker to use as the container's cgroup
 137         // parent. Note: Ideally we would use the same field for both
 138         // expectCgroupParent and setCgroupParent, and just make it
 139         // default to "docker". However, when using docker < 1.10 with
 140         // systemd, specifying a non-empty cgroup parent (even the
 141         // default value "docker") hits a docker bug
 142         // (https://github.com/docker/docker/issues/17126). Using two
 143         // separate fields makes it possible to use the "expect cgroup
 144         // parent to be X" feature even on sites where the "specify
 145         // cgroup parent" feature breaks.
 146         setCgroupParent string
 147
 148         cStateLock sync.Mutex
 149         cCancelled bool // StopContainer() invoked
 150
 151         enableMemoryLimit bool
 152         enableNetwork     string // one of "default" or "always"
 153         networkMode       string // "none", "host", or "" -- passed through to executor
 154         arvMountLog       *ThrottledLogger
 155
 156         containerWatchdogInterval time.Duration
 157
 158         gateway Gateway
 159 }
 160
 161 // setupSignals sets up signal handling to gracefully terminate the
 162 // underlying container and update state when receiving a TERM, INT or
 163 // QUIT signal.
 164 func (runner *ContainerRunner) setupSignals() {
 165         runner.SigChan = make(chan os.Signal, 1)
 166         signal.Notify(runner.SigChan, syscall.SIGTERM)
 167         signal.Notify(runner.SigChan, syscall.SIGINT)
 168         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 169
 170         go func(sig chan os.Signal) {
 171                 for s := range sig {
 172                         runner.stop(s)
 173                 }
 174         }(runner.SigChan)
 175 }
 176
 177 // stop the underlying container.
 178 func (runner *ContainerRunner) stop(sig os.Signal) {
 179         runner.cStateLock.Lock()
 180         defer runner.cStateLock.Unlock()
 181         if sig != nil {
 182                 runner.CrunchLog.Printf("caught signal: %v", sig)
 183         }
 184         runner.cCancelled = true
 185         runner.CrunchLog.Printf("stopping container")
 186         err := runner.executor.Stop()
 187         if err != nil {
 188                 runner.CrunchLog.Printf("error stopping container: %s", err)
 189         }
 190 }
 191
 192 var errorBlacklist = []string{
 193         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 194         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 195         "(?ms).*grpc: the connection is unavailable.*",
 196 }
 197 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)")
 198
 199 func (runner *ContainerRunner) runBrokenNodeHook() {
 200         if *brokenNodeHook == "" {
 201                 path := filepath.Join(lockdir, brokenfile)
 202                 runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
 203                 f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
 204                 if err != nil {
 205                         runner.CrunchLog.Printf("Error writing %s: %s", path, err)
 206                         return
 207                 }
 208                 f.Close()
 209         } else {
 210                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 211                 // run killme script
 212                 c := exec.Command(*brokenNodeHook)
 213                 c.Stdout = runner.CrunchLog
 214                 c.Stderr = runner.CrunchLog
 215                 err := c.Run()
 216                 if err != nil {
 217                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 218                 }
 219         }
 220 }
 221
 222 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 223         for _, d := range errorBlacklist {
 224                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 225                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 226                         runner.runBrokenNodeHook()
 227                         return true
 228                 }
 229         }
 230         return false
 231 }
 232
 233 // LoadImage determines the docker image id from the container record and
 234 // checks if it is available in the local Docker image store.  If not, it loads
 235 // the image from Keep.
 236 func (runner *ContainerRunner) LoadImage() (string, error) {
 237         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 238
 239         d, err := os.Open(runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage)
 240         if err != nil {
 241                 return "", err
 242         }
 243         defer d.Close()
 244         allfiles, err := d.Readdirnames(-1)
 245         if err != nil {
 246                 return "", err
 247         }
 248         var tarfiles []string
 249         for _, fnm := range allfiles {
 250                 if strings.HasSuffix(fnm, ".tar") {
 251                         tarfiles = append(tarfiles, fnm)
 252                 }
 253         }
 254         if len(tarfiles) == 0 {
 255                 return "", fmt.Errorf("image collection does not include a .tar image file")
 256         }
 257         if len(tarfiles) > 1 {
 258                 return "", fmt.Errorf("cannot choose from multiple tar files in image collection: %v", tarfiles)
 259         }
 260         imageID := tarfiles[0][:len(tarfiles[0])-4]
 261         imageFile := runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage + "/" + tarfiles[0]
 262         runner.CrunchLog.Printf("Using Docker image id %q", imageID)
 263
 264         if !runner.executor.ImageLoaded(imageID) {
 265                 runner.CrunchLog.Print("Loading Docker image from keep")
 266                 err = runner.executor.LoadImage(imageFile)
 267                 if err != nil {
 268                         return "", err
 269                 }
 270         } else {
 271                 runner.CrunchLog.Print("Docker image is available")
 272         }
 273         return imageID, nil
 274 }
 275
 276 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 277         c = exec.Command("arv-mount", arvMountCmd...)
 278
 279         // Copy our environment, but override ARVADOS_API_TOKEN with
 280         // the container auth token.
 281         c.Env = nil
 282         for _, s := range os.Environ() {
 283                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 284                         c.Env = append(c.Env, s)
 285                 }
 286         }
 287         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 288
 289         w, err := runner.NewLogWriter("arv-mount")
 290         if err != nil {
 291                 return nil, err
 292         }
 293         runner.arvMountLog = NewThrottledLogger(w)
 294         c.Stdout = runner.arvMountLog
 295         c.Stderr = io.MultiWriter(runner.arvMountLog, os.Stderr)
 296
 297         runner.CrunchLog.Printf("Running %v", c.Args)
 298
 299         err = c.Start()
 300         if err != nil {
 301                 return nil, err
 302         }
 303
 304         statReadme := make(chan bool)
 305         runner.ArvMountExit = make(chan error)
 306
 307         keepStatting := true
 308         go func() {
 309                 for keepStatting {
 310                         time.Sleep(100 * time.Millisecond)
 311                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 312                         if err == nil {
 313                                 keepStatting = false
 314                                 statReadme <- true
 315                         }
 316                 }
 317                 close(statReadme)
 318         }()
 319
 320         go func() {
 321                 mnterr := c.Wait()
 322                 if mnterr != nil {
 323                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 324                 }
 325                 runner.ArvMountExit <- mnterr
 326                 close(runner.ArvMountExit)
 327         }()
 328
 329         select {
 330         case <-statReadme:
 331                 break
 332         case err := <-runner.ArvMountExit:
 333                 runner.ArvMount = nil
 334                 keepStatting = false
 335                 return nil, err
 336         }
 337
 338         return c, nil
 339 }
 340
 341 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 342         if runner.ArvMountPoint == "" {
 343                 runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
 344         }
 345         return
 346 }
 347
 348 func copyfile(src string, dst string) (err error) {
 349         srcfile, err := os.Open(src)
 350         if err != nil {
 351                 return
 352         }
 353
 354         os.MkdirAll(path.Dir(dst), 0777)
 355
 356         dstfile, err := os.Create(dst)
 357         if err != nil {
 358                 return
 359         }
 360         _, err = io.Copy(dstfile, srcfile)
 361         if err != nil {
 362                 return
 363         }
 364
 365         err = srcfile.Close()
 366         err2 := dstfile.Close()
 367
 368         if err != nil {
 369                 return
 370         }
 371
 372         if err2 != nil {
 373                 return err2
 374         }
 375
 376         return nil
 377 }
 378
 379 func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
 380         bindmounts := map[string]bindmount{}
 381         err := runner.SetupArvMountPoint("keep")
 382         if err != nil {
 383                 return nil, fmt.Errorf("While creating keep mount temp dir: %v", err)
 384         }
 385
 386         token, err := runner.ContainerToken()
 387         if err != nil {
 388                 return nil, fmt.Errorf("could not get container token: %s", err)
 389         }
 390         runner.CrunchLog.Printf("container token %q", token)
 391
 392         pdhOnly := true
 393         tmpcount := 0
 394         arvMountCmd := []string{
 395                 "--foreground",
 396                 "--allow-other",
 397                 "--read-write",
 398                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 399
 400         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 401                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 402         }
 403
 404         collectionPaths := []string{}
 405         needCertMount := true
 406         type copyFile struct {
 407                 src  string
 408                 bind string
 409         }
 410         var copyFiles []copyFile
 411
 412         var binds []string
 413         for bind := range runner.Container.Mounts {
 414                 binds = append(binds, bind)
 415         }
 416         for bind := range runner.SecretMounts {
 417                 if _, ok := runner.Container.Mounts[bind]; ok {
 418                         return nil, fmt.Errorf("secret mount %q conflicts with regular mount", bind)
 419                 }
 420                 if runner.SecretMounts[bind].Kind != "json" &&
 421                         runner.SecretMounts[bind].Kind != "text" {
 422                         return nil, fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
 423                                 bind, runner.SecretMounts[bind].Kind)
 424                 }
 425                 binds = append(binds, bind)
 426         }
 427         sort.Strings(binds)
 428
 429         for _, bind := range binds {
 430                 mnt, ok := runner.Container.Mounts[bind]
 431                 if !ok {
 432                         mnt = runner.SecretMounts[bind]
 433                 }
 434                 if bind == "stdout" || bind == "stderr" {
 435                         // Is it a "file" mount kind?
 436                         if mnt.Kind != "file" {
 437                                 return nil, fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
 438                         }
 439
 440                         // Does path start with OutputPath?
 441                         prefix := runner.Container.OutputPath
 442                         if !strings.HasSuffix(prefix, "/") {
 443                                 prefix += "/"
 444                         }
 445                         if !strings.HasPrefix(mnt.Path, prefix) {
 446                                 return nil, fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 447                         }
 448                 }
 449
 450                 if bind == "stdin" {
 451                         // Is it a "collection" mount kind?
 452                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 453                                 return nil, fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
 454                         }
 455                 }
 456
 457                 if bind == "/etc/arvados/ca-certificates.crt" {
 458                         needCertMount = false
 459                 }
 460
 461                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 462                         if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
 463                                 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)
 464                         }
 465                 }
 466
 467                 switch {
 468                 case mnt.Kind == "collection" && bind != "stdin":
 469                         var src string
 470                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 471                                 return nil, fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 472                         }
 473                         if mnt.UUID != "" {
 474                                 if mnt.Writable {
 475                                         return nil, fmt.Errorf("writing to existing collections currently not permitted")
 476                                 }
 477                                 pdhOnly = false
 478                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 479                         } else if mnt.PortableDataHash != "" {
 480                                 if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 481                                         return nil, fmt.Errorf("can never write to a collection specified by portable data hash")
 482                                 }
 483                                 idx := strings.Index(mnt.PortableDataHash, "/")
 484                                 if idx > 0 {
 485                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 486                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 487                                         runner.Container.Mounts[bind] = mnt
 488                                 }
 489                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 490                                 if mnt.Path != "" && mnt.Path != "." {
 491                                         if strings.HasPrefix(mnt.Path, "./") {
 492                                                 mnt.Path = mnt.Path[2:]
 493                                         } else if strings.HasPrefix(mnt.Path, "/") {
 494                                                 mnt.Path = mnt.Path[1:]
 495                                         }
 496                                         src += "/" + mnt.Path
 497                                 }
 498                         } else {
 499                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 500                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 501                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 502                                 tmpcount++
 503                         }
 504                         if mnt.Writable {
 505                                 if bind == runner.Container.OutputPath {
 506                                         runner.HostOutputDir = src
 507                                         bindmounts[bind] = bindmount{HostPath: src}
 508                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 509                                         copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 510                                 } else {
 511                                         bindmounts[bind] = bindmount{HostPath: src}
 512                                 }
 513                         } else {
 514                                 bindmounts[bind] = bindmount{HostPath: src, ReadOnly: true}
 515                         }
 516                         collectionPaths = append(collectionPaths, src)
 517
 518                 case mnt.Kind == "tmp":
 519                         var tmpdir string
 520                         tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
 521                         if err != nil {
 522                                 return nil, fmt.Errorf("while creating mount temp dir: %v", err)
 523                         }
 524                         st, staterr := os.Stat(tmpdir)
 525                         if staterr != nil {
 526                                 return nil, fmt.Errorf("while Stat on temp dir: %v", staterr)
 527                         }
 528                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 529                         if staterr != nil {
 530                                 return nil, fmt.Errorf("while Chmod temp dir: %v", err)
 531                         }
 532                         bindmounts[bind] = bindmount{HostPath: tmpdir}
 533                         if bind == runner.Container.OutputPath {
 534                                 runner.HostOutputDir = tmpdir
 535                         }
 536
 537                 case mnt.Kind == "json" || mnt.Kind == "text":
 538                         var filedata []byte
 539                         if mnt.Kind == "json" {
 540                                 filedata, err = json.Marshal(mnt.Content)
 541                                 if err != nil {
 542                                         return nil, fmt.Errorf("encoding json data: %v", err)
 543                                 }
 544                         } else {
 545                                 text, ok := mnt.Content.(string)
 546                                 if !ok {
 547                                         return nil, fmt.Errorf("content for mount %q must be a string", bind)
 548                                 }
 549                                 filedata = []byte(text)
 550                         }
 551
 552                         tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
 553                         if err != nil {
 554                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 555                         }
 556                         tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
 557                         err = ioutil.WriteFile(tmpfn, filedata, 0444)
 558                         if err != nil {
 559                                 return nil, fmt.Errorf("writing temp file: %v", err)
 560                         }
 561                         if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 562                                 copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 563                         } else {
 564                                 bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
 565                         }
 566
 567                 case mnt.Kind == "git_tree":
 568                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
 569                         if err != nil {
 570                                 return nil, fmt.Errorf("creating temp dir: %v", err)
 571                         }
 572                         err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
 573                         if err != nil {
 574                                 return nil, err
 575                         }
 576                         bindmounts[bind] = bindmount{HostPath: tmpdir, ReadOnly: true}
 577                 }
 578         }
 579
 580         if runner.HostOutputDir == "" {
 581                 return nil, fmt.Errorf("output path does not correspond to a writable mount point")
 582         }
 583
 584         if needCertMount && runner.Container.RuntimeConstraints.API {
 585                 for _, certfile := range arvadosclient.CertFiles {
 586                         _, err := os.Stat(certfile)
 587                         if err == nil {
 588                                 bindmounts["/etc/arvados/ca-certificates.crt"] = bindmount{HostPath: certfile, ReadOnly: true}
 589                                 break
 590                         }
 591                 }
 592         }
 593
 594         if pdhOnly {
 595                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 596         } else {
 597                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 598         }
 599         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 600
 601         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 602         if err != nil {
 603                 return nil, fmt.Errorf("while trying to start arv-mount: %v", err)
 604         }
 605
 606         for _, p := range collectionPaths {
 607                 _, err = os.Stat(p)
 608                 if err != nil {
 609                         return nil, fmt.Errorf("while checking that input files exist: %v", err)
 610                 }
 611         }
 612
 613         for _, cp := range copyFiles {
 614                 st, err := os.Stat(cp.src)
 615                 if err != nil {
 616                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 617                 }
 618                 if st.IsDir() {
 619                         err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
 620                                 if walkerr != nil {
 621                                         return walkerr
 622                                 }
 623                                 target := path.Join(cp.bind, walkpath[len(cp.src):])
 624                                 if walkinfo.Mode().IsRegular() {
 625                                         copyerr := copyfile(walkpath, target)
 626                                         if copyerr != nil {
 627                                                 return copyerr
 628                                         }
 629                                         return os.Chmod(target, walkinfo.Mode()|0777)
 630                                 } else if walkinfo.Mode().IsDir() {
 631                                         mkerr := os.MkdirAll(target, 0777)
 632                                         if mkerr != nil {
 633                                                 return mkerr
 634                                         }
 635                                         return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 636                                 } else {
 637                                         return fmt.Errorf("source %q is not a regular file or directory", cp.src)
 638                                 }
 639                         })
 640                 } else if st.Mode().IsRegular() {
 641                         err = copyfile(cp.src, cp.bind)
 642                         if err == nil {
 643                                 err = os.Chmod(cp.bind, st.Mode()|0777)
 644                         }
 645                 }
 646                 if err != nil {
 647                         return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 648                 }
 649         }
 650
 651         return bindmounts, nil
 652 }
 653
 654 func (runner *ContainerRunner) stopHoststat() error {
 655         if runner.hoststatReporter == nil {
 656                 return nil
 657         }
 658         runner.hoststatReporter.Stop()
 659         err := runner.hoststatLogger.Close()
 660         if err != nil {
 661                 return fmt.Errorf("error closing hoststat logs: %v", err)
 662         }
 663         return nil
 664 }
 665
 666 func (runner *ContainerRunner) startHoststat() error {
 667         w, err := runner.NewLogWriter("hoststat")
 668         if err != nil {
 669                 return err
 670         }
 671         runner.hoststatLogger = NewThrottledLogger(w)
 672         runner.hoststatReporter = &crunchstat.Reporter{
 673                 Logger:     log.New(runner.hoststatLogger, "", 0),
 674                 CgroupRoot: runner.cgroupRoot,
 675                 PollPeriod: runner.statInterval,
 676         }
 677         runner.hoststatReporter.Start()
 678         return nil
 679 }
 680
 681 func (runner *ContainerRunner) startCrunchstat() error {
 682         w, err := runner.NewLogWriter("crunchstat")
 683         if err != nil {
 684                 return err
 685         }
 686         runner.statLogger = NewThrottledLogger(w)
 687         runner.statReporter = &crunchstat.Reporter{
 688                 CID:          runner.executor.CgroupID(),
 689                 Logger:       log.New(runner.statLogger, "", 0),
 690                 CgroupParent: runner.expectCgroupParent,
 691                 CgroupRoot:   runner.cgroupRoot,
 692                 PollPeriod:   runner.statInterval,
 693                 TempDir:      runner.parentTemp,
 694         }
 695         runner.statReporter.Start()
 696         return nil
 697 }
 698
 699 type infoCommand struct {
 700         label string
 701         cmd   []string
 702 }
 703
 704 // LogHostInfo logs info about the current host, for debugging and
 705 // accounting purposes. Although it's logged as "node-info", this is
 706 // about the environment where crunch-run is actually running, which
 707 // might differ from what's described in the node record (see
 708 // LogNodeRecord).
 709 func (runner *ContainerRunner) LogHostInfo() (err error) {
 710         w, err := runner.NewLogWriter("node-info")
 711         if err != nil {
 712                 return
 713         }
 714
 715         commands := []infoCommand{
 716                 {
 717                         label: "Host Information",
 718                         cmd:   []string{"uname", "-a"},
 719                 },
 720                 {
 721                         label: "CPU Information",
 722                         cmd:   []string{"cat", "/proc/cpuinfo"},
 723                 },
 724                 {
 725                         label: "Memory Information",
 726                         cmd:   []string{"cat", "/proc/meminfo"},
 727                 },
 728                 {
 729                         label: "Disk Space",
 730                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 731                 },
 732                 {
 733                         label: "Disk INodes",
 734                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 735                 },
 736         }
 737
 738         // Run commands with informational output to be logged.
 739         for _, command := range commands {
 740                 fmt.Fprintln(w, command.label)
 741                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 742                 cmd.Stdout = w
 743                 cmd.Stderr = w
 744                 if err := cmd.Run(); err != nil {
 745                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 746                         fmt.Fprintln(w, err)
 747                         return err
 748                 }
 749                 fmt.Fprintln(w, "")
 750         }
 751
 752         err = w.Close()
 753         if err != nil {
 754                 return fmt.Errorf("While closing node-info logs: %v", err)
 755         }
 756         return nil
 757 }
 758
 759 // LogContainerRecord gets and saves the raw JSON container record from the API server
 760 func (runner *ContainerRunner) LogContainerRecord() error {
 761         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 762         if !logged && err == nil {
 763                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 764         }
 765         return err
 766 }
 767
 768 // LogNodeRecord logs the current host's InstanceType config entry (or
 769 // the arvados#node record, if running via crunch-dispatch-slurm).
 770 func (runner *ContainerRunner) LogNodeRecord() error {
 771         if it := os.Getenv("InstanceType"); it != "" {
 772                 // Dispatched via arvados-dispatch-cloud. Save
 773                 // InstanceType config fragment received from
 774                 // dispatcher on stdin.
 775                 w, err := runner.LogCollection.OpenFile("node.json", os.O_CREATE|os.O_WRONLY, 0666)
 776                 if err != nil {
 777                         return err
 778                 }
 779                 defer w.Close()
 780                 _, err = io.WriteString(w, it)
 781                 if err != nil {
 782                         return err
 783                 }
 784                 return w.Close()
 785         }
 786         // Dispatched via crunch-dispatch-slurm. Look up
 787         // apiserver's node record corresponding to
 788         // $SLURMD_NODENAME.
 789         hostname := os.Getenv("SLURMD_NODENAME")
 790         if hostname == "" {
 791                 hostname, _ = os.Hostname()
 792         }
 793         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 794                 // The "info" field has admin-only info when
 795                 // obtained with a privileged token, and
 796                 // should not be logged.
 797                 node, ok := resp.(map[string]interface{})
 798                 if ok {
 799                         delete(node, "info")
 800                 }
 801         })
 802         return err
 803 }
 804
 805 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 806         writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
 807         if err != nil {
 808                 return false, err
 809         }
 810         w := &ArvLogWriter{
 811                 ArvClient:     runner.DispatcherArvClient,
 812                 UUID:          runner.Container.UUID,
 813                 loggingStream: label,
 814                 writeCloser:   writer,
 815         }
 816
 817         reader, err := runner.DispatcherArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 818         if err != nil {
 819                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 820         }
 821         defer reader.Close()
 822
 823         dec := json.NewDecoder(reader)
 824         dec.UseNumber()
 825         var resp map[string]interface{}
 826         if err = dec.Decode(&resp); err != nil {
 827                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 828         }
 829         items, ok := resp["items"].([]interface{})
 830         if !ok {
 831                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 832         } else if len(items) < 1 {
 833                 return false, nil
 834         }
 835         if munge != nil {
 836                 munge(items[0])
 837         }
 838         // Re-encode it using indentation to improve readability
 839         enc := json.NewEncoder(w)
 840         enc.SetIndent("", "    ")
 841         if err = enc.Encode(items[0]); err != nil {
 842                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 843         }
 844         err = w.Close()
 845         if err != nil {
 846                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 847         }
 848         return true, nil
 849 }
 850
 851 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 852         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 853         index := strings.LastIndex(stdoutPath, "/")
 854         if index > 0 {
 855                 subdirs := stdoutPath[:index]
 856                 if subdirs != "" {
 857                         st, err := os.Stat(runner.HostOutputDir)
 858                         if err != nil {
 859                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 860                         }
 861                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 862                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 863                         if err != nil {
 864                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 865                         }
 866                 }
 867         }
 868         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 869         if err != nil {
 870                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 871         }
 872
 873         return stdoutFile, nil
 874 }
 875
 876 // CreateContainer creates the docker container.
 877 func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[string]bindmount) error {
 878         var stdin io.ReadCloser
 879         if mnt, ok := runner.Container.Mounts["stdin"]; ok {
 880                 switch mnt.Kind {
 881                 case "collection":
 882                         var collID string
 883                         if mnt.UUID != "" {
 884                                 collID = mnt.UUID
 885                         } else {
 886                                 collID = mnt.PortableDataHash
 887                         }
 888                         path := runner.ArvMountPoint + "/by_id/" + collID + "/" + mnt.Path
 889                         f, err := os.Open(path)
 890                         if err != nil {
 891                                 return err
 892                         }
 893                         stdin = f
 894                 case "json":
 895                         j, err := json.Marshal(mnt.Content)
 896                         if err != nil {
 897                                 return fmt.Errorf("error encoding stdin json data: %v", err)
 898                         }
 899                         stdin = ioutil.NopCloser(bytes.NewReader(j))
 900                 default:
 901                         return fmt.Errorf("stdin mount has unsupported kind %q", mnt.Kind)
 902                 }
 903         }
 904
 905         var stdout, stderr io.WriteCloser
 906         if mnt, ok := runner.Container.Mounts["stdout"]; ok {
 907                 f, err := runner.getStdoutFile(mnt.Path)
 908                 if err != nil {
 909                         return err
 910                 }
 911                 stdout = f
 912         } else if w, err := runner.NewLogWriter("stdout"); err != nil {
 913                 return err
 914         } else {
 915                 stdout = NewThrottledLogger(w)
 916         }
 917
 918         if mnt, ok := runner.Container.Mounts["stderr"]; ok {
 919                 f, err := runner.getStdoutFile(mnt.Path)
 920                 if err != nil {
 921                         return err
 922                 }
 923                 stderr = f
 924         } else if w, err := runner.NewLogWriter("stderr"); err != nil {
 925                 return err
 926         } else {
 927                 stderr = NewThrottledLogger(w)
 928         }
 929
 930         env := runner.Container.Environment
 931         enableNetwork := runner.enableNetwork == "always"
 932         if runner.Container.RuntimeConstraints.API {
 933                 enableNetwork = true
 934                 tok, err := runner.ContainerToken()
 935                 if err != nil {
 936                         return err
 937                 }
 938                 env = map[string]string{}
 939                 for k, v := range runner.Container.Environment {
 940                         env[k] = v
 941                 }
 942                 env["ARVADOS_API_TOKEN"] = tok
 943                 env["ARVADOS_API_HOST"] = os.Getenv("ARVADOS_API_HOST")
 944                 env["ARVADOS_API_HOST_INSECURE"] = os.Getenv("ARVADOS_API_HOST_INSECURE")
 945         }
 946         workdir := runner.Container.Cwd
 947         if workdir == "." {
 948                 // both "" and "." mean default
 949                 workdir = ""
 950         }
 951         ram := runner.Container.RuntimeConstraints.RAM
 952         if !runner.enableMemoryLimit {
 953                 ram = 0
 954         }
 955         return runner.executor.Create(containerSpec{
 956                 Image:         imageID,
 957                 VCPUs:         runner.Container.RuntimeConstraints.VCPUs,
 958                 RAM:           ram,
 959                 WorkingDir:    workdir,
 960                 Env:           env,
 961                 BindMounts:    bindmounts,
 962                 Command:       runner.Container.Command,
 963                 EnableNetwork: enableNetwork,
 964                 NetworkMode:   runner.networkMode,
 965                 CgroupParent:  runner.setCgroupParent,
 966                 Stdin:         stdin,
 967                 Stdout:        stdout,
 968                 Stderr:        stderr,
 969         })
 970 }
 971
 972 // StartContainer starts the docker container created by CreateContainer.
 973 func (runner *ContainerRunner) StartContainer() error {
 974         runner.CrunchLog.Printf("Starting container")
 975         runner.cStateLock.Lock()
 976         defer runner.cStateLock.Unlock()
 977         if runner.cCancelled {
 978                 return ErrCancelled
 979         }
 980         err := runner.executor.Start()
 981         if err != nil {
 982                 var advice string
 983                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
 984                         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])
 985                 }
 986                 return fmt.Errorf("could not start container: %v%s", err, advice)
 987         }
 988         return nil
 989 }
 990
 991 // WaitFinish waits for the container to terminate, capture the exit code, and
 992 // close the stdout/stderr logging.
 993 func (runner *ContainerRunner) WaitFinish() error {
 994         runner.CrunchLog.Print("Waiting for container to finish")
 995         var timeout <-chan time.Time
 996         if s := runner.Container.SchedulingParameters.MaxRunTime; s > 0 {
 997                 timeout = time.After(time.Duration(s) * time.Second)
 998         }
 999         ctx, cancel := context.WithCancel(context.Background())
1000         defer cancel()
1001         go func() {
1002                 select {
1003                 case <-timeout:
1004                         runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
1005                         runner.stop(nil)
1006                 case <-runner.ArvMountExit:
1007                         runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
1008                         runner.stop(nil)
1009                 case <-ctx.Done():
1010                 }
1011         }()
1012         exitcode, err := runner.executor.Wait(ctx)
1013         if err != nil {
1014                 runner.checkBrokenNode(err)
1015                 return err
1016         }
1017         runner.ExitCode = &exitcode
1018
1019         if runner.statReporter != nil {
1020                 runner.statReporter.Stop()
1021                 err = runner.statLogger.Close()
1022                 if err != nil {
1023                         runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
1024                 }
1025         }
1026         return nil
1027 }
1028
1029 func (runner *ContainerRunner) updateLogs() {
1030         ticker := time.NewTicker(crunchLogUpdatePeriod / 360)
1031         defer ticker.Stop()
1032
1033         sigusr1 := make(chan os.Signal, 1)
1034         signal.Notify(sigusr1, syscall.SIGUSR1)
1035         defer signal.Stop(sigusr1)
1036
1037         saveAtTime := time.Now().Add(crunchLogUpdatePeriod)
1038         saveAtSize := crunchLogUpdateSize
1039         var savedSize int64
1040         for {
1041                 select {
1042                 case <-ticker.C:
1043                 case <-sigusr1:
1044                         saveAtTime = time.Now()
1045                 }
1046                 runner.logMtx.Lock()
1047                 done := runner.LogsPDH != nil
1048                 runner.logMtx.Unlock()
1049                 if done {
1050                         return
1051                 }
1052                 size := runner.LogCollection.Size()
1053                 if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) {
1054                         continue
1055                 }
1056                 saveAtTime = time.Now().Add(crunchLogUpdatePeriod)
1057                 saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize
1058                 saved, err := runner.saveLogCollection(false)
1059                 if err != nil {
1060                         runner.CrunchLog.Printf("error updating log collection: %s", err)
1061                         continue
1062                 }
1063
1064                 var updated arvados.Container
1065                 err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
1066                         "container": arvadosclient.Dict{"log": saved.PortableDataHash},
1067                 }, &updated)
1068                 if err != nil {
1069                         runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
1070                         continue
1071                 }
1072
1073                 savedSize = size
1074         }
1075 }
1076
1077 // CaptureOutput saves data from the container's output directory if
1078 // needed, and updates the container output accordingly.
1079 func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) error {
1080         if runner.Container.RuntimeConstraints.API {
1081                 // Output may have been set directly by the container, so
1082                 // refresh the container record to check.
1083                 err := runner.DispatcherArvClient.Get("containers", runner.Container.UUID,
1084                         nil, &runner.Container)
1085                 if err != nil {
1086                         return err
1087                 }
1088                 if runner.Container.Output != "" {
1089                         // Container output is already set.
1090                         runner.OutputPDH = &runner.Container.Output
1091                         return nil
1092                 }
1093         }
1094
1095         txt, err := (&copier{
1096                 client:        runner.containerClient,
1097                 arvClient:     runner.ContainerArvClient,
1098                 keepClient:    runner.ContainerKeepClient,
1099                 hostOutputDir: runner.HostOutputDir,
1100                 ctrOutputDir:  runner.Container.OutputPath,
1101                 bindmounts:    bindmounts,
1102                 mounts:        runner.Container.Mounts,
1103                 secretMounts:  runner.SecretMounts,
1104                 logger:        runner.CrunchLog,
1105         }).Copy()
1106         if err != nil {
1107                 return err
1108         }
1109         if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 {
1110                 runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n)
1111                 fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.containerClient, runner.ContainerKeepClient)
1112                 if err != nil {
1113                         return err
1114                 }
1115                 txt, err = fs.MarshalManifest(".")
1116                 if err != nil {
1117                         return err
1118                 }
1119         }
1120         var resp arvados.Collection
1121         err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
1122                 "ensure_unique_name": true,
1123                 "collection": arvadosclient.Dict{
1124                         "is_trashed":    true,
1125                         "name":          "output for " + runner.Container.UUID,
1126                         "manifest_text": txt,
1127                 },
1128         }, &resp)
1129         if err != nil {
1130                 return fmt.Errorf("error creating output collection: %v", err)
1131         }
1132         runner.OutputPDH = &resp.PortableDataHash
1133         return nil
1134 }
1135
1136 func (runner *ContainerRunner) CleanupDirs() {
1137         if runner.ArvMount != nil {
1138                 var delay int64 = 8
1139                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1140                 umount.Stdout = runner.CrunchLog
1141                 umount.Stderr = runner.CrunchLog
1142                 runner.CrunchLog.Printf("Running %v", umount.Args)
1143                 umnterr := umount.Start()
1144
1145                 if umnterr != nil {
1146                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1147                 } else {
1148                         // If arv-mount --unmount gets stuck for any reason, we
1149                         // don't want to wait for it forever.  Do Wait() in a goroutine
1150                         // so it doesn't block crunch-run.
1151                         umountExit := make(chan error)
1152                         go func() {
1153                                 mnterr := umount.Wait()
1154                                 if mnterr != nil {
1155                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1156                                 }
1157                                 umountExit <- mnterr
1158                         }()
1159
1160                         for again := true; again; {
1161                                 again = false
1162                                 select {
1163                                 case <-umountExit:
1164                                         umount = nil
1165                                         again = true
1166                                 case <-runner.ArvMountExit:
1167                                         break
1168                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1169                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1170                                         if umount != nil {
1171                                                 umount.Process.Kill()
1172                                         }
1173                                         runner.ArvMount.Process.Kill()
1174                                 }
1175                         }
1176                 }
1177         }
1178
1179         if runner.ArvMountPoint != "" {
1180                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1181                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1182                 }
1183         }
1184
1185         if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
1186                 runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
1187         }
1188 }
1189
1190 // CommitLogs posts the collection containing the final container logs.
1191 func (runner *ContainerRunner) CommitLogs() error {
1192         func() {
1193                 // Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
1194                 runner.cStateLock.Lock()
1195                 defer runner.cStateLock.Unlock()
1196
1197                 runner.CrunchLog.Print(runner.finalState)
1198
1199                 if runner.arvMountLog != nil {
1200                         runner.arvMountLog.Close()
1201                 }
1202                 runner.CrunchLog.Close()
1203
1204                 // Closing CrunchLog above allows them to be committed to Keep at this
1205                 // point, but re-open crunch log with ArvClient in case there are any
1206                 // other further errors (such as failing to write the log to Keep!)
1207                 // while shutting down
1208                 runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
1209                         ArvClient:     runner.DispatcherArvClient,
1210                         UUID:          runner.Container.UUID,
1211                         loggingStream: "crunch-run",
1212                         writeCloser:   nil,
1213                 })
1214                 runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1215         }()
1216
1217         if runner.LogsPDH != nil {
1218                 // If we have already assigned something to LogsPDH,
1219                 // we must be closing the re-opened log, which won't
1220                 // end up getting attached to the container record and
1221                 // therefore doesn't need to be saved as a collection
1222                 // -- it exists only to send logs to other channels.
1223                 return nil
1224         }
1225         saved, err := runner.saveLogCollection(true)
1226         if err != nil {
1227                 return fmt.Errorf("error saving log collection: %s", err)
1228         }
1229         runner.logMtx.Lock()
1230         defer runner.logMtx.Unlock()
1231         runner.LogsPDH = &saved.PortableDataHash
1232         return nil
1233 }
1234
1235 func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
1236         runner.logMtx.Lock()
1237         defer runner.logMtx.Unlock()
1238         if runner.LogsPDH != nil {
1239                 // Already finalized.
1240                 return
1241         }
1242         updates := arvadosclient.Dict{
1243                 "name": "logs for " + runner.Container.UUID,
1244         }
1245         mt, err1 := runner.LogCollection.MarshalManifest(".")
1246         if err1 == nil {
1247                 // Only send updated manifest text if there was no
1248                 // error.
1249                 updates["manifest_text"] = mt
1250         }
1251
1252         // Even if flushing the manifest had an error, we still want
1253         // to update the log record, if possible, to push the trash_at
1254         // and delete_at times into the future.  Details on bug
1255         // #17293.
1256         if final {
1257                 updates["is_trashed"] = true
1258         } else {
1259                 exp := time.Now().Add(crunchLogUpdatePeriod * 24)
1260                 updates["trash_at"] = exp
1261                 updates["delete_at"] = exp
1262         }
1263         reqBody := arvadosclient.Dict{"collection": updates}
1264         var err2 error
1265         if runner.logUUID == "" {
1266                 reqBody["ensure_unique_name"] = true
1267                 err2 = runner.DispatcherArvClient.Create("collections", reqBody, &response)
1268         } else {
1269                 err2 = runner.DispatcherArvClient.Update("collections", runner.logUUID, reqBody, &response)
1270         }
1271         if err2 == nil {
1272                 runner.logUUID = response.UUID
1273         }
1274
1275         if err1 != nil || err2 != nil {
1276                 err = fmt.Errorf("error recording logs: %q, %q", err1, err2)
1277         }
1278         return
1279 }
1280
1281 // UpdateContainerRunning updates the container state to "Running"
1282 func (runner *ContainerRunner) UpdateContainerRunning() error {
1283         runner.cStateLock.Lock()
1284         defer runner.cStateLock.Unlock()
1285         if runner.cCancelled {
1286                 return ErrCancelled
1287         }
1288         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID,
1289                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running", "gateway_address": runner.gateway.Address}}, nil)
1290 }
1291
1292 // ContainerToken returns the api_token the container (and any
1293 // arv-mount processes) are allowed to use.
1294 func (runner *ContainerRunner) ContainerToken() (string, error) {
1295         if runner.token != "" {
1296                 return runner.token, nil
1297         }
1298
1299         var auth arvados.APIClientAuthorization
1300         err := runner.DispatcherArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1301         if err != nil {
1302                 return "", err
1303         }
1304         runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID)
1305         return runner.token, nil
1306 }
1307
1308 // UpdateContainerFinal updates the container record state on API
1309 // server to "Complete" or "Cancelled"
1310 func (runner *ContainerRunner) UpdateContainerFinal() error {
1311         update := arvadosclient.Dict{}
1312         update["state"] = runner.finalState
1313         if runner.LogsPDH != nil {
1314                 update["log"] = *runner.LogsPDH
1315         }
1316         if runner.finalState == "Complete" {
1317                 if runner.ExitCode != nil {
1318                         update["exit_code"] = *runner.ExitCode
1319                 }
1320                 if runner.OutputPDH != nil {
1321                         update["output"] = *runner.OutputPDH
1322                 }
1323         }
1324         return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1325 }
1326
1327 // IsCancelled returns the value of Cancelled, with goroutine safety.
1328 func (runner *ContainerRunner) IsCancelled() bool {
1329         runner.cStateLock.Lock()
1330         defer runner.cStateLock.Unlock()
1331         return runner.cCancelled
1332 }
1333
1334 // NewArvLogWriter creates an ArvLogWriter
1335 func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) {
1336         writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
1337         if err != nil {
1338                 return nil, err
1339         }
1340         return &ArvLogWriter{
1341                 ArvClient:     runner.DispatcherArvClient,
1342                 UUID:          runner.Container.UUID,
1343                 loggingStream: name,
1344                 writeCloser:   writer,
1345         }, nil
1346 }
1347
1348 // Run the full container lifecycle.
1349 func (runner *ContainerRunner) Run() (err error) {
1350         runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
1351         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1352
1353         hostname, hosterr := os.Hostname()
1354         if hosterr != nil {
1355                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1356         } else {
1357                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1358         }
1359
1360         runner.finalState = "Queued"
1361
1362         defer func() {
1363                 runner.CleanupDirs()
1364
1365                 runner.CrunchLog.Printf("crunch-run finished")
1366                 runner.CrunchLog.Close()
1367         }()
1368
1369         err = runner.fetchContainerRecord()
1370         if err != nil {
1371                 return
1372         }
1373         if runner.Container.State != "Locked" {
1374                 return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
1375         }
1376
1377         var bindmounts map[string]bindmount
1378         defer func() {
1379                 // checkErr prints e (unless it's nil) and sets err to
1380                 // e (unless err is already non-nil). Thus, if err
1381                 // hasn't already been assigned when Run() returns,
1382                 // this cleanup func will cause Run() to return the
1383                 // first non-nil error that is passed to checkErr().
1384                 checkErr := func(errorIn string, e error) {
1385                         if e == nil {
1386                                 return
1387                         }
1388                         runner.CrunchLog.Printf("error in %s: %v", errorIn, e)
1389                         if err == nil {
1390                                 err = e
1391                         }
1392                         if runner.finalState == "Complete" {
1393                                 // There was an error in the finalization.
1394                                 runner.finalState = "Cancelled"
1395                         }
1396                 }
1397
1398                 // Log the error encountered in Run(), if any
1399                 checkErr("Run", err)
1400
1401                 if runner.finalState == "Queued" {
1402                         runner.UpdateContainerFinal()
1403                         return
1404                 }
1405
1406                 if runner.IsCancelled() {
1407                         runner.finalState = "Cancelled"
1408                         // but don't return yet -- we still want to
1409                         // capture partial output and write logs
1410                 }
1411
1412                 if bindmounts != nil {
1413                         checkErr("CaptureOutput", runner.CaptureOutput(bindmounts))
1414                 }
1415                 checkErr("stopHoststat", runner.stopHoststat())
1416                 checkErr("CommitLogs", runner.CommitLogs())
1417                 checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
1418         }()
1419
1420         runner.setupSignals()
1421         err = runner.startHoststat()
1422         if err != nil {
1423                 return
1424         }
1425
1426         // set up FUSE mount and binds
1427         bindmounts, err = runner.SetupMounts()
1428         if err != nil {
1429                 runner.finalState = "Cancelled"
1430                 err = fmt.Errorf("While setting up mounts: %v", err)
1431                 return
1432         }
1433
1434         // check for and/or load image
1435         imageID, err := runner.LoadImage()
1436         if err != nil {
1437                 if !runner.checkBrokenNode(err) {
1438                         // Failed to load image but not due to a "broken node"
1439                         // condition, probably user error.
1440                         runner.finalState = "Cancelled"
1441                 }
1442                 err = fmt.Errorf("While loading container image: %v", err)
1443                 return
1444         }
1445
1446         err = runner.CreateContainer(imageID, bindmounts)
1447         if err != nil {
1448                 return
1449         }
1450         err = runner.LogHostInfo()
1451         if err != nil {
1452                 return
1453         }
1454         err = runner.LogNodeRecord()
1455         if err != nil {
1456                 return
1457         }
1458         err = runner.LogContainerRecord()
1459         if err != nil {
1460                 return
1461         }
1462
1463         if runner.IsCancelled() {
1464                 return
1465         }
1466
1467         err = runner.UpdateContainerRunning()
1468         if err != nil {
1469                 return
1470         }
1471         runner.finalState = "Cancelled"
1472
1473         err = runner.startCrunchstat()
1474         if err != nil {
1475                 return
1476         }
1477
1478         err = runner.StartContainer()
1479         if err != nil {
1480                 runner.checkBrokenNode(err)
1481                 return
1482         }
1483
1484         err = runner.WaitFinish()
1485         if err == nil && !runner.IsCancelled() {
1486                 runner.finalState = "Complete"
1487         }
1488         return
1489 }
1490
1491 // Fetch the current container record (uuid = runner.Container.UUID)
1492 // into runner.Container.
1493 func (runner *ContainerRunner) fetchContainerRecord() error {
1494         reader, err := runner.DispatcherArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1495         if err != nil {
1496                 return fmt.Errorf("error fetching container record: %v", err)
1497         }
1498         defer reader.Close()
1499
1500         dec := json.NewDecoder(reader)
1501         dec.UseNumber()
1502         err = dec.Decode(&runner.Container)
1503         if err != nil {
1504                 return fmt.Errorf("error decoding container record: %v", err)
1505         }
1506
1507         var sm struct {
1508                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
1509         }
1510
1511         containerToken, err := runner.ContainerToken()
1512         if err != nil {
1513                 return fmt.Errorf("error getting container token: %v", err)
1514         }
1515
1516         runner.ContainerArvClient, runner.ContainerKeepClient,
1517                 runner.containerClient, err = runner.MkArvClient(containerToken)
1518         if err != nil {
1519                 return fmt.Errorf("error creating container API client: %v", err)
1520         }
1521
1522         err = runner.ContainerArvClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
1523         if err != nil {
1524                 if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
1525                         return fmt.Errorf("error fetching secret_mounts: %v", err)
1526                 }
1527                 // ok && apierr.HttpStatusCode == 404, which means
1528                 // secret_mounts isn't supported by this API server.
1529         }
1530         runner.SecretMounts = sm.SecretMounts
1531
1532         return nil
1533 }
1534
1535 // NewContainerRunner creates a new container runner.
1536 func NewContainerRunner(dispatcherClient *arvados.Client,
1537         dispatcherArvClient IArvadosClient,
1538         dispatcherKeepClient IKeepClient,
1539         containerUUID string) (*ContainerRunner, error) {
1540
1541         cr := &ContainerRunner{
1542                 dispatcherClient:     dispatcherClient,
1543                 DispatcherArvClient:  dispatcherArvClient,
1544                 DispatcherKeepClient: dispatcherKeepClient,
1545         }
1546         cr.NewLogWriter = cr.NewArvLogWriter
1547         cr.RunArvMount = cr.ArvMountCmd
1548         cr.MkTempDir = ioutil.TempDir
1549         cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
1550                 cl, err := arvadosclient.MakeArvadosClient()
1551                 if err != nil {
1552                         return nil, nil, nil, err
1553                 }
1554                 cl.ApiToken = token
1555                 kc, err := keepclient.MakeKeepClient(cl)
1556                 if err != nil {
1557                         return nil, nil, nil, err
1558                 }
1559                 c2 := arvados.NewClientFromEnv()
1560                 c2.AuthToken = token
1561                 return cl, kc, c2, nil
1562         }
1563         var err error
1564         cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.dispatcherClient, cr.DispatcherKeepClient)
1565         if err != nil {
1566                 return nil, err
1567         }
1568         cr.Container.UUID = containerUUID
1569         w, err := cr.NewLogWriter("crunch-run")
1570         if err != nil {
1571                 return nil, err
1572         }
1573         cr.CrunchLog = NewThrottledLogger(w)
1574         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1575
1576         loadLogThrottleParams(dispatcherArvClient)
1577         go cr.updateLogs()
1578
1579         return cr, nil
1580 }
1581
1582 func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
1583         flags := flag.NewFlagSet(prog, flag.ContinueOnError)
1584         statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1585         cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1586         cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1587         cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1588         caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
1589         detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
1590         stdinEnv := flags.Bool("stdin-env", false, "Load environment variables from JSON message on stdin")
1591         sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
1592         kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
1593         list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
1594         enableMemoryLimit := flags.Bool("enable-memory-limit", true, "tell container runtime to limit container's memory usage")
1595         enableNetwork := flags.String("container-enable-networking", "default", "enable networking \"always\" (for all containers) or \"default\" (for containers that request it)")
1596         networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
1597         memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
1598         runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
1599         flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
1600
1601         ignoreDetachFlag := false
1602         if len(args) > 0 && args[0] == "-no-detach" {
1603                 // This process was invoked by a parent process, which
1604                 // has passed along its own arguments, including
1605                 // -detach, after the leading -no-detach flag.  Strip
1606                 // the leading -no-detach flag (it's not recognized by
1607                 // flags.Parse()) and ignore the -detach flag that
1608                 // comes later.
1609                 args = args[1:]
1610                 ignoreDetachFlag = true
1611         }
1612
1613         if err := flags.Parse(args); err == flag.ErrHelp {
1614                 return 0
1615         } else if err != nil {
1616                 log.Print(err)
1617                 return 1
1618         }
1619
1620         if *stdinEnv && !ignoreDetachFlag {
1621                 // Load env vars on stdin if asked (but not in a
1622                 // detached child process, in which case stdin is
1623                 // /dev/null).
1624                 err := loadEnv(os.Stdin)
1625                 if err != nil {
1626                         log.Print(err)
1627                         return 1
1628                 }
1629         }
1630
1631         containerUUID := flags.Arg(0)
1632
1633         switch {
1634         case *detach && !ignoreDetachFlag:
1635                 return Detach(containerUUID, prog, args, os.Stdout, os.Stderr)
1636         case *kill >= 0:
1637                 return KillProcess(containerUUID, syscall.Signal(*kill), os.Stdout, os.Stderr)
1638         case *list:
1639                 return ListProcesses(os.Stdout, os.Stderr)
1640         }
1641
1642         if containerUUID == "" {
1643                 log.Printf("usage: %s [options] UUID", prog)
1644                 return 1
1645         }
1646
1647         log.Printf("crunch-run %s started", cmd.Version.String())
1648         time.Sleep(*sleep)
1649
1650         if *caCertsPath != "" {
1651                 arvadosclient.CertFiles = []string{*caCertsPath}
1652         }
1653
1654         api, err := arvadosclient.MakeArvadosClient()
1655         if err != nil {
1656                 log.Printf("%s: %v", containerUUID, err)
1657                 return 1
1658         }
1659         api.Retries = 8
1660
1661         kc, kcerr := keepclient.MakeKeepClient(api)
1662         if kcerr != nil {
1663                 log.Printf("%s: %v", containerUUID, kcerr)
1664                 return 1
1665         }
1666         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1667         kc.Retries = 4
1668
1669         cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, containerUUID)
1670         if err != nil {
1671                 log.Print(err)
1672                 return 1
1673         }
1674
1675         switch *runtimeEngine {
1676         case "docker":
1677                 cr.executor, err = newDockerExecutor(containerUUID, cr.CrunchLog.Printf, cr.containerWatchdogInterval)
1678         case "singularity":
1679                 cr.executor, err = newSingularityExecutor(cr.CrunchLog.Printf)
1680         default:
1681                 cr.CrunchLog.Printf("%s: unsupported RuntimeEngine %q", containerUUID, *runtimeEngine)
1682                 cr.CrunchLog.Close()
1683                 return 1
1684         }
1685         if err != nil {
1686                 cr.CrunchLog.Printf("%s: %v", containerUUID, err)
1687                 cr.checkBrokenNode(err)
1688                 cr.CrunchLog.Close()
1689                 return 1
1690         }
1691         defer cr.executor.Close()
1692
1693         gwAuthSecret := os.Getenv("GatewayAuthSecret")
1694         os.Unsetenv("GatewayAuthSecret")
1695         if gwAuthSecret == "" {
1696                 // not safe to run a gateway service without an auth
1697                 // secret
1698         } else if gwListen := os.Getenv("GatewayAddress"); gwListen == "" {
1699                 // dispatcher did not tell us which external IP
1700                 // address to advertise --> no gateway service
1701         } else if de, ok := cr.executor.(*dockerExecutor); ok {
1702                 cr.gateway = Gateway{
1703                         Address:            gwListen,
1704                         AuthSecret:         gwAuthSecret,
1705                         ContainerUUID:      containerUUID,
1706                         DockerContainerID:  &de.containerID,
1707                         Log:                cr.CrunchLog,
1708                         ContainerIPAddress: dockerContainerIPAddress(&de.containerID),
1709                 }
1710                 err = cr.gateway.Start()
1711                 if err != nil {
1712                         log.Printf("error starting gateway server: %s", err)
1713                         return 1
1714                 }
1715         }
1716
1717         parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerUUID+".")
1718         if tmperr != nil {
1719                 log.Printf("%s: %v", containerUUID, tmperr)
1720                 return 1
1721         }
1722
1723         cr.parentTemp = parentTemp
1724         cr.statInterval = *statInterval
1725         cr.cgroupRoot = *cgroupRoot
1726         cr.expectCgroupParent = *cgroupParent
1727         cr.enableMemoryLimit = *enableMemoryLimit
1728         cr.enableNetwork = *enableNetwork
1729         cr.networkMode = *networkMode
1730         if *cgroupParentSubsystem != "" {
1731                 p := findCgroup(*cgroupParentSubsystem)
1732                 cr.setCgroupParent = p
1733                 cr.expectCgroupParent = p
1734         }
1735
1736         runerr := cr.Run()
1737
1738         if *memprofile != "" {
1739                 f, err := os.Create(*memprofile)
1740                 if err != nil {
1741                         log.Printf("could not create memory profile: %s", err)
1742                 }
1743                 runtime.GC() // get up-to-date statistics
1744                 if err := pprof.WriteHeapProfile(f); err != nil {
1745                         log.Printf("could not write memory profile: %s", err)
1746                 }
1747                 closeerr := f.Close()
1748                 if closeerr != nil {
1749                         log.Printf("closing memprofile file: %s", err)
1750                 }
1751         }
1752
1753         if runerr != nil {
1754                 log.Printf("%s: %v", containerUUID, runerr)
1755                 return 1
1756         }
1757         return 0
1758 }
1759
1760 func loadEnv(rdr io.Reader) error {
1761         buf, err := ioutil.ReadAll(rdr)
1762         if err != nil {
1763                 return fmt.Errorf("read stdin: %s", err)
1764         }
1765         var env map[string]string
1766         err = json.Unmarshal(buf, &env)
1767         if err != nil {
1768                 return fmt.Errorf("decode stdin: %s", err)
1769         }
1770         for k, v := range env {
1771                 err = os.Setenv(k, v)
1772                 if err != nil {
1773                         return fmt.Errorf("setenv(%q): %s", k, err)
1774                 }
1775         }
1776         return nil
1777 }