services/crunch-run/crunchrun.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package main
   6
   7 import (
   8         "bytes"
   9         "encoding/json"
  10         "errors"
  11         "flag"
  12         "fmt"
  13         "io"
  14         "io/ioutil"
  15         "log"
  16         "os"
  17         "os/exec"
  18         "os/signal"
  19         "path"
  20         "path/filepath"
  21         "regexp"
  22         "runtime"
  23         "runtime/pprof"
  24         "sort"
  25         "strings"
  26         "sync"
  27         "syscall"
  28         "time"
  29
  30         "git.curoverse.com/arvados.git/lib/crunchstat"
  31         "git.curoverse.com/arvados.git/sdk/go/arvados"
  32         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  33         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  34         "git.curoverse.com/arvados.git/sdk/go/manifest"
  35         "golang.org/x/net/context"
  36
  37         dockertypes "github.com/docker/docker/api/types"
  38         dockercontainer "github.com/docker/docker/api/types/container"
  39         dockernetwork "github.com/docker/docker/api/types/network"
  40         dockerclient "github.com/docker/docker/client"
  41 )
  42
  43 var version = "dev"
  44
  45 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  46 type IArvadosClient interface {
  47         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  48         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  49         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  50         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  51         CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
  52         Discovery(key string) (interface{}, error)
  53 }
  54
  55 // ErrCancelled is the error returned when the container is cancelled.
  56 var ErrCancelled = errors.New("Cancelled")
  57
  58 // IKeepClient is the minimal Keep API methods used by crunch-run.
  59 type IKeepClient interface {
  60         PutHB(hash string, buf []byte) (string, int, error)
  61         ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
  62         ClearBlockCache()
  63 }
  64
  65 // NewLogWriter is a factory function to create a new log writer.
  66 type NewLogWriter func(name string) io.WriteCloser
  67
  68 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  69
  70 type MkTempDir func(string, string) (string, error)
  71
  72 // ThinDockerClient is the minimal Docker client interface used by crunch-run.
  73 type ThinDockerClient interface {
  74         ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error)
  75         ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
  76                 networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error)
  77         ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error
  78         ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error
  79         ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error)
  80         ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error)
  81         ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error)
  82         ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error)
  83 }
  84
  85 // ContainerRunner is the main stateful struct used for a single execution of a
  86 // container.
  87 type ContainerRunner struct {
  88         Docker    ThinDockerClient
  89         ArvClient IArvadosClient
  90         Kc        IKeepClient
  91         arvados.Container
  92         ContainerConfig dockercontainer.Config
  93         dockercontainer.HostConfig
  94         token       string
  95         ContainerID string
  96         ExitCode    *int
  97         NewLogWriter
  98         loggingDone   chan bool
  99         CrunchLog     *ThrottledLogger
 100         Stdout        io.WriteCloser
 101         Stderr        io.WriteCloser
 102         LogCollection *CollectionWriter
 103         LogsPDH       *string
 104         RunArvMount
 105         MkTempDir
 106         ArvMount      *exec.Cmd
 107         ArvMountPoint string
 108         HostOutputDir string
 109         Binds         []string
 110         Volumes       map[string]struct{}
 111         OutputPDH     *string
 112         SigChan       chan os.Signal
 113         ArvMountExit  chan error
 114         finalState    string
 115         parentTemp    string
 116
 117         statLogger       io.WriteCloser
 118         statReporter     *crunchstat.Reporter
 119         hoststatLogger   io.WriteCloser
 120         hoststatReporter *crunchstat.Reporter
 121         statInterval     time.Duration
 122         cgroupRoot       string
 123         // What we expect the container's cgroup parent to be.
 124         expectCgroupParent string
 125         // What we tell docker to use as the container's cgroup
 126         // parent. Note: Ideally we would use the same field for both
 127         // expectCgroupParent and setCgroupParent, and just make it
 128         // default to "docker". However, when using docker < 1.10 with
 129         // systemd, specifying a non-empty cgroup parent (even the
 130         // default value "docker") hits a docker bug
 131         // (https://github.com/docker/docker/issues/17126). Using two
 132         // separate fields makes it possible to use the "expect cgroup
 133         // parent to be X" feature even on sites where the "specify
 134         // cgroup parent" feature breaks.
 135         setCgroupParent string
 136
 137         cStateLock sync.Mutex
 138         cCancelled bool // StopContainer() invoked
 139
 140         enableNetwork string // one of "default" or "always"
 141         networkMode   string // passed through to HostConfig.NetworkMode
 142         arvMountLog   *ThrottledLogger
 143 }
 144
 145 // setupSignals sets up signal handling to gracefully terminate the underlying
 146 // Docker container and update state when receiving a TERM, INT or QUIT signal.
 147 func (runner *ContainerRunner) setupSignals() {
 148         runner.SigChan = make(chan os.Signal, 1)
 149         signal.Notify(runner.SigChan, syscall.SIGTERM)
 150         signal.Notify(runner.SigChan, syscall.SIGINT)
 151         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 152
 153         go func(sig chan os.Signal) {
 154                 for s := range sig {
 155                         runner.stop(s)
 156                 }
 157         }(runner.SigChan)
 158 }
 159
 160 // stop the underlying Docker container.
 161 func (runner *ContainerRunner) stop(sig os.Signal) {
 162         runner.cStateLock.Lock()
 163         defer runner.cStateLock.Unlock()
 164         if sig != nil {
 165                 runner.CrunchLog.Printf("caught signal: %v", sig)
 166         }
 167         if runner.ContainerID == "" {
 168                 return
 169         }
 170         runner.cCancelled = true
 171         runner.CrunchLog.Printf("removing container")
 172         err := runner.Docker.ContainerRemove(context.TODO(), runner.ContainerID, dockertypes.ContainerRemoveOptions{Force: true})
 173         if err != nil {
 174                 runner.CrunchLog.Printf("error removing container: %s", err)
 175         }
 176 }
 177
 178 var errorBlacklist = []string{
 179         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 180         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 181 }
 182 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)")
 183
 184 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 185         for _, d := range errorBlacklist {
 186                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 187                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 188                         if *brokenNodeHook == "" {
 189                                 runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
 190                         } else {
 191                                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 192                                 // run killme script
 193                                 c := exec.Command(*brokenNodeHook)
 194                                 c.Stdout = runner.CrunchLog
 195                                 c.Stderr = runner.CrunchLog
 196                                 err := c.Run()
 197                                 if err != nil {
 198                                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 199                                 }
 200                         }
 201                         return true
 202                 }
 203         }
 204         return false
 205 }
 206
 207 // LoadImage determines the docker image id from the container record and
 208 // checks if it is available in the local Docker image store.  If not, it loads
 209 // the image from Keep.
 210 func (runner *ContainerRunner) LoadImage() (err error) {
 211
 212         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 213
 214         var collection arvados.Collection
 215         err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
 216         if err != nil {
 217                 return fmt.Errorf("While getting container image collection: %v", err)
 218         }
 219         manifest := manifest.Manifest{Text: collection.ManifestText}
 220         var img, imageID string
 221         for ms := range manifest.StreamIter() {
 222                 img = ms.FileStreamSegments[0].Name
 223                 if !strings.HasSuffix(img, ".tar") {
 224                         return fmt.Errorf("First file in the container image collection does not end in .tar")
 225                 }
 226                 imageID = img[:len(img)-4]
 227         }
 228
 229         runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
 230
 231         _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
 232         if err != nil {
 233                 runner.CrunchLog.Print("Loading Docker image from keep")
 234
 235                 var readCloser io.ReadCloser
 236                 readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
 237                 if err != nil {
 238                         return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
 239                 }
 240
 241                 response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, true)
 242                 if err != nil {
 243                         return fmt.Errorf("While loading container image into Docker: %v", err)
 244                 }
 245
 246                 defer response.Body.Close()
 247                 rbody, err := ioutil.ReadAll(response.Body)
 248                 if err != nil {
 249                         return fmt.Errorf("Reading response to image load: %v", err)
 250                 }
 251                 runner.CrunchLog.Printf("Docker response: %s", rbody)
 252         } else {
 253                 runner.CrunchLog.Print("Docker image is available")
 254         }
 255
 256         runner.ContainerConfig.Image = imageID
 257
 258         runner.Kc.ClearBlockCache()
 259
 260         return nil
 261 }
 262
 263 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 264         c = exec.Command("arv-mount", arvMountCmd...)
 265
 266         // Copy our environment, but override ARVADOS_API_TOKEN with
 267         // the container auth token.
 268         c.Env = nil
 269         for _, s := range os.Environ() {
 270                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 271                         c.Env = append(c.Env, s)
 272                 }
 273         }
 274         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 275
 276         runner.arvMountLog = NewThrottledLogger(runner.NewLogWriter("arv-mount"))
 277         c.Stdout = runner.arvMountLog
 278         c.Stderr = runner.arvMountLog
 279
 280         runner.CrunchLog.Printf("Running %v", c.Args)
 281
 282         err = c.Start()
 283         if err != nil {
 284                 return nil, err
 285         }
 286
 287         statReadme := make(chan bool)
 288         runner.ArvMountExit = make(chan error)
 289
 290         keepStatting := true
 291         go func() {
 292                 for keepStatting {
 293                         time.Sleep(100 * time.Millisecond)
 294                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 295                         if err == nil {
 296                                 keepStatting = false
 297                                 statReadme <- true
 298                         }
 299                 }
 300                 close(statReadme)
 301         }()
 302
 303         go func() {
 304                 mnterr := c.Wait()
 305                 if mnterr != nil {
 306                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 307                 }
 308                 runner.ArvMountExit <- mnterr
 309                 close(runner.ArvMountExit)
 310         }()
 311
 312         select {
 313         case <-statReadme:
 314                 break
 315         case err := <-runner.ArvMountExit:
 316                 runner.ArvMount = nil
 317                 keepStatting = false
 318                 return nil, err
 319         }
 320
 321         return c, nil
 322 }
 323
 324 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 325         if runner.ArvMountPoint == "" {
 326                 runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
 327         }
 328         return
 329 }
 330
 331 func copyfile(src string, dst string) (err error) {
 332         srcfile, err := os.Open(src)
 333         if err != nil {
 334                 return
 335         }
 336
 337         os.MkdirAll(path.Dir(dst), 0777)
 338
 339         dstfile, err := os.Create(dst)
 340         if err != nil {
 341                 return
 342         }
 343         _, err = io.Copy(dstfile, srcfile)
 344         if err != nil {
 345                 return
 346         }
 347
 348         err = srcfile.Close()
 349         err2 := dstfile.Close()
 350
 351         if err != nil {
 352                 return
 353         }
 354
 355         if err2 != nil {
 356                 return err2
 357         }
 358
 359         return nil
 360 }
 361
 362 func (runner *ContainerRunner) SetupMounts() (err error) {
 363         err = runner.SetupArvMountPoint("keep")
 364         if err != nil {
 365                 return fmt.Errorf("While creating keep mount temp dir: %v", err)
 366         }
 367
 368         token, err := runner.ContainerToken()
 369         if err != nil {
 370                 return fmt.Errorf("could not get container token: %s", err)
 371         }
 372
 373         pdhOnly := true
 374         tmpcount := 0
 375         arvMountCmd := []string{
 376                 "--foreground",
 377                 "--allow-other",
 378                 "--read-write",
 379                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 380
 381         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 382                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 383         }
 384
 385         collectionPaths := []string{}
 386         runner.Binds = nil
 387         runner.Volumes = make(map[string]struct{})
 388         needCertMount := true
 389         type copyFile struct {
 390                 src  string
 391                 bind string
 392         }
 393         var copyFiles []copyFile
 394
 395         var binds []string
 396         for bind := range runner.Container.Mounts {
 397                 binds = append(binds, bind)
 398         }
 399         sort.Strings(binds)
 400
 401         for _, bind := range binds {
 402                 mnt := runner.Container.Mounts[bind]
 403                 if bind == "stdout" || bind == "stderr" {
 404                         // Is it a "file" mount kind?
 405                         if mnt.Kind != "file" {
 406                                 return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind)
 407                         }
 408
 409                         // Does path start with OutputPath?
 410                         prefix := runner.Container.OutputPath
 411                         if !strings.HasSuffix(prefix, "/") {
 412                                 prefix += "/"
 413                         }
 414                         if !strings.HasPrefix(mnt.Path, prefix) {
 415                                 return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 416                         }
 417                 }
 418
 419                 if bind == "stdin" {
 420                         // Is it a "collection" mount kind?
 421                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 422                                 return fmt.Errorf("Unsupported mount kind '%s' for stdin. Only 'collection' or 'json' are supported.", mnt.Kind)
 423                         }
 424                 }
 425
 426                 if bind == "/etc/arvados/ca-certificates.crt" {
 427                         needCertMount = false
 428                 }
 429
 430                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 431                         if mnt.Kind != "collection" {
 432                                 return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind)
 433                         }
 434                 }
 435
 436                 switch {
 437                 case mnt.Kind == "collection" && bind != "stdin":
 438                         var src string
 439                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 440                                 return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 441                         }
 442                         if mnt.UUID != "" {
 443                                 if mnt.Writable {
 444                                         return fmt.Errorf("Writing to existing collections currently not permitted.")
 445                                 }
 446                                 pdhOnly = false
 447                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 448                         } else if mnt.PortableDataHash != "" {
 449                                 if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 450                                         return fmt.Errorf("Can never write to a collection specified by portable data hash")
 451                                 }
 452                                 idx := strings.Index(mnt.PortableDataHash, "/")
 453                                 if idx > 0 {
 454                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 455                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 456                                         runner.Container.Mounts[bind] = mnt
 457                                 }
 458                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 459                                 if mnt.Path != "" && mnt.Path != "." {
 460                                         if strings.HasPrefix(mnt.Path, "./") {
 461                                                 mnt.Path = mnt.Path[2:]
 462                                         } else if strings.HasPrefix(mnt.Path, "/") {
 463                                                 mnt.Path = mnt.Path[1:]
 464                                         }
 465                                         src += "/" + mnt.Path
 466                                 }
 467                         } else {
 468                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 469                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 470                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 471                                 tmpcount += 1
 472                         }
 473                         if mnt.Writable {
 474                                 if bind == runner.Container.OutputPath {
 475                                         runner.HostOutputDir = src
 476                                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 477                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 478                                         copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 479                                 } else {
 480                                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 481                                 }
 482                         } else {
 483                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
 484                         }
 485                         collectionPaths = append(collectionPaths, src)
 486
 487                 case mnt.Kind == "tmp":
 488                         var tmpdir string
 489                         tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
 490                         if err != nil {
 491                                 return fmt.Errorf("While creating mount temp dir: %v", err)
 492                         }
 493                         st, staterr := os.Stat(tmpdir)
 494                         if staterr != nil {
 495                                 return fmt.Errorf("While Stat on temp dir: %v", staterr)
 496                         }
 497                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 498                         if staterr != nil {
 499                                 return fmt.Errorf("While Chmod temp dir: %v", err)
 500                         }
 501                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
 502                         if bind == runner.Container.OutputPath {
 503                                 runner.HostOutputDir = tmpdir
 504                         }
 505
 506                 case mnt.Kind == "json":
 507                         jsondata, err := json.Marshal(mnt.Content)
 508                         if err != nil {
 509                                 return fmt.Errorf("encoding json data: %v", err)
 510                         }
 511                         // Create a tempdir with a single file
 512                         // (instead of just a tempfile): this way we
 513                         // can ensure the file is world-readable
 514                         // inside the container, without having to
 515                         // make it world-readable on the docker host.
 516                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "json")
 517                         if err != nil {
 518                                 return fmt.Errorf("creating temp dir: %v", err)
 519                         }
 520                         tmpfn := filepath.Join(tmpdir, "mountdata.json")
 521                         err = ioutil.WriteFile(tmpfn, jsondata, 0644)
 522                         if err != nil {
 523                                 return fmt.Errorf("writing temp file: %v", err)
 524                         }
 525                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
 526
 527                 case mnt.Kind == "git_tree":
 528                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
 529                         if err != nil {
 530                                 return fmt.Errorf("creating temp dir: %v", err)
 531                         }
 532                         err = gitMount(mnt).extractTree(runner.ArvClient, tmpdir, token)
 533                         if err != nil {
 534                                 return err
 535                         }
 536                         runner.Binds = append(runner.Binds, tmpdir+":"+bind+":ro")
 537                 }
 538         }
 539
 540         if runner.HostOutputDir == "" {
 541                 return fmt.Errorf("Output path does not correspond to a writable mount point")
 542         }
 543
 544         if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
 545                 for _, certfile := range arvadosclient.CertFiles {
 546                         _, err := os.Stat(certfile)
 547                         if err == nil {
 548                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
 549                                 break
 550                         }
 551                 }
 552         }
 553
 554         if pdhOnly {
 555                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 556         } else {
 557                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 558         }
 559         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 560
 561         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 562         if err != nil {
 563                 return fmt.Errorf("While trying to start arv-mount: %v", err)
 564         }
 565
 566         for _, p := range collectionPaths {
 567                 _, err = os.Stat(p)
 568                 if err != nil {
 569                         return fmt.Errorf("While checking that input files exist: %v", err)
 570                 }
 571         }
 572
 573         for _, cp := range copyFiles {
 574                 st, err := os.Stat(cp.src)
 575                 if err != nil {
 576                         return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 577                 }
 578                 if st.IsDir() {
 579                         err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
 580                                 if walkerr != nil {
 581                                         return walkerr
 582                                 }
 583                                 target := path.Join(cp.bind, walkpath[len(cp.src):])
 584                                 if walkinfo.Mode().IsRegular() {
 585                                         copyerr := copyfile(walkpath, target)
 586                                         if copyerr != nil {
 587                                                 return copyerr
 588                                         }
 589                                         return os.Chmod(target, walkinfo.Mode()|0777)
 590                                 } else if walkinfo.Mode().IsDir() {
 591                                         mkerr := os.MkdirAll(target, 0777)
 592                                         if mkerr != nil {
 593                                                 return mkerr
 594                                         }
 595                                         return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 596                                 } else {
 597                                         return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
 598                                 }
 599                         })
 600                 } else if st.Mode().IsRegular() {
 601                         err = copyfile(cp.src, cp.bind)
 602                         if err == nil {
 603                                 err = os.Chmod(cp.bind, st.Mode()|0777)
 604                         }
 605                 }
 606                 if err != nil {
 607                         return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 608                 }
 609         }
 610
 611         return nil
 612 }
 613
 614 func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
 615         // Handle docker log protocol
 616         // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
 617         defer close(runner.loggingDone)
 618
 619         header := make([]byte, 8)
 620         var err error
 621         for err == nil {
 622                 _, err = io.ReadAtLeast(containerReader, header, 8)
 623                 if err != nil {
 624                         if err == io.EOF {
 625                                 err = nil
 626                         }
 627                         break
 628                 }
 629                 readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
 630                 if header[0] == 1 {
 631                         // stdout
 632                         _, err = io.CopyN(runner.Stdout, containerReader, readsize)
 633                 } else {
 634                         // stderr
 635                         _, err = io.CopyN(runner.Stderr, containerReader, readsize)
 636                 }
 637         }
 638
 639         if err != nil {
 640                 runner.CrunchLog.Printf("error reading docker logs: %v", err)
 641         }
 642
 643         err = runner.Stdout.Close()
 644         if err != nil {
 645                 runner.CrunchLog.Printf("error closing stdout logs: %v", err)
 646         }
 647
 648         err = runner.Stderr.Close()
 649         if err != nil {
 650                 runner.CrunchLog.Printf("error closing stderr logs: %v", err)
 651         }
 652
 653         if runner.statReporter != nil {
 654                 runner.statReporter.Stop()
 655                 err = runner.statLogger.Close()
 656                 if err != nil {
 657                         runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
 658                 }
 659         }
 660 }
 661
 662 func (runner *ContainerRunner) stopHoststat() error {
 663         if runner.hoststatReporter == nil {
 664                 return nil
 665         }
 666         runner.hoststatReporter.Stop()
 667         err := runner.hoststatLogger.Close()
 668         if err != nil {
 669                 return fmt.Errorf("error closing hoststat logs: %v", err)
 670         }
 671         return nil
 672 }
 673
 674 func (runner *ContainerRunner) startHoststat() {
 675         runner.hoststatLogger = NewThrottledLogger(runner.NewLogWriter("hoststat"))
 676         runner.hoststatReporter = &crunchstat.Reporter{
 677                 Logger:     log.New(runner.hoststatLogger, "", 0),
 678                 CgroupRoot: runner.cgroupRoot,
 679                 PollPeriod: runner.statInterval,
 680         }
 681         runner.hoststatReporter.Start()
 682 }
 683
 684 func (runner *ContainerRunner) startCrunchstat() {
 685         runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
 686         runner.statReporter = &crunchstat.Reporter{
 687                 CID:          runner.ContainerID,
 688                 Logger:       log.New(runner.statLogger, "", 0),
 689                 CgroupParent: runner.expectCgroupParent,
 690                 CgroupRoot:   runner.cgroupRoot,
 691                 PollPeriod:   runner.statInterval,
 692         }
 693         runner.statReporter.Start()
 694 }
 695
 696 type infoCommand struct {
 697         label string
 698         cmd   []string
 699 }
 700
 701 // LogHostInfo logs info about the current host, for debugging and
 702 // accounting purposes. Although it's logged as "node-info", this is
 703 // about the environment where crunch-run is actually running, which
 704 // might differ from what's described in the node record (see
 705 // LogNodeRecord).
 706 func (runner *ContainerRunner) LogHostInfo() (err error) {
 707         w := runner.NewLogWriter("node-info")
 708
 709         commands := []infoCommand{
 710                 {
 711                         label: "Host Information",
 712                         cmd:   []string{"uname", "-a"},
 713                 },
 714                 {
 715                         label: "CPU Information",
 716                         cmd:   []string{"cat", "/proc/cpuinfo"},
 717                 },
 718                 {
 719                         label: "Memory Information",
 720                         cmd:   []string{"cat", "/proc/meminfo"},
 721                 },
 722                 {
 723                         label: "Disk Space",
 724                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 725                 },
 726                 {
 727                         label: "Disk INodes",
 728                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 729                 },
 730         }
 731
 732         // Run commands with informational output to be logged.
 733         for _, command := range commands {
 734                 fmt.Fprintln(w, command.label)
 735                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 736                 cmd.Stdout = w
 737                 cmd.Stderr = w
 738                 if err := cmd.Run(); err != nil {
 739                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 740                         fmt.Fprintln(w, err)
 741                         return err
 742                 }
 743                 fmt.Fprintln(w, "")
 744         }
 745
 746         err = w.Close()
 747         if err != nil {
 748                 return fmt.Errorf("While closing node-info logs: %v", err)
 749         }
 750         return nil
 751 }
 752
 753 // LogContainerRecord gets and saves the raw JSON container record from the API server
 754 func (runner *ContainerRunner) LogContainerRecord() error {
 755         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 756         if !logged && err == nil {
 757                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 758         }
 759         return err
 760 }
 761
 762 // LogNodeRecord logs arvados#node record corresponding to the current host.
 763 func (runner *ContainerRunner) LogNodeRecord() error {
 764         hostname := os.Getenv("SLURMD_NODENAME")
 765         if hostname == "" {
 766                 hostname, _ = os.Hostname()
 767         }
 768         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 769                 // The "info" field has admin-only info when obtained
 770                 // with a privileged token, and should not be logged.
 771                 node, ok := resp.(map[string]interface{})
 772                 if ok {
 773                         delete(node, "info")
 774                 }
 775         })
 776         return err
 777 }
 778
 779 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 780         w := &ArvLogWriter{
 781                 ArvClient:     runner.ArvClient,
 782                 UUID:          runner.Container.UUID,
 783                 loggingStream: label,
 784                 writeCloser:   runner.LogCollection.Open(label + ".json"),
 785         }
 786
 787         reader, err := runner.ArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 788         if err != nil {
 789                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 790         }
 791         defer reader.Close()
 792
 793         dec := json.NewDecoder(reader)
 794         dec.UseNumber()
 795         var resp map[string]interface{}
 796         if err = dec.Decode(&resp); err != nil {
 797                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 798         }
 799         items, ok := resp["items"].([]interface{})
 800         if !ok {
 801                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 802         } else if len(items) < 1 {
 803                 return false, nil
 804         }
 805         if munge != nil {
 806                 munge(items[0])
 807         }
 808         // Re-encode it using indentation to improve readability
 809         enc := json.NewEncoder(w)
 810         enc.SetIndent("", "    ")
 811         if err = enc.Encode(items[0]); err != nil {
 812                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 813         }
 814         err = w.Close()
 815         if err != nil {
 816                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 817         }
 818         return true, nil
 819 }
 820
 821 // AttachStreams connects the docker container stdin, stdout and stderr logs
 822 // to the Arvados logger which logs to Keep and the API server logs table.
 823 func (runner *ContainerRunner) AttachStreams() (err error) {
 824
 825         runner.CrunchLog.Print("Attaching container streams")
 826
 827         // If stdin mount is provided, attach it to the docker container
 828         var stdinRdr arvados.File
 829         var stdinJson []byte
 830         if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
 831                 if stdinMnt.Kind == "collection" {
 832                         var stdinColl arvados.Collection
 833                         collId := stdinMnt.UUID
 834                         if collId == "" {
 835                                 collId = stdinMnt.PortableDataHash
 836                         }
 837                         err = runner.ArvClient.Get("collections", collId, nil, &stdinColl)
 838                         if err != nil {
 839                                 return fmt.Errorf("While getting stding collection: %v", err)
 840                         }
 841
 842                         stdinRdr, err = runner.Kc.ManifestFileReader(manifest.Manifest{Text: stdinColl.ManifestText}, stdinMnt.Path)
 843                         if os.IsNotExist(err) {
 844                                 return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
 845                         } else if err != nil {
 846                                 return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
 847                         }
 848                 } else if stdinMnt.Kind == "json" {
 849                         stdinJson, err = json.Marshal(stdinMnt.Content)
 850                         if err != nil {
 851                                 return fmt.Errorf("While encoding stdin json data: %v", err)
 852                         }
 853                 }
 854         }
 855
 856         stdinUsed := stdinRdr != nil || len(stdinJson) != 0
 857         response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
 858                 dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, Stdout: true, Stderr: true})
 859         if err != nil {
 860                 return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
 861         }
 862
 863         runner.loggingDone = make(chan bool)
 864
 865         if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
 866                 stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
 867                 if err != nil {
 868                         return err
 869                 }
 870                 runner.Stdout = stdoutFile
 871         } else {
 872                 runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
 873         }
 874
 875         if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
 876                 stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
 877                 if err != nil {
 878                         return err
 879                 }
 880                 runner.Stderr = stderrFile
 881         } else {
 882                 runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
 883         }
 884
 885         if stdinRdr != nil {
 886                 go func() {
 887                         _, err := io.Copy(response.Conn, stdinRdr)
 888                         if err != nil {
 889                                 runner.CrunchLog.Print("While writing stdin collection to docker container %q", err)
 890                                 runner.stop(nil)
 891                         }
 892                         stdinRdr.Close()
 893                         response.CloseWrite()
 894                 }()
 895         } else if len(stdinJson) != 0 {
 896                 go func() {
 897                         _, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
 898                         if err != nil {
 899                                 runner.CrunchLog.Print("While writing stdin json to docker container %q", err)
 900                                 runner.stop(nil)
 901                         }
 902                         response.CloseWrite()
 903                 }()
 904         }
 905
 906         go runner.ProcessDockerAttach(response.Reader)
 907
 908         return nil
 909 }
 910
 911 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 912         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 913         index := strings.LastIndex(stdoutPath, "/")
 914         if index > 0 {
 915                 subdirs := stdoutPath[:index]
 916                 if subdirs != "" {
 917                         st, err := os.Stat(runner.HostOutputDir)
 918                         if err != nil {
 919                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 920                         }
 921                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 922                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 923                         if err != nil {
 924                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 925                         }
 926                 }
 927         }
 928         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 929         if err != nil {
 930                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 931         }
 932
 933         return stdoutFile, nil
 934 }
 935
 936 // CreateContainer creates the docker container.
 937 func (runner *ContainerRunner) CreateContainer() error {
 938         runner.CrunchLog.Print("Creating Docker container")
 939
 940         runner.ContainerConfig.Cmd = runner.Container.Command
 941         if runner.Container.Cwd != "." {
 942                 runner.ContainerConfig.WorkingDir = runner.Container.Cwd
 943         }
 944
 945         for k, v := range runner.Container.Environment {
 946                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
 947         }
 948
 949         runner.ContainerConfig.Volumes = runner.Volumes
 950
 951         runner.HostConfig = dockercontainer.HostConfig{
 952                 Binds: runner.Binds,
 953                 LogConfig: dockercontainer.LogConfig{
 954                         Type: "none",
 955                 },
 956                 Resources: dockercontainer.Resources{
 957                         CgroupParent: runner.setCgroupParent,
 958                 },
 959         }
 960
 961         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
 962                 tok, err := runner.ContainerToken()
 963                 if err != nil {
 964                         return err
 965                 }
 966                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
 967                         "ARVADOS_API_TOKEN="+tok,
 968                         "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
 969                         "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
 970                 )
 971                 runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 972         } else {
 973                 if runner.enableNetwork == "always" {
 974                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
 975                 } else {
 976                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
 977                 }
 978         }
 979
 980         _, stdinUsed := runner.Container.Mounts["stdin"]
 981         runner.ContainerConfig.OpenStdin = stdinUsed
 982         runner.ContainerConfig.StdinOnce = stdinUsed
 983         runner.ContainerConfig.AttachStdin = stdinUsed
 984         runner.ContainerConfig.AttachStdout = true
 985         runner.ContainerConfig.AttachStderr = true
 986
 987         createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
 988         if err != nil {
 989                 return fmt.Errorf("While creating container: %v", err)
 990         }
 991
 992         runner.ContainerID = createdBody.ID
 993
 994         return runner.AttachStreams()
 995 }
 996
 997 // StartContainer starts the docker container created by CreateContainer.
 998 func (runner *ContainerRunner) StartContainer() error {
 999         runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
1000         runner.cStateLock.Lock()
1001         defer runner.cStateLock.Unlock()
1002         if runner.cCancelled {
1003                 return ErrCancelled
1004         }
1005         err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
1006                 dockertypes.ContainerStartOptions{})
1007         if err != nil {
1008                 var advice string
1009                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
1010                         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])
1011                 }
1012                 return fmt.Errorf("could not start container: %v%s", err, advice)
1013         }
1014         return nil
1015 }
1016
1017 // WaitFinish waits for the container to terminate, capture the exit code, and
1018 // close the stdout/stderr logging.
1019 func (runner *ContainerRunner) WaitFinish() error {
1020         runner.CrunchLog.Print("Waiting for container to finish")
1021
1022         waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning)
1023         arvMountExit := runner.ArvMountExit
1024         for {
1025                 select {
1026                 case waitBody := <-waitOk:
1027                         runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode)
1028                         code := int(waitBody.StatusCode)
1029                         runner.ExitCode = &code
1030
1031                         // wait for stdout/stderr to complete
1032                         <-runner.loggingDone
1033                         return nil
1034
1035                 case err := <-waitErr:
1036                         return fmt.Errorf("container wait: %v", err)
1037
1038                 case <-arvMountExit:
1039                         runner.CrunchLog.Printf("arv-mount exited while container is still running.  Stopping container.")
1040                         runner.stop(nil)
1041                         // arvMountExit will always be ready now that
1042                         // it's closed, but that doesn't interest us.
1043                         arvMountExit = nil
1044                 }
1045         }
1046 }
1047
1048 var ErrNotInOutputDir = fmt.Errorf("Must point to path within the output directory")
1049
1050 func (runner *ContainerRunner) derefOutputSymlink(path string, startinfo os.FileInfo) (tgt string, readlinktgt string, info os.FileInfo, err error) {
1051         // Follow symlinks if necessary
1052         info = startinfo
1053         tgt = path
1054         readlinktgt = ""
1055         nextlink := path
1056         for followed := 0; info.Mode()&os.ModeSymlink != 0; followed++ {
1057                 if followed >= limitFollowSymlinks {
1058                         // Got stuck in a loop or just a pathological number of links, give up.
1059                         err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
1060                         return
1061                 }
1062
1063                 readlinktgt, err = os.Readlink(nextlink)
1064                 if err != nil {
1065                         return
1066                 }
1067
1068                 tgt = readlinktgt
1069                 if !strings.HasPrefix(tgt, "/") {
1070                         // Relative symlink, resolve it to host path
1071                         tgt = filepath.Join(filepath.Dir(path), tgt)
1072                 }
1073                 if strings.HasPrefix(tgt, runner.Container.OutputPath+"/") && !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
1074                         // Absolute symlink to container output path, adjust it to host output path.
1075                         tgt = filepath.Join(runner.HostOutputDir, tgt[len(runner.Container.OutputPath):])
1076                 }
1077                 if !strings.HasPrefix(tgt, runner.HostOutputDir+"/") {
1078                         // After dereferencing, symlink target must either be
1079                         // within output directory, or must point to a
1080                         // collection mount.
1081                         err = ErrNotInOutputDir
1082                         return
1083                 }
1084
1085                 info, err = os.Lstat(tgt)
1086                 if err != nil {
1087                         // tgt
1088                         err = fmt.Errorf("Symlink in output %q points to invalid location %q: %v",
1089                                 path[len(runner.HostOutputDir):], readlinktgt, err)
1090                         return
1091                 }
1092
1093                 nextlink = tgt
1094         }
1095
1096         return
1097 }
1098
1099 var limitFollowSymlinks = 10
1100
1101 // UploadFile uploads files within the output directory, with special handling
1102 // for symlinks. If the symlink leads to a keep mount, copy the manifest text
1103 // from the keep mount into the output manifestText.  Ensure that whether
1104 // symlinks are relative or absolute, every symlink target (even targets that
1105 // are symlinks themselves) must point to a path in either the output directory
1106 // or a collection mount.
1107 //
1108 // Assumes initial value of "path" is absolute, and located within runner.HostOutputDir.
1109 func (runner *ContainerRunner) UploadOutputFile(
1110         path string,
1111         info os.FileInfo,
1112         infoerr error,
1113         binds []string,
1114         walkUpload *WalkUpload,
1115         relocateFrom string,
1116         relocateTo string,
1117         followed int) (manifestText string, err error) {
1118
1119         if infoerr != nil {
1120                 return "", infoerr
1121         }
1122
1123         if info.Mode().IsDir() {
1124                 // if empty, need to create a .keep file
1125                 dir, direrr := os.Open(path)
1126                 if direrr != nil {
1127                         return "", direrr
1128                 }
1129                 defer dir.Close()
1130                 names, eof := dir.Readdirnames(1)
1131                 if len(names) == 0 && eof == io.EOF && path != runner.HostOutputDir {
1132                         containerPath := runner.OutputPath + path[len(runner.HostOutputDir):]
1133                         for _, bind := range binds {
1134                                 mnt := runner.Container.Mounts[bind]
1135                                 // Check if there is a bind for this
1136                                 // directory, in which case assume we don't need .keep
1137                                 if (containerPath == bind || strings.HasPrefix(containerPath, bind+"/")) && mnt.PortableDataHash != "d41d8cd98f00b204e9800998ecf8427e+0" {
1138                                         return
1139                                 }
1140                         }
1141                         outputSuffix := path[len(runner.HostOutputDir)+1:]
1142                         return fmt.Sprintf("./%v d41d8cd98f00b204e9800998ecf8427e+0 0:0:.keep\n", outputSuffix), nil
1143                 }
1144                 return
1145         }
1146
1147         if followed >= limitFollowSymlinks {
1148                 // Got stuck in a loop or just a pathological number of
1149                 // directory links, give up.
1150                 err = fmt.Errorf("Followed more than %v symlinks from path %q", limitFollowSymlinks, path)
1151                 return
1152         }
1153
1154         // "path" is the actual path we are visiting
1155         // "tgt" is the target of "path" (a non-symlink) after following symlinks
1156         // "relocated" is the path in the output manifest where the file should be placed,
1157         // but has HostOutputDir as a prefix.
1158
1159         // The destination path in the output manifest may need to be
1160         // logically relocated to some other path in order to appear
1161         // in the correct location as a result of following a symlink.
1162         // Remove the relocateFrom prefix and replace it with
1163         // relocateTo.
1164         relocated := relocateTo + path[len(relocateFrom):]
1165
1166         tgt, readlinktgt, info, derefErr := runner.derefOutputSymlink(path, info)
1167         if derefErr != nil && derefErr != ErrNotInOutputDir {
1168                 return "", derefErr
1169         }
1170
1171         // go through mounts and try reverse map to collection reference
1172         for _, bind := range binds {
1173                 mnt := runner.Container.Mounts[bind]
1174                 if (tgt == bind || strings.HasPrefix(tgt, bind+"/")) && !mnt.Writable {
1175                         // get path relative to bind
1176                         targetSuffix := tgt[len(bind):]
1177
1178                         // Copy mount and adjust the path to add path relative to the bind
1179                         adjustedMount := mnt
1180                         adjustedMount.Path = filepath.Join(adjustedMount.Path, targetSuffix)
1181
1182                         // Terminates in this keep mount, so add the
1183                         // manifest text at appropriate location.
1184                         outputSuffix := relocated[len(runner.HostOutputDir):]
1185                         manifestText, err = runner.getCollectionManifestForPath(adjustedMount, outputSuffix)
1186                         return
1187                 }
1188         }
1189
1190         // If target is not a collection mount, it must be located within the
1191         // output directory, otherwise it is an error.
1192         if derefErr == ErrNotInOutputDir {
1193                 err = fmt.Errorf("Symlink in output %q points to invalid location %q, must point to path within the output directory.",
1194                         path[len(runner.HostOutputDir):], readlinktgt)
1195                 return
1196         }
1197
1198         if info.Mode().IsRegular() {
1199                 return "", walkUpload.UploadFile(relocated, tgt)
1200         }
1201
1202         if info.Mode().IsDir() {
1203                 // Symlink leads to directory.  Walk() doesn't follow
1204                 // directory symlinks, so we walk the target directory
1205                 // instead.  Within the walk, file paths are relocated
1206                 // so they appear under the original symlink path.
1207                 err = filepath.Walk(tgt, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
1208                         var m string
1209                         m, walkerr = runner.UploadOutputFile(walkpath, walkinfo, walkerr,
1210                                 binds, walkUpload, tgt, relocated, followed+1)
1211                         if walkerr == nil {
1212                                 manifestText = manifestText + m
1213                         }
1214                         return walkerr
1215                 })
1216                 return
1217         }
1218
1219         return
1220 }
1221
1222 // HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
1223 func (runner *ContainerRunner) CaptureOutput() error {
1224         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
1225                 // Output may have been set directly by the container, so
1226                 // refresh the container record to check.
1227                 err := runner.ArvClient.Get("containers", runner.Container.UUID,
1228                         nil, &runner.Container)
1229                 if err != nil {
1230                         return err
1231                 }
1232                 if runner.Container.Output != "" {
1233                         // Container output is already set.
1234                         runner.OutputPDH = &runner.Container.Output
1235                         return nil
1236                 }
1237         }
1238
1239         if runner.HostOutputDir == "" {
1240                 return nil
1241         }
1242
1243         _, err := os.Stat(runner.HostOutputDir)
1244         if err != nil {
1245                 return fmt.Errorf("While checking host output path: %v", err)
1246         }
1247
1248         // Pre-populate output from the configured mount points
1249         var binds []string
1250         for bind, mnt := range runner.Container.Mounts {
1251                 if mnt.Kind == "collection" {
1252                         binds = append(binds, bind)
1253                 }
1254         }
1255         sort.Strings(binds)
1256
1257         var manifestText string
1258
1259         collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
1260         _, err = os.Stat(collectionMetafile)
1261         if err != nil {
1262                 // Regular directory
1263
1264                 cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
1265                 walkUpload := cw.BeginUpload(runner.HostOutputDir, runner.CrunchLog.Logger)
1266
1267                 var m string
1268                 err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error {
1269                         m, err = runner.UploadOutputFile(path, info, err, binds, walkUpload, "", "", 0)
1270                         if err == nil {
1271                                 manifestText = manifestText + m
1272                         }
1273                         return err
1274                 })
1275
1276                 cw.EndUpload(walkUpload)
1277
1278                 if err != nil {
1279                         return fmt.Errorf("While uploading output files: %v", err)
1280                 }
1281
1282                 m, err = cw.ManifestText()
1283                 manifestText = manifestText + m
1284                 if err != nil {
1285                         return fmt.Errorf("While uploading output files: %v", err)
1286                 }
1287         } else {
1288                 // FUSE mount directory
1289                 file, openerr := os.Open(collectionMetafile)
1290                 if openerr != nil {
1291                         return fmt.Errorf("While opening FUSE metafile: %v", err)
1292                 }
1293                 defer file.Close()
1294
1295                 var rec arvados.Collection
1296                 err = json.NewDecoder(file).Decode(&rec)
1297                 if err != nil {
1298                         return fmt.Errorf("While reading FUSE metafile: %v", err)
1299                 }
1300                 manifestText = rec.ManifestText
1301         }
1302
1303         for _, bind := range binds {
1304                 mnt := runner.Container.Mounts[bind]
1305
1306                 bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
1307
1308                 if bindSuffix == bind || len(bindSuffix) <= 0 {
1309                         // either does not start with OutputPath or is OutputPath itself
1310                         continue
1311                 }
1312
1313                 if mnt.ExcludeFromOutput == true || mnt.Writable {
1314                         continue
1315                 }
1316
1317                 // append to manifest_text
1318                 m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
1319                 if err != nil {
1320                         return err
1321                 }
1322
1323                 manifestText = manifestText + m
1324         }
1325
1326         // Save output
1327         var response arvados.Collection
1328         manifest := manifest.Manifest{Text: manifestText}
1329         manifestText = manifest.Extract(".", ".").Text
1330         err = runner.ArvClient.Create("collections",
1331                 arvadosclient.Dict{
1332                         "ensure_unique_name": true,
1333                         "collection": arvadosclient.Dict{
1334                                 "is_trashed":    true,
1335                                 "name":          "output for " + runner.Container.UUID,
1336                                 "manifest_text": manifestText}},
1337                 &response)
1338         if err != nil {
1339                 return fmt.Errorf("While creating output collection: %v", err)
1340         }
1341         runner.OutputPDH = &response.PortableDataHash
1342         return nil
1343 }
1344
1345 var outputCollections = make(map[string]arvados.Collection)
1346
1347 // Fetch the collection for the mnt.PortableDataHash
1348 // Return the manifest_text fragment corresponding to the specified mnt.Path
1349 //  after making any required updates.
1350 //  Ex:
1351 //    If mnt.Path is not specified,
1352 //      return the entire manifest_text after replacing any "." with bindSuffix
1353 //    If mnt.Path corresponds to one stream,
1354 //      return the manifest_text for that stream after replacing that stream name with bindSuffix
1355 //    Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
1356 //      for that stream after replacing stream name with bindSuffix minus the last word
1357 //      and the file name with last word of the bindSuffix
1358 //  Allowed path examples:
1359 //    "path":"/"
1360 //    "path":"/subdir1"
1361 //    "path":"/subdir1/subdir2"
1362 //    "path":"/subdir/filename" etc
1363 func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
1364         collection := outputCollections[mnt.PortableDataHash]
1365         if collection.PortableDataHash == "" {
1366                 err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
1367                 if err != nil {
1368                         return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
1369                 }
1370                 outputCollections[mnt.PortableDataHash] = collection
1371         }
1372
1373         if collection.ManifestText == "" {
1374                 runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
1375                 return "", nil
1376         }
1377
1378         mft := manifest.Manifest{Text: collection.ManifestText}
1379         extracted := mft.Extract(mnt.Path, bindSuffix)
1380         if extracted.Err != nil {
1381                 return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
1382         }
1383         return extracted.Text, nil
1384 }
1385
1386 func (runner *ContainerRunner) CleanupDirs() {
1387         if runner.ArvMount != nil {
1388                 var delay int64 = 8
1389                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1390                 umount.Stdout = runner.CrunchLog
1391                 umount.Stderr = runner.CrunchLog
1392                 runner.CrunchLog.Printf("Running %v", umount.Args)
1393                 umnterr := umount.Start()
1394
1395                 if umnterr != nil {
1396                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1397                 } else {
1398                         // If arv-mount --unmount gets stuck for any reason, we
1399                         // don't want to wait for it forever.  Do Wait() in a goroutine
1400                         // so it doesn't block crunch-run.
1401                         umountExit := make(chan error)
1402                         go func() {
1403                                 mnterr := umount.Wait()
1404                                 if mnterr != nil {
1405                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1406                                 }
1407                                 umountExit <- mnterr
1408                         }()
1409
1410                         for again := true; again; {
1411                                 again = false
1412                                 select {
1413                                 case <-umountExit:
1414                                         umount = nil
1415                                         again = true
1416                                 case <-runner.ArvMountExit:
1417                                         break
1418                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1419                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1420                                         if umount != nil {
1421                                                 umount.Process.Kill()
1422                                         }
1423                                         runner.ArvMount.Process.Kill()
1424                                 }
1425                         }
1426                 }
1427         }
1428
1429         if runner.ArvMountPoint != "" {
1430                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1431                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1432                 }
1433         }
1434
1435         if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
1436                 runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
1437         }
1438 }
1439
1440 // CommitLogs posts the collection containing the final container logs.
1441 func (runner *ContainerRunner) CommitLogs() error {
1442         func() {
1443                 // Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
1444                 runner.cStateLock.Lock()
1445                 defer runner.cStateLock.Unlock()
1446
1447                 runner.CrunchLog.Print(runner.finalState)
1448
1449                 if runner.arvMountLog != nil {
1450                         runner.arvMountLog.Close()
1451                 }
1452                 runner.CrunchLog.Close()
1453
1454                 // Closing CrunchLog above allows them to be committed to Keep at this
1455                 // point, but re-open crunch log with ArvClient in case there are any
1456                 // other further errors (such as failing to write the log to Keep!)
1457                 // while shutting down
1458                 runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{ArvClient: runner.ArvClient,
1459                         UUID: runner.Container.UUID, loggingStream: "crunch-run", writeCloser: nil})
1460                 runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1461         }()
1462
1463         if runner.LogsPDH != nil {
1464                 // If we have already assigned something to LogsPDH,
1465                 // we must be closing the re-opened log, which won't
1466                 // end up getting attached to the container record and
1467                 // therefore doesn't need to be saved as a collection
1468                 // -- it exists only to send logs to other channels.
1469                 return nil
1470         }
1471
1472         mt, err := runner.LogCollection.ManifestText()
1473         if err != nil {
1474                 return fmt.Errorf("While creating log manifest: %v", err)
1475         }
1476
1477         var response arvados.Collection
1478         err = runner.ArvClient.Create("collections",
1479                 arvadosclient.Dict{
1480                         "ensure_unique_name": true,
1481                         "collection": arvadosclient.Dict{
1482                                 "is_trashed":    true,
1483                                 "name":          "logs for " + runner.Container.UUID,
1484                                 "manifest_text": mt}},
1485                 &response)
1486         if err != nil {
1487                 return fmt.Errorf("While creating log collection: %v", err)
1488         }
1489         runner.LogsPDH = &response.PortableDataHash
1490         return nil
1491 }
1492
1493 // UpdateContainerRunning updates the container state to "Running"
1494 func (runner *ContainerRunner) UpdateContainerRunning() error {
1495         runner.cStateLock.Lock()
1496         defer runner.cStateLock.Unlock()
1497         if runner.cCancelled {
1498                 return ErrCancelled
1499         }
1500         return runner.ArvClient.Update("containers", runner.Container.UUID,
1501                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
1502 }
1503
1504 // ContainerToken returns the api_token the container (and any
1505 // arv-mount processes) are allowed to use.
1506 func (runner *ContainerRunner) ContainerToken() (string, error) {
1507         if runner.token != "" {
1508                 return runner.token, nil
1509         }
1510
1511         var auth arvados.APIClientAuthorization
1512         err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1513         if err != nil {
1514                 return "", err
1515         }
1516         runner.token = auth.APIToken
1517         return runner.token, nil
1518 }
1519
1520 // UpdateContainerComplete updates the container record state on API
1521 // server to "Complete" or "Cancelled"
1522 func (runner *ContainerRunner) UpdateContainerFinal() error {
1523         update := arvadosclient.Dict{}
1524         update["state"] = runner.finalState
1525         if runner.LogsPDH != nil {
1526                 update["log"] = *runner.LogsPDH
1527         }
1528         if runner.finalState == "Complete" {
1529                 if runner.ExitCode != nil {
1530                         update["exit_code"] = *runner.ExitCode
1531                 }
1532                 if runner.OutputPDH != nil {
1533                         update["output"] = *runner.OutputPDH
1534                 }
1535         }
1536         return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1537 }
1538
1539 // IsCancelled returns the value of Cancelled, with goroutine safety.
1540 func (runner *ContainerRunner) IsCancelled() bool {
1541         runner.cStateLock.Lock()
1542         defer runner.cStateLock.Unlock()
1543         return runner.cCancelled
1544 }
1545
1546 // NewArvLogWriter creates an ArvLogWriter
1547 func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser {
1548         return &ArvLogWriter{
1549                 ArvClient:     runner.ArvClient,
1550                 UUID:          runner.Container.UUID,
1551                 loggingStream: name,
1552                 writeCloser:   runner.LogCollection.Open(name + ".txt")}
1553 }
1554
1555 // Run the full container lifecycle.
1556 func (runner *ContainerRunner) Run() (err error) {
1557         runner.CrunchLog.Printf("crunch-run %s started", version)
1558         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1559
1560         hostname, hosterr := os.Hostname()
1561         if hosterr != nil {
1562                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1563         } else {
1564                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1565         }
1566
1567         runner.finalState = "Queued"
1568
1569         defer func() {
1570                 runner.CleanupDirs()
1571
1572                 runner.CrunchLog.Printf("crunch-run finished")
1573                 runner.CrunchLog.Close()
1574         }()
1575
1576         defer func() {
1577                 // checkErr prints e (unless it's nil) and sets err to
1578                 // e (unless err is already non-nil). Thus, if err
1579                 // hasn't already been assigned when Run() returns,
1580                 // this cleanup func will cause Run() to return the
1581                 // first non-nil error that is passed to checkErr().
1582                 checkErr := func(e error) {
1583                         if e == nil {
1584                                 return
1585                         }
1586                         runner.CrunchLog.Print(e)
1587                         if err == nil {
1588                                 err = e
1589                         }
1590                         if runner.finalState == "Complete" {
1591                                 // There was an error in the finalization.
1592                                 runner.finalState = "Cancelled"
1593                         }
1594                 }
1595
1596                 // Log the error encountered in Run(), if any
1597                 checkErr(err)
1598
1599                 if runner.finalState == "Queued" {
1600                         runner.UpdateContainerFinal()
1601                         return
1602                 }
1603
1604                 if runner.IsCancelled() {
1605                         runner.finalState = "Cancelled"
1606                         // but don't return yet -- we still want to
1607                         // capture partial output and write logs
1608                 }
1609
1610                 checkErr(runner.CaptureOutput())
1611                 checkErr(runner.stopHoststat())
1612                 checkErr(runner.CommitLogs())
1613                 checkErr(runner.UpdateContainerFinal())
1614         }()
1615
1616         err = runner.fetchContainerRecord()
1617         if err != nil {
1618                 return
1619         }
1620         runner.setupSignals()
1621         runner.startHoststat()
1622
1623         // check for and/or load image
1624         err = runner.LoadImage()
1625         if err != nil {
1626                 if !runner.checkBrokenNode(err) {
1627                         // Failed to load image but not due to a "broken node"
1628                         // condition, probably user error.
1629                         runner.finalState = "Cancelled"
1630                 }
1631                 err = fmt.Errorf("While loading container image: %v", err)
1632                 return
1633         }
1634
1635         // set up FUSE mount and binds
1636         err = runner.SetupMounts()
1637         if err != nil {
1638                 runner.finalState = "Cancelled"
1639                 err = fmt.Errorf("While setting up mounts: %v", err)
1640                 return
1641         }
1642
1643         err = runner.CreateContainer()
1644         if err != nil {
1645                 return
1646         }
1647         err = runner.LogHostInfo()
1648         if err != nil {
1649                 return
1650         }
1651         err = runner.LogNodeRecord()
1652         if err != nil {
1653                 return
1654         }
1655         err = runner.LogContainerRecord()
1656         if err != nil {
1657                 return
1658         }
1659
1660         if runner.IsCancelled() {
1661                 return
1662         }
1663
1664         err = runner.UpdateContainerRunning()
1665         if err != nil {
1666                 return
1667         }
1668         runner.finalState = "Cancelled"
1669
1670         runner.startCrunchstat()
1671
1672         err = runner.StartContainer()
1673         if err != nil {
1674                 runner.checkBrokenNode(err)
1675                 return
1676         }
1677
1678         err = runner.WaitFinish()
1679         if err == nil && !runner.IsCancelled() {
1680                 runner.finalState = "Complete"
1681         }
1682         return
1683 }
1684
1685 // Fetch the current container record (uuid = runner.Container.UUID)
1686 // into runner.Container.
1687 func (runner *ContainerRunner) fetchContainerRecord() error {
1688         reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1689         if err != nil {
1690                 return fmt.Errorf("error fetching container record: %v", err)
1691         }
1692         defer reader.Close()
1693
1694         dec := json.NewDecoder(reader)
1695         dec.UseNumber()
1696         err = dec.Decode(&runner.Container)
1697         if err != nil {
1698                 return fmt.Errorf("error decoding container record: %v", err)
1699         }
1700         return nil
1701 }
1702
1703 // NewContainerRunner creates a new container runner.
1704 func NewContainerRunner(api IArvadosClient,
1705         kc IKeepClient,
1706         docker ThinDockerClient,
1707         containerUUID string) *ContainerRunner {
1708
1709         cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
1710         cr.NewLogWriter = cr.NewArvLogWriter
1711         cr.RunArvMount = cr.ArvMountCmd
1712         cr.MkTempDir = ioutil.TempDir
1713         cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
1714         cr.Container.UUID = containerUUID
1715         cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
1716         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1717
1718         loadLogThrottleParams(api)
1719
1720         return cr
1721 }
1722
1723 func main() {
1724         statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1725         cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1726         cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1727         cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1728         caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
1729         enableNetwork := flag.String("container-enable-networking", "default",
1730                 `Specify if networking should be enabled for container.  One of 'default', 'always':
1731         default: only enable networking if container requests it.
1732         always:  containers always have networking enabled
1733         `)
1734         networkMode := flag.String("container-network-mode", "default",
1735                 `Set networking mode for container.  Corresponds to Docker network mode (--net).
1736         `)
1737         memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container")
1738         getVersion := flag.Bool("version", false, "Print version information and exit.")
1739         flag.Parse()
1740
1741         // Print version information if requested
1742         if *getVersion {
1743                 fmt.Printf("crunch-run %s\n", version)
1744                 return
1745         }
1746
1747         log.Printf("crunch-run %s started", version)
1748
1749         containerId := flag.Arg(0)
1750
1751         if *caCertsPath != "" {
1752                 arvadosclient.CertFiles = []string{*caCertsPath}
1753         }
1754
1755         api, err := arvadosclient.MakeArvadosClient()
1756         if err != nil {
1757                 log.Fatalf("%s: %v", containerId, err)
1758         }
1759         api.Retries = 8
1760
1761         kc, kcerr := keepclient.MakeKeepClient(api)
1762         if kcerr != nil {
1763                 log.Fatalf("%s: %v", containerId, kcerr)
1764         }
1765         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1766         kc.Retries = 4
1767
1768         // API version 1.21 corresponds to Docker 1.9, which is currently the
1769         // minimum version we want to support.
1770         docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
1771
1772         cr := NewContainerRunner(api, kc, docker, containerId)
1773         if dockererr != nil {
1774                 cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
1775                 cr.checkBrokenNode(dockererr)
1776                 cr.CrunchLog.Close()
1777                 os.Exit(1)
1778         }
1779
1780         parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerId+".")
1781         if tmperr != nil {
1782                 log.Fatalf("%s: %v", containerId, tmperr)
1783         }
1784
1785         cr.parentTemp = parentTemp
1786         cr.statInterval = *statInterval
1787         cr.cgroupRoot = *cgroupRoot
1788         cr.expectCgroupParent = *cgroupParent
1789         cr.enableNetwork = *enableNetwork
1790         cr.networkMode = *networkMode
1791         if *cgroupParentSubsystem != "" {
1792                 p := findCgroup(*cgroupParentSubsystem)
1793                 cr.setCgroupParent = p
1794                 cr.expectCgroupParent = p
1795         }
1796
1797         runerr := cr.Run()
1798
1799         if *memprofile != "" {
1800                 f, err := os.Create(*memprofile)
1801                 if err != nil {
1802                         log.Printf("could not create memory profile: ", err)
1803                 }
1804                 runtime.GC() // get up-to-date statistics
1805                 if err := pprof.WriteHeapProfile(f); err != nil {
1806                         log.Printf("could not write memory profile: ", err)
1807                 }
1808                 closeerr := f.Close()
1809                 if closeerr != nil {
1810                         log.Printf("closing memprofile file: ", err)
1811                 }
1812         }
1813
1814         if runerr != nil {
1815                 log.Fatalf("%s: %v", containerId, runerr)
1816         }
1817 }