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         "github.com/shirou/gopsutil/process"
  36         "golang.org/x/net/context"
  37
  38         dockertypes "github.com/docker/docker/api/types"
  39         dockercontainer "github.com/docker/docker/api/types/container"
  40         dockernetwork "github.com/docker/docker/api/types/network"
  41         dockerclient "github.com/docker/docker/client"
  42 )
  43
  44 var version = "dev"
  45
  46 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  47 type IArvadosClient interface {
  48         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  49         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  50         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  51         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  52         CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
  53         Discovery(key string) (interface{}, error)
  54 }
  55
  56 // ErrCancelled is the error returned when the container is cancelled.
  57 var ErrCancelled = errors.New("Cancelled")
  58
  59 // IKeepClient is the minimal Keep API methods used by crunch-run.
  60 type IKeepClient interface {
  61         PutB(buf []byte) (string, int, error)
  62         ReadAt(locator string, p []byte, off int) (int, error)
  63         ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
  64         ClearBlockCache()
  65 }
  66
  67 // NewLogWriter is a factory function to create a new log writer.
  68 type NewLogWriter func(name string) (io.WriteCloser, error)
  69
  70 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  71
  72 type MkTempDir func(string, string) (string, error)
  73
  74 // ThinDockerClient is the minimal Docker client interface used by crunch-run.
  75 type ThinDockerClient interface {
  76         ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error)
  77         ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
  78                 networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error)
  79         ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error
  80         ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error
  81         ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error)
  82         ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error)
  83         ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error)
  84         ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error)
  85 }
  86
  87 type PsProcess interface {
  88         CmdlineSlice() ([]string, error)
  89 }
  90
  91 // ContainerRunner is the main stateful struct used for a single execution of a
  92 // container.
  93 type ContainerRunner struct {
  94         Docker    ThinDockerClient
  95         client    *arvados.Client
  96         ArvClient IArvadosClient
  97         Kc        IKeepClient
  98         arvados.Container
  99         ContainerConfig dockercontainer.Config
 100         dockercontainer.HostConfig
 101         token       string
 102         ContainerID string
 103         ExitCode    *int
 104         NewLogWriter
 105         loggingDone   chan bool
 106         CrunchLog     *ThrottledLogger
 107         Stdout        io.WriteCloser
 108         Stderr        io.WriteCloser
 109         LogCollection arvados.CollectionFileSystem
 110         LogsPDH       *string
 111         RunArvMount
 112         MkTempDir
 113         ArvMount      *exec.Cmd
 114         ArvMountPoint string
 115         HostOutputDir string
 116         Binds         []string
 117         Volumes       map[string]struct{}
 118         OutputPDH     *string
 119         SigChan       chan os.Signal
 120         ArvMountExit  chan error
 121         SecretMounts  map[string]arvados.Mount
 122         MkArvClient   func(token string) (IArvadosClient, error)
 123         finalState    string
 124         parentTemp    string
 125
 126         ListProcesses func() ([]PsProcess, error)
 127
 128         statLogger       io.WriteCloser
 129         statReporter     *crunchstat.Reporter
 130         hoststatLogger   io.WriteCloser
 131         hoststatReporter *crunchstat.Reporter
 132         statInterval     time.Duration
 133         cgroupRoot       string
 134         // What we expect the container's cgroup parent to be.
 135         expectCgroupParent string
 136         // What we tell docker to use as the container's cgroup
 137         // parent. Note: Ideally we would use the same field for both
 138         // expectCgroupParent and setCgroupParent, and just make it
 139         // default to "docker". However, when using docker < 1.10 with
 140         // systemd, specifying a non-empty cgroup parent (even the
 141         // default value "docker") hits a docker bug
 142         // (https://github.com/docker/docker/issues/17126). Using two
 143         // separate fields makes it possible to use the "expect cgroup
 144         // parent to be X" feature even on sites where the "specify
 145         // cgroup parent" feature breaks.
 146         setCgroupParent string
 147
 148         cStateLock sync.Mutex
 149         cCancelled bool // StopContainer() invoked
 150
 151         enableNetwork   string // one of "default" or "always"
 152         networkMode     string // passed through to HostConfig.NetworkMode
 153         arvMountLog     *ThrottledLogger
 154         checkContainerd time.Duration
 155 }
 156
 157 // setupSignals sets up signal handling to gracefully terminate the underlying
 158 // Docker container and update state when receiving a TERM, INT or QUIT signal.
 159 func (runner *ContainerRunner) setupSignals() {
 160         runner.SigChan = make(chan os.Signal, 1)
 161         signal.Notify(runner.SigChan, syscall.SIGTERM)
 162         signal.Notify(runner.SigChan, syscall.SIGINT)
 163         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 164
 165         go func(sig chan os.Signal) {
 166                 for s := range sig {
 167                         runner.stop(s)
 168                 }
 169         }(runner.SigChan)
 170 }
 171
 172 // stop the underlying Docker container.
 173 func (runner *ContainerRunner) stop(sig os.Signal) {
 174         runner.cStateLock.Lock()
 175         defer runner.cStateLock.Unlock()
 176         if sig != nil {
 177                 runner.CrunchLog.Printf("caught signal: %v", sig)
 178         }
 179         if runner.ContainerID == "" {
 180                 return
 181         }
 182         runner.cCancelled = true
 183         runner.CrunchLog.Printf("removing container")
 184         err := runner.Docker.ContainerRemove(context.TODO(), runner.ContainerID, dockertypes.ContainerRemoveOptions{Force: true})
 185         if err != nil {
 186                 runner.CrunchLog.Printf("error removing container: %s", err)
 187         }
 188 }
 189
 190 var errorBlacklist = []string{
 191         "(?ms).*[Cc]annot connect to the Docker daemon.*",
 192         "(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
 193 }
 194 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)")
 195
 196 func (runner *ContainerRunner) runBrokenNodeHook() {
 197         if *brokenNodeHook == "" {
 198                 runner.CrunchLog.Printf("No broken node hook provided, cannot mark node as broken.")
 199         } else {
 200                 runner.CrunchLog.Printf("Running broken node hook %q", *brokenNodeHook)
 201                 // run killme script
 202                 c := exec.Command(*brokenNodeHook)
 203                 c.Stdout = runner.CrunchLog
 204                 c.Stderr = runner.CrunchLog
 205                 err := c.Run()
 206                 if err != nil {
 207                         runner.CrunchLog.Printf("Error running broken node hook: %v", err)
 208                 }
 209         }
 210 }
 211
 212 func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
 213         for _, d := range errorBlacklist {
 214                 if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
 215                         runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
 216                         runner.runBrokenNodeHook()
 217                         return true
 218                 }
 219         }
 220         return false
 221 }
 222
 223 // LoadImage determines the docker image id from the container record and
 224 // checks if it is available in the local Docker image store.  If not, it loads
 225 // the image from Keep.
 226 func (runner *ContainerRunner) LoadImage() (err error) {
 227
 228         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 229
 230         var collection arvados.Collection
 231         err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
 232         if err != nil {
 233                 return fmt.Errorf("While getting container image collection: %v", err)
 234         }
 235         manifest := manifest.Manifest{Text: collection.ManifestText}
 236         var img, imageID string
 237         for ms := range manifest.StreamIter() {
 238                 img = ms.FileStreamSegments[0].Name
 239                 if !strings.HasSuffix(img, ".tar") {
 240                         return fmt.Errorf("First file in the container image collection does not end in .tar")
 241                 }
 242                 imageID = img[:len(img)-4]
 243         }
 244
 245         runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
 246
 247         _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
 248         if err != nil {
 249                 runner.CrunchLog.Print("Loading Docker image from keep")
 250
 251                 var readCloser io.ReadCloser
 252                 readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
 253                 if err != nil {
 254                         return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
 255                 }
 256
 257                 response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, true)
 258                 if err != nil {
 259                         return fmt.Errorf("While loading container image into Docker: %v", err)
 260                 }
 261
 262                 defer response.Body.Close()
 263                 rbody, err := ioutil.ReadAll(response.Body)
 264                 if err != nil {
 265                         return fmt.Errorf("Reading response to image load: %v", err)
 266                 }
 267                 runner.CrunchLog.Printf("Docker response: %s", rbody)
 268         } else {
 269                 runner.CrunchLog.Print("Docker image is available")
 270         }
 271
 272         runner.ContainerConfig.Image = imageID
 273
 274         runner.Kc.ClearBlockCache()
 275
 276         return nil
 277 }
 278
 279 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 280         c = exec.Command("arv-mount", arvMountCmd...)
 281
 282         // Copy our environment, but override ARVADOS_API_TOKEN with
 283         // the container auth token.
 284         c.Env = nil
 285         for _, s := range os.Environ() {
 286                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 287                         c.Env = append(c.Env, s)
 288                 }
 289         }
 290         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 291
 292         w, err := runner.NewLogWriter("arv-mount")
 293         if err != nil {
 294                 return nil, err
 295         }
 296         runner.arvMountLog = NewThrottledLogger(w)
 297         c.Stdout = runner.arvMountLog
 298         c.Stderr = runner.arvMountLog
 299
 300         runner.CrunchLog.Printf("Running %v", c.Args)
 301
 302         err = c.Start()
 303         if err != nil {
 304                 return nil, err
 305         }
 306
 307         statReadme := make(chan bool)
 308         runner.ArvMountExit = make(chan error)
 309
 310         keepStatting := true
 311         go func() {
 312                 for keepStatting {
 313                         time.Sleep(100 * time.Millisecond)
 314                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 315                         if err == nil {
 316                                 keepStatting = false
 317                                 statReadme <- true
 318                         }
 319                 }
 320                 close(statReadme)
 321         }()
 322
 323         go func() {
 324                 mnterr := c.Wait()
 325                 if mnterr != nil {
 326                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 327                 }
 328                 runner.ArvMountExit <- mnterr
 329                 close(runner.ArvMountExit)
 330         }()
 331
 332         select {
 333         case <-statReadme:
 334                 break
 335         case err := <-runner.ArvMountExit:
 336                 runner.ArvMount = nil
 337                 keepStatting = false
 338                 return nil, err
 339         }
 340
 341         return c, nil
 342 }
 343
 344 func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
 345         if runner.ArvMountPoint == "" {
 346                 runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
 347         }
 348         return
 349 }
 350
 351 func copyfile(src string, dst string) (err error) {
 352         srcfile, err := os.Open(src)
 353         if err != nil {
 354                 return
 355         }
 356
 357         os.MkdirAll(path.Dir(dst), 0777)
 358
 359         dstfile, err := os.Create(dst)
 360         if err != nil {
 361                 return
 362         }
 363         _, err = io.Copy(dstfile, srcfile)
 364         if err != nil {
 365                 return
 366         }
 367
 368         err = srcfile.Close()
 369         err2 := dstfile.Close()
 370
 371         if err != nil {
 372                 return
 373         }
 374
 375         if err2 != nil {
 376                 return err2
 377         }
 378
 379         return nil
 380 }
 381
 382 func (runner *ContainerRunner) SetupMounts() (err error) {
 383         err = runner.SetupArvMountPoint("keep")
 384         if err != nil {
 385                 return fmt.Errorf("While creating keep mount temp dir: %v", err)
 386         }
 387
 388         token, err := runner.ContainerToken()
 389         if err != nil {
 390                 return fmt.Errorf("could not get container token: %s", err)
 391         }
 392
 393         pdhOnly := true
 394         tmpcount := 0
 395         arvMountCmd := []string{
 396                 "--foreground",
 397                 "--allow-other",
 398                 "--read-write",
 399                 fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
 400
 401         if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
 402                 arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
 403         }
 404
 405         collectionPaths := []string{}
 406         runner.Binds = nil
 407         runner.Volumes = make(map[string]struct{})
 408         needCertMount := true
 409         type copyFile struct {
 410                 src  string
 411                 bind string
 412         }
 413         var copyFiles []copyFile
 414
 415         var binds []string
 416         for bind := range runner.Container.Mounts {
 417                 binds = append(binds, bind)
 418         }
 419         for bind := range runner.SecretMounts {
 420                 if _, ok := runner.Container.Mounts[bind]; ok {
 421                         return fmt.Errorf("Secret mount %q conflicts with regular mount", bind)
 422                 }
 423                 if runner.SecretMounts[bind].Kind != "json" &&
 424                         runner.SecretMounts[bind].Kind != "text" {
 425                         return fmt.Errorf("Secret mount %q type is %q but only 'json' and 'text' are permitted.",
 426                                 bind, runner.SecretMounts[bind].Kind)
 427                 }
 428                 binds = append(binds, bind)
 429         }
 430         sort.Strings(binds)
 431
 432         for _, bind := range binds {
 433                 mnt, ok := runner.Container.Mounts[bind]
 434                 if !ok {
 435                         mnt = runner.SecretMounts[bind]
 436                 }
 437                 if bind == "stdout" || bind == "stderr" {
 438                         // Is it a "file" mount kind?
 439                         if mnt.Kind != "file" {
 440                                 return fmt.Errorf("Unsupported mount kind '%s' for %s. Only 'file' is supported.", mnt.Kind, bind)
 441                         }
 442
 443                         // Does path start with OutputPath?
 444                         prefix := runner.Container.OutputPath
 445                         if !strings.HasSuffix(prefix, "/") {
 446                                 prefix += "/"
 447                         }
 448                         if !strings.HasPrefix(mnt.Path, prefix) {
 449                                 return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
 450                         }
 451                 }
 452
 453                 if bind == "stdin" {
 454                         // Is it a "collection" mount kind?
 455                         if mnt.Kind != "collection" && mnt.Kind != "json" {
 456                                 return fmt.Errorf("Unsupported mount kind '%s' for stdin. Only 'collection' or 'json' are supported.", mnt.Kind)
 457                         }
 458                 }
 459
 460                 if bind == "/etc/arvados/ca-certificates.crt" {
 461                         needCertMount = false
 462                 }
 463
 464                 if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
 465                         if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
 466                                 return fmt.Errorf("Only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
 467                         }
 468                 }
 469
 470                 switch {
 471                 case mnt.Kind == "collection" && bind != "stdin":
 472                         var src string
 473                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 474                                 return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 475                         }
 476                         if mnt.UUID != "" {
 477                                 if mnt.Writable {
 478                                         return fmt.Errorf("Writing to existing collections currently not permitted.")
 479                                 }
 480                                 pdhOnly = false
 481                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 482                         } else if mnt.PortableDataHash != "" {
 483                                 if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 484                                         return fmt.Errorf("Can never write to a collection specified by portable data hash")
 485                                 }
 486                                 idx := strings.Index(mnt.PortableDataHash, "/")
 487                                 if idx > 0 {
 488                                         mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
 489                                         mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
 490                                         runner.Container.Mounts[bind] = mnt
 491                                 }
 492                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 493                                 if mnt.Path != "" && mnt.Path != "." {
 494                                         if strings.HasPrefix(mnt.Path, "./") {
 495                                                 mnt.Path = mnt.Path[2:]
 496                                         } else if strings.HasPrefix(mnt.Path, "/") {
 497                                                 mnt.Path = mnt.Path[1:]
 498                                         }
 499                                         src += "/" + mnt.Path
 500                                 }
 501                         } else {
 502                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 503                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 504                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 505                                 tmpcount += 1
 506                         }
 507                         if mnt.Writable {
 508                                 if bind == runner.Container.OutputPath {
 509                                         runner.HostOutputDir = src
 510                                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 511                                 } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 512                                         copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 513                                 } else {
 514                                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 515                                 }
 516                         } else {
 517                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
 518                         }
 519                         collectionPaths = append(collectionPaths, src)
 520
 521                 case mnt.Kind == "tmp":
 522                         var tmpdir string
 523                         tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
 524                         if err != nil {
 525                                 return fmt.Errorf("While creating mount temp dir: %v", err)
 526                         }
 527                         st, staterr := os.Stat(tmpdir)
 528                         if staterr != nil {
 529                                 return fmt.Errorf("While Stat on temp dir: %v", staterr)
 530                         }
 531                         err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
 532                         if staterr != nil {
 533                                 return fmt.Errorf("While Chmod temp dir: %v", err)
 534                         }
 535                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
 536                         if bind == runner.Container.OutputPath {
 537                                 runner.HostOutputDir = tmpdir
 538                         }
 539
 540                 case mnt.Kind == "json" || mnt.Kind == "text":
 541                         var filedata []byte
 542                         if mnt.Kind == "json" {
 543                                 filedata, err = json.Marshal(mnt.Content)
 544                                 if err != nil {
 545                                         return fmt.Errorf("encoding json data: %v", err)
 546                                 }
 547                         } else {
 548                                 text, ok := mnt.Content.(string)
 549                                 if !ok {
 550                                         return fmt.Errorf("content for mount %q must be a string", bind)
 551                                 }
 552                                 filedata = []byte(text)
 553                         }
 554
 555                         tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
 556                         if err != nil {
 557                                 return fmt.Errorf("creating temp dir: %v", err)
 558                         }
 559                         tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
 560                         err = ioutil.WriteFile(tmpfn, filedata, 0444)
 561                         if err != nil {
 562                                 return fmt.Errorf("writing temp file: %v", err)
 563                         }
 564                         if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
 565                                 copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
 566                         } else {
 567                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
 568                         }
 569
 570                 case mnt.Kind == "git_tree":
 571                         tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
 572                         if err != nil {
 573                                 return fmt.Errorf("creating temp dir: %v", err)
 574                         }
 575                         err = gitMount(mnt).extractTree(runner.ArvClient, tmpdir, token)
 576                         if err != nil {
 577                                 return err
 578                         }
 579                         runner.Binds = append(runner.Binds, tmpdir+":"+bind+":ro")
 580                 }
 581         }
 582
 583         if runner.HostOutputDir == "" {
 584                 return fmt.Errorf("Output path does not correspond to a writable mount point")
 585         }
 586
 587         if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
 588                 for _, certfile := range arvadosclient.CertFiles {
 589                         _, err := os.Stat(certfile)
 590                         if err == nil {
 591                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
 592                                 break
 593                         }
 594                 }
 595         }
 596
 597         if pdhOnly {
 598                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 599         } else {
 600                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 601         }
 602         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 603
 604         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 605         if err != nil {
 606                 return fmt.Errorf("While trying to start arv-mount: %v", err)
 607         }
 608
 609         for _, p := range collectionPaths {
 610                 _, err = os.Stat(p)
 611                 if err != nil {
 612                         return fmt.Errorf("While checking that input files exist: %v", err)
 613                 }
 614         }
 615
 616         for _, cp := range copyFiles {
 617                 st, err := os.Stat(cp.src)
 618                 if err != nil {
 619                         return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 620                 }
 621                 if st.IsDir() {
 622                         err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
 623                                 if walkerr != nil {
 624                                         return walkerr
 625                                 }
 626                                 target := path.Join(cp.bind, walkpath[len(cp.src):])
 627                                 if walkinfo.Mode().IsRegular() {
 628                                         copyerr := copyfile(walkpath, target)
 629                                         if copyerr != nil {
 630                                                 return copyerr
 631                                         }
 632                                         return os.Chmod(target, walkinfo.Mode()|0777)
 633                                 } else if walkinfo.Mode().IsDir() {
 634                                         mkerr := os.MkdirAll(target, 0777)
 635                                         if mkerr != nil {
 636                                                 return mkerr
 637                                         }
 638                                         return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 639                                 } else {
 640                                         return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
 641                                 }
 642                         })
 643                 } else if st.Mode().IsRegular() {
 644                         err = copyfile(cp.src, cp.bind)
 645                         if err == nil {
 646                                 err = os.Chmod(cp.bind, st.Mode()|0777)
 647                         }
 648                 }
 649                 if err != nil {
 650                         return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
 651                 }
 652         }
 653
 654         return nil
 655 }
 656
 657 func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
 658         // Handle docker log protocol
 659         // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
 660         defer close(runner.loggingDone)
 661
 662         header := make([]byte, 8)
 663         var err error
 664         for err == nil {
 665                 _, err = io.ReadAtLeast(containerReader, header, 8)
 666                 if err != nil {
 667                         if err == io.EOF {
 668                                 err = nil
 669                         }
 670                         break
 671                 }
 672                 readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
 673                 if header[0] == 1 {
 674                         // stdout
 675                         _, err = io.CopyN(runner.Stdout, containerReader, readsize)
 676                 } else {
 677                         // stderr
 678                         _, err = io.CopyN(runner.Stderr, containerReader, readsize)
 679                 }
 680         }
 681
 682         if err != nil {
 683                 runner.CrunchLog.Printf("error reading docker logs: %v", err)
 684         }
 685
 686         err = runner.Stdout.Close()
 687         if err != nil {
 688                 runner.CrunchLog.Printf("error closing stdout logs: %v", err)
 689         }
 690
 691         err = runner.Stderr.Close()
 692         if err != nil {
 693                 runner.CrunchLog.Printf("error closing stderr logs: %v", err)
 694         }
 695
 696         if runner.statReporter != nil {
 697                 runner.statReporter.Stop()
 698                 err = runner.statLogger.Close()
 699                 if err != nil {
 700                         runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
 701                 }
 702         }
 703 }
 704
 705 func (runner *ContainerRunner) stopHoststat() error {
 706         if runner.hoststatReporter == nil {
 707                 return nil
 708         }
 709         runner.hoststatReporter.Stop()
 710         err := runner.hoststatLogger.Close()
 711         if err != nil {
 712                 return fmt.Errorf("error closing hoststat logs: %v", err)
 713         }
 714         return nil
 715 }
 716
 717 func (runner *ContainerRunner) startHoststat() error {
 718         w, err := runner.NewLogWriter("hoststat")
 719         if err != nil {
 720                 return err
 721         }
 722         runner.hoststatLogger = NewThrottledLogger(w)
 723         runner.hoststatReporter = &crunchstat.Reporter{
 724                 Logger:     log.New(runner.hoststatLogger, "", 0),
 725                 CgroupRoot: runner.cgroupRoot,
 726                 PollPeriod: runner.statInterval,
 727         }
 728         runner.hoststatReporter.Start()
 729         return nil
 730 }
 731
 732 func (runner *ContainerRunner) startCrunchstat() error {
 733         w, err := runner.NewLogWriter("crunchstat")
 734         if err != nil {
 735                 return err
 736         }
 737         runner.statLogger = NewThrottledLogger(w)
 738         runner.statReporter = &crunchstat.Reporter{
 739                 CID:          runner.ContainerID,
 740                 Logger:       log.New(runner.statLogger, "", 0),
 741                 CgroupParent: runner.expectCgroupParent,
 742                 CgroupRoot:   runner.cgroupRoot,
 743                 PollPeriod:   runner.statInterval,
 744         }
 745         runner.statReporter.Start()
 746         return nil
 747 }
 748
 749 type infoCommand struct {
 750         label string
 751         cmd   []string
 752 }
 753
 754 // LogHostInfo logs info about the current host, for debugging and
 755 // accounting purposes. Although it's logged as "node-info", this is
 756 // about the environment where crunch-run is actually running, which
 757 // might differ from what's described in the node record (see
 758 // LogNodeRecord).
 759 func (runner *ContainerRunner) LogHostInfo() (err error) {
 760         w, err := runner.NewLogWriter("node-info")
 761         if err != nil {
 762                 return
 763         }
 764
 765         commands := []infoCommand{
 766                 {
 767                         label: "Host Information",
 768                         cmd:   []string{"uname", "-a"},
 769                 },
 770                 {
 771                         label: "CPU Information",
 772                         cmd:   []string{"cat", "/proc/cpuinfo"},
 773                 },
 774                 {
 775                         label: "Memory Information",
 776                         cmd:   []string{"cat", "/proc/meminfo"},
 777                 },
 778                 {
 779                         label: "Disk Space",
 780                         cmd:   []string{"df", "-m", "/", os.TempDir()},
 781                 },
 782                 {
 783                         label: "Disk INodes",
 784                         cmd:   []string{"df", "-i", "/", os.TempDir()},
 785                 },
 786         }
 787
 788         // Run commands with informational output to be logged.
 789         for _, command := range commands {
 790                 fmt.Fprintln(w, command.label)
 791                 cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
 792                 cmd.Stdout = w
 793                 cmd.Stderr = w
 794                 if err := cmd.Run(); err != nil {
 795                         err = fmt.Errorf("While running command %q: %v", command.cmd, err)
 796                         fmt.Fprintln(w, err)
 797                         return err
 798                 }
 799                 fmt.Fprintln(w, "")
 800         }
 801
 802         err = w.Close()
 803         if err != nil {
 804                 return fmt.Errorf("While closing node-info logs: %v", err)
 805         }
 806         return nil
 807 }
 808
 809 // LogContainerRecord gets and saves the raw JSON container record from the API server
 810 func (runner *ContainerRunner) LogContainerRecord() error {
 811         logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
 812         if !logged && err == nil {
 813                 err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
 814         }
 815         return err
 816 }
 817
 818 // LogNodeRecord logs arvados#node record corresponding to the current host.
 819 func (runner *ContainerRunner) LogNodeRecord() error {
 820         hostname := os.Getenv("SLURMD_NODENAME")
 821         if hostname == "" {
 822                 hostname, _ = os.Hostname()
 823         }
 824         _, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
 825                 // The "info" field has admin-only info when obtained
 826                 // with a privileged token, and should not be logged.
 827                 node, ok := resp.(map[string]interface{})
 828                 if ok {
 829                         delete(node, "info")
 830                 }
 831         })
 832         return err
 833 }
 834
 835 func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
 836         writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
 837         if err != nil {
 838                 return false, err
 839         }
 840         w := &ArvLogWriter{
 841                 ArvClient:     runner.ArvClient,
 842                 UUID:          runner.Container.UUID,
 843                 loggingStream: label,
 844                 writeCloser:   writer,
 845         }
 846
 847         reader, err := runner.ArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
 848         if err != nil {
 849                 return false, fmt.Errorf("error getting %s record: %v", label, err)
 850         }
 851         defer reader.Close()
 852
 853         dec := json.NewDecoder(reader)
 854         dec.UseNumber()
 855         var resp map[string]interface{}
 856         if err = dec.Decode(&resp); err != nil {
 857                 return false, fmt.Errorf("error decoding %s list response: %v", label, err)
 858         }
 859         items, ok := resp["items"].([]interface{})
 860         if !ok {
 861                 return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
 862         } else if len(items) < 1 {
 863                 return false, nil
 864         }
 865         if munge != nil {
 866                 munge(items[0])
 867         }
 868         // Re-encode it using indentation to improve readability
 869         enc := json.NewEncoder(w)
 870         enc.SetIndent("", "    ")
 871         if err = enc.Encode(items[0]); err != nil {
 872                 return false, fmt.Errorf("error logging %s record: %v", label, err)
 873         }
 874         err = w.Close()
 875         if err != nil {
 876                 return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
 877         }
 878         return true, nil
 879 }
 880
 881 // AttachStreams connects the docker container stdin, stdout and stderr logs
 882 // to the Arvados logger which logs to Keep and the API server logs table.
 883 func (runner *ContainerRunner) AttachStreams() (err error) {
 884
 885         runner.CrunchLog.Print("Attaching container streams")
 886
 887         // If stdin mount is provided, attach it to the docker container
 888         var stdinRdr arvados.File
 889         var stdinJson []byte
 890         if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
 891                 if stdinMnt.Kind == "collection" {
 892                         var stdinColl arvados.Collection
 893                         collId := stdinMnt.UUID
 894                         if collId == "" {
 895                                 collId = stdinMnt.PortableDataHash
 896                         }
 897                         err = runner.ArvClient.Get("collections", collId, nil, &stdinColl)
 898                         if err != nil {
 899                                 return fmt.Errorf("While getting stding collection: %v", err)
 900                         }
 901
 902                         stdinRdr, err = runner.Kc.ManifestFileReader(manifest.Manifest{Text: stdinColl.ManifestText}, stdinMnt.Path)
 903                         if os.IsNotExist(err) {
 904                                 return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
 905                         } else if err != nil {
 906                                 return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
 907                         }
 908                 } else if stdinMnt.Kind == "json" {
 909                         stdinJson, err = json.Marshal(stdinMnt.Content)
 910                         if err != nil {
 911                                 return fmt.Errorf("While encoding stdin json data: %v", err)
 912                         }
 913                 }
 914         }
 915
 916         stdinUsed := stdinRdr != nil || len(stdinJson) != 0
 917         response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
 918                 dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, Stdout: true, Stderr: true})
 919         if err != nil {
 920                 return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
 921         }
 922
 923         runner.loggingDone = make(chan bool)
 924
 925         if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
 926                 stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
 927                 if err != nil {
 928                         return err
 929                 }
 930                 runner.Stdout = stdoutFile
 931         } else if w, err := runner.NewLogWriter("stdout"); err != nil {
 932                 return err
 933         } else {
 934                 runner.Stdout = NewThrottledLogger(w)
 935         }
 936
 937         if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
 938                 stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
 939                 if err != nil {
 940                         return err
 941                 }
 942                 runner.Stderr = stderrFile
 943         } else if w, err := runner.NewLogWriter("stderr"); err != nil {
 944                 return err
 945         } else {
 946                 runner.Stderr = NewThrottledLogger(w)
 947         }
 948
 949         if stdinRdr != nil {
 950                 go func() {
 951                         _, err := io.Copy(response.Conn, stdinRdr)
 952                         if err != nil {
 953                                 runner.CrunchLog.Print("While writing stdin collection to docker container %q", err)
 954                                 runner.stop(nil)
 955                         }
 956                         stdinRdr.Close()
 957                         response.CloseWrite()
 958                 }()
 959         } else if len(stdinJson) != 0 {
 960                 go func() {
 961                         _, err := io.Copy(response.Conn, bytes.NewReader(stdinJson))
 962                         if err != nil {
 963                                 runner.CrunchLog.Print("While writing stdin json to docker container %q", err)
 964                                 runner.stop(nil)
 965                         }
 966                         response.CloseWrite()
 967                 }()
 968         }
 969
 970         go runner.ProcessDockerAttach(response.Reader)
 971
 972         return nil
 973 }
 974
 975 func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
 976         stdoutPath := mntPath[len(runner.Container.OutputPath):]
 977         index := strings.LastIndex(stdoutPath, "/")
 978         if index > 0 {
 979                 subdirs := stdoutPath[:index]
 980                 if subdirs != "" {
 981                         st, err := os.Stat(runner.HostOutputDir)
 982                         if err != nil {
 983                                 return nil, fmt.Errorf("While Stat on temp dir: %v", err)
 984                         }
 985                         stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
 986                         err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 987                         if err != nil {
 988                                 return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 989                         }
 990                 }
 991         }
 992         stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
 993         if err != nil {
 994                 return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
 995         }
 996
 997         return stdoutFile, nil
 998 }
 999
1000 // CreateContainer creates the docker container.
1001 func (runner *ContainerRunner) CreateContainer() error {
1002         runner.CrunchLog.Print("Creating Docker container")
1003
1004         runner.ContainerConfig.Cmd = runner.Container.Command
1005         if runner.Container.Cwd != "." {
1006                 runner.ContainerConfig.WorkingDir = runner.Container.Cwd
1007         }
1008
1009         for k, v := range runner.Container.Environment {
1010                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
1011         }
1012
1013         runner.ContainerConfig.Volumes = runner.Volumes
1014
1015         maxRAM := int64(runner.Container.RuntimeConstraints.RAM)
1016         if maxRAM < 4*1024*1024 {
1017                 // Docker daemon won't let you set a limit less than 4 MiB
1018                 maxRAM = 4 * 1024 * 1024
1019         }
1020         runner.HostConfig = dockercontainer.HostConfig{
1021                 Binds: runner.Binds,
1022                 LogConfig: dockercontainer.LogConfig{
1023                         Type: "none",
1024                 },
1025                 Resources: dockercontainer.Resources{
1026                         CgroupParent: runner.setCgroupParent,
1027                         NanoCPUs:     int64(runner.Container.RuntimeConstraints.VCPUs) * 1000000000,
1028                         Memory:       maxRAM, // RAM
1029                         MemorySwap:   maxRAM, // RAM+swap
1030                         KernelMemory: maxRAM, // kernel portion
1031                 },
1032         }
1033
1034         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
1035                 tok, err := runner.ContainerToken()
1036                 if err != nil {
1037                         return err
1038                 }
1039                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
1040                         "ARVADOS_API_TOKEN="+tok,
1041                         "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
1042                         "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
1043                 )
1044                 runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
1045         } else {
1046                 if runner.enableNetwork == "always" {
1047                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
1048                 } else {
1049                         runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
1050                 }
1051         }
1052
1053         _, stdinUsed := runner.Container.Mounts["stdin"]
1054         runner.ContainerConfig.OpenStdin = stdinUsed
1055         runner.ContainerConfig.StdinOnce = stdinUsed
1056         runner.ContainerConfig.AttachStdin = stdinUsed
1057         runner.ContainerConfig.AttachStdout = true
1058         runner.ContainerConfig.AttachStderr = true
1059
1060         createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
1061         if err != nil {
1062                 return fmt.Errorf("While creating container: %v", err)
1063         }
1064
1065         runner.ContainerID = createdBody.ID
1066
1067         return runner.AttachStreams()
1068 }
1069
1070 // StartContainer starts the docker container created by CreateContainer.
1071 func (runner *ContainerRunner) StartContainer() error {
1072         runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
1073         runner.cStateLock.Lock()
1074         defer runner.cStateLock.Unlock()
1075         if runner.cCancelled {
1076                 return ErrCancelled
1077         }
1078         err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
1079                 dockertypes.ContainerStartOptions{})
1080         if err != nil {
1081                 var advice string
1082                 if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
1083                         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])
1084                 }
1085                 return fmt.Errorf("could not start container: %v%s", err, advice)
1086         }
1087         return nil
1088 }
1089
1090 // checkContainerd checks if "containerd" is present in the process list.
1091 func (runner *ContainerRunner) CheckContainerd() error {
1092         if runner.checkContainerd == 0 {
1093                 return nil
1094         }
1095         p, _ := runner.ListProcesses()
1096         for _, i := range p {
1097                 e, _ := i.CmdlineSlice()
1098                 if len(e) > 0 {
1099                         if strings.Index(e[0], "containerd") > -1 {
1100                                 return nil
1101                         }
1102                 }
1103         }
1104
1105         // Not found
1106         runner.runBrokenNodeHook()
1107         runner.stop(nil)
1108         return fmt.Errorf("'containerd' not found in process list.")
1109 }
1110
1111 // WaitFinish waits for the container to terminate, capture the exit code, and
1112 // close the stdout/stderr logging.
1113 func (runner *ContainerRunner) WaitFinish() error {
1114         var runTimeExceeded <-chan time.Time
1115         runner.CrunchLog.Print("Waiting for container to finish")
1116
1117         waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning)
1118         arvMountExit := runner.ArvMountExit
1119         if timeout := runner.Container.SchedulingParameters.MaxRunTime; timeout > 0 {
1120                 runTimeExceeded = time.After(time.Duration(timeout) * time.Second)
1121         }
1122
1123         containerdGone := make(chan error)
1124         defer func() {
1125                 close(containerdGone)
1126         }()
1127         if runner.checkContainerd > 0 {
1128                 go func() {
1129                         ticker := time.NewTicker(time.Duration(runner.checkContainerd))
1130                         defer ticker.Stop()
1131                         for {
1132                                 select {
1133                                 case <-ticker.C:
1134                                         if ck := runner.CheckContainerd(); ck != nil {
1135                                                 containerdGone <- ck
1136                                                 return
1137                                         }
1138                                 case <-containerdGone:
1139                                         break
1140                                 }
1141                         }
1142                 }()
1143         }
1144
1145         for {
1146                 select {
1147                 case waitBody := <-waitOk:
1148                         runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode)
1149                         code := int(waitBody.StatusCode)
1150                         runner.ExitCode = &code
1151
1152                         // wait for stdout/stderr to complete
1153                         <-runner.loggingDone
1154                         return nil
1155
1156                 case err := <-waitErr:
1157                         return fmt.Errorf("container wait: %v", err)
1158
1159                 case <-arvMountExit:
1160                         runner.CrunchLog.Printf("arv-mount exited while container is still running.  Stopping container.")
1161                         runner.stop(nil)
1162                         // arvMountExit will always be ready now that
1163                         // it's closed, but that doesn't interest us.
1164                         arvMountExit = nil
1165
1166                 case <-runTimeExceeded:
1167                         runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
1168                         runner.stop(nil)
1169                         runTimeExceeded = nil
1170
1171                 case err := <-containerdGone:
1172                         return err
1173                 }
1174         }
1175 }
1176
1177 // CaptureOutput saves data from the container's output directory if
1178 // needed, and updates the container output accordingly.
1179 func (runner *ContainerRunner) CaptureOutput() error {
1180         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
1181                 // Output may have been set directly by the container, so
1182                 // refresh the container record to check.
1183                 err := runner.ArvClient.Get("containers", runner.Container.UUID,
1184                         nil, &runner.Container)
1185                 if err != nil {
1186                         return err
1187                 }
1188                 if runner.Container.Output != "" {
1189                         // Container output is already set.
1190                         runner.OutputPDH = &runner.Container.Output
1191                         return nil
1192                 }
1193         }
1194
1195         txt, err := (&copier{
1196                 client:        runner.client,
1197                 arvClient:     runner.ArvClient,
1198                 keepClient:    runner.Kc,
1199                 hostOutputDir: runner.HostOutputDir,
1200                 ctrOutputDir:  runner.Container.OutputPath,
1201                 binds:         runner.Binds,
1202                 mounts:        runner.Container.Mounts,
1203                 secretMounts:  runner.SecretMounts,
1204                 logger:        runner.CrunchLog,
1205         }).Copy()
1206         if err != nil {
1207                 return err
1208         }
1209         var resp arvados.Collection
1210         err = runner.ArvClient.Create("collections", arvadosclient.Dict{
1211                 "ensure_unique_name": true,
1212                 "collection": arvadosclient.Dict{
1213                         "is_trashed":    true,
1214                         "name":          "output for " + runner.Container.UUID,
1215                         "manifest_text": txt,
1216                 },
1217         }, &resp)
1218         if err != nil {
1219                 return fmt.Errorf("error creating output collection: %v", err)
1220         }
1221         runner.OutputPDH = &resp.PortableDataHash
1222         return nil
1223 }
1224
1225 func (runner *ContainerRunner) CleanupDirs() {
1226         if runner.ArvMount != nil {
1227                 var delay int64 = 8
1228                 umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
1229                 umount.Stdout = runner.CrunchLog
1230                 umount.Stderr = runner.CrunchLog
1231                 runner.CrunchLog.Printf("Running %v", umount.Args)
1232                 umnterr := umount.Start()
1233
1234                 if umnterr != nil {
1235                         runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
1236                 } else {
1237                         // If arv-mount --unmount gets stuck for any reason, we
1238                         // don't want to wait for it forever.  Do Wait() in a goroutine
1239                         // so it doesn't block crunch-run.
1240                         umountExit := make(chan error)
1241                         go func() {
1242                                 mnterr := umount.Wait()
1243                                 if mnterr != nil {
1244                                         runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
1245                                 }
1246                                 umountExit <- mnterr
1247                         }()
1248
1249                         for again := true; again; {
1250                                 again = false
1251                                 select {
1252                                 case <-umountExit:
1253                                         umount = nil
1254                                         again = true
1255                                 case <-runner.ArvMountExit:
1256                                         break
1257                                 case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
1258                                         runner.CrunchLog.Printf("Timed out waiting for unmount")
1259                                         if umount != nil {
1260                                                 umount.Process.Kill()
1261                                         }
1262                                         runner.ArvMount.Process.Kill()
1263                                 }
1264                         }
1265                 }
1266         }
1267
1268         if runner.ArvMountPoint != "" {
1269                 if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
1270                         runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
1271                 }
1272         }
1273
1274         if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
1275                 runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
1276         }
1277 }
1278
1279 // CommitLogs posts the collection containing the final container logs.
1280 func (runner *ContainerRunner) CommitLogs() error {
1281         func() {
1282                 // Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
1283                 runner.cStateLock.Lock()
1284                 defer runner.cStateLock.Unlock()
1285
1286                 runner.CrunchLog.Print(runner.finalState)
1287
1288                 if runner.arvMountLog != nil {
1289                         runner.arvMountLog.Close()
1290                 }
1291                 runner.CrunchLog.Close()
1292
1293                 // Closing CrunchLog above allows them to be committed to Keep at this
1294                 // point, but re-open crunch log with ArvClient in case there are any
1295                 // other further errors (such as failing to write the log to Keep!)
1296                 // while shutting down
1297                 runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
1298                         ArvClient:     runner.ArvClient,
1299                         UUID:          runner.Container.UUID,
1300                         loggingStream: "crunch-run",
1301                         writeCloser:   nil,
1302                 })
1303                 runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
1304         }()
1305
1306         if runner.LogsPDH != nil {
1307                 // If we have already assigned something to LogsPDH,
1308                 // we must be closing the re-opened log, which won't
1309                 // end up getting attached to the container record and
1310                 // therefore doesn't need to be saved as a collection
1311                 // -- it exists only to send logs to other channels.
1312                 return nil
1313         }
1314
1315         mt, err := runner.LogCollection.MarshalManifest(".")
1316         if err != nil {
1317                 return fmt.Errorf("While creating log manifest: %v", err)
1318         }
1319
1320         var response arvados.Collection
1321         err = runner.ArvClient.Create("collections",
1322                 arvadosclient.Dict{
1323                         "ensure_unique_name": true,
1324                         "collection": arvadosclient.Dict{
1325                                 "is_trashed":    true,
1326                                 "name":          "logs for " + runner.Container.UUID,
1327                                 "manifest_text": mt}},
1328                 &response)
1329         if err != nil {
1330                 return fmt.Errorf("While creating log collection: %v", err)
1331         }
1332         runner.LogsPDH = &response.PortableDataHash
1333         return nil
1334 }
1335
1336 // UpdateContainerRunning updates the container state to "Running"
1337 func (runner *ContainerRunner) UpdateContainerRunning() error {
1338         runner.cStateLock.Lock()
1339         defer runner.cStateLock.Unlock()
1340         if runner.cCancelled {
1341                 return ErrCancelled
1342         }
1343         return runner.ArvClient.Update("containers", runner.Container.UUID,
1344                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
1345 }
1346
1347 // ContainerToken returns the api_token the container (and any
1348 // arv-mount processes) are allowed to use.
1349 func (runner *ContainerRunner) ContainerToken() (string, error) {
1350         if runner.token != "" {
1351                 return runner.token, nil
1352         }
1353
1354         var auth arvados.APIClientAuthorization
1355         err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
1356         if err != nil {
1357                 return "", err
1358         }
1359         runner.token = auth.APIToken
1360         return runner.token, nil
1361 }
1362
1363 // UpdateContainerComplete updates the container record state on API
1364 // server to "Complete" or "Cancelled"
1365 func (runner *ContainerRunner) UpdateContainerFinal() error {
1366         update := arvadosclient.Dict{}
1367         update["state"] = runner.finalState
1368         if runner.LogsPDH != nil {
1369                 update["log"] = *runner.LogsPDH
1370         }
1371         if runner.finalState == "Complete" {
1372                 if runner.ExitCode != nil {
1373                         update["exit_code"] = *runner.ExitCode
1374                 }
1375                 if runner.OutputPDH != nil {
1376                         update["output"] = *runner.OutputPDH
1377                 }
1378         }
1379         return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
1380 }
1381
1382 // IsCancelled returns the value of Cancelled, with goroutine safety.
1383 func (runner *ContainerRunner) IsCancelled() bool {
1384         runner.cStateLock.Lock()
1385         defer runner.cStateLock.Unlock()
1386         return runner.cCancelled
1387 }
1388
1389 // NewArvLogWriter creates an ArvLogWriter
1390 func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) {
1391         writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
1392         if err != nil {
1393                 return nil, err
1394         }
1395         return &ArvLogWriter{
1396                 ArvClient:     runner.ArvClient,
1397                 UUID:          runner.Container.UUID,
1398                 loggingStream: name,
1399                 writeCloser:   writer,
1400         }, nil
1401 }
1402
1403 // Run the full container lifecycle.
1404 func (runner *ContainerRunner) Run() (err error) {
1405         runner.CrunchLog.Printf("crunch-run %s started", version)
1406         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
1407
1408         hostname, hosterr := os.Hostname()
1409         if hosterr != nil {
1410                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
1411         } else {
1412                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
1413         }
1414
1415         runner.finalState = "Queued"
1416
1417         defer func() {
1418                 runner.CleanupDirs()
1419
1420                 runner.CrunchLog.Printf("crunch-run finished")
1421                 runner.CrunchLog.Close()
1422         }()
1423
1424         defer func() {
1425                 // checkErr prints e (unless it's nil) and sets err to
1426                 // e (unless err is already non-nil). Thus, if err
1427                 // hasn't already been assigned when Run() returns,
1428                 // this cleanup func will cause Run() to return the
1429                 // first non-nil error that is passed to checkErr().
1430                 checkErr := func(e error) {
1431                         if e == nil {
1432                                 return
1433                         }
1434                         runner.CrunchLog.Print(e)
1435                         if err == nil {
1436                                 err = e
1437                         }
1438                         if runner.finalState == "Complete" {
1439                                 // There was an error in the finalization.
1440                                 runner.finalState = "Cancelled"
1441                         }
1442                 }
1443
1444                 // Log the error encountered in Run(), if any
1445                 checkErr(err)
1446
1447                 if runner.finalState == "Queued" {
1448                         runner.UpdateContainerFinal()
1449                         return
1450                 }
1451
1452                 if runner.IsCancelled() {
1453                         runner.finalState = "Cancelled"
1454                         // but don't return yet -- we still want to
1455                         // capture partial output and write logs
1456                 }
1457
1458                 checkErr(runner.CaptureOutput())
1459                 checkErr(runner.stopHoststat())
1460                 checkErr(runner.CommitLogs())
1461                 checkErr(runner.UpdateContainerFinal())
1462         }()
1463
1464         err = runner.fetchContainerRecord()
1465         if err != nil {
1466                 return
1467         }
1468         runner.setupSignals()
1469         err = runner.startHoststat()
1470         if err != nil {
1471                 return
1472         }
1473
1474         // Sanity check that containerd is running.
1475         err = runner.CheckContainerd()
1476         if err != nil {
1477                 return
1478         }
1479
1480         // check for and/or load image
1481         err = runner.LoadImage()
1482         if err != nil {
1483                 if !runner.checkBrokenNode(err) {
1484                         // Failed to load image but not due to a "broken node"
1485                         // condition, probably user error.
1486                         runner.finalState = "Cancelled"
1487                 }
1488                 err = fmt.Errorf("While loading container image: %v", err)
1489                 return
1490         }
1491
1492         // set up FUSE mount and binds
1493         err = runner.SetupMounts()
1494         if err != nil {
1495                 runner.finalState = "Cancelled"
1496                 err = fmt.Errorf("While setting up mounts: %v", err)
1497                 return
1498         }
1499
1500         err = runner.CreateContainer()
1501         if err != nil {
1502                 return
1503         }
1504         err = runner.LogHostInfo()
1505         if err != nil {
1506                 return
1507         }
1508         err = runner.LogNodeRecord()
1509         if err != nil {
1510                 return
1511         }
1512         err = runner.LogContainerRecord()
1513         if err != nil {
1514                 return
1515         }
1516
1517         if runner.IsCancelled() {
1518                 return
1519         }
1520
1521         err = runner.UpdateContainerRunning()
1522         if err != nil {
1523                 return
1524         }
1525         runner.finalState = "Cancelled"
1526
1527         err = runner.startCrunchstat()
1528         if err != nil {
1529                 return
1530         }
1531
1532         err = runner.StartContainer()
1533         if err != nil {
1534                 runner.checkBrokenNode(err)
1535                 return
1536         }
1537
1538         err = runner.WaitFinish()
1539         if err == nil && !runner.IsCancelled() {
1540                 runner.finalState = "Complete"
1541         }
1542         return
1543 }
1544
1545 // Fetch the current container record (uuid = runner.Container.UUID)
1546 // into runner.Container.
1547 func (runner *ContainerRunner) fetchContainerRecord() error {
1548         reader, err := runner.ArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
1549         if err != nil {
1550                 return fmt.Errorf("error fetching container record: %v", err)
1551         }
1552         defer reader.Close()
1553
1554         dec := json.NewDecoder(reader)
1555         dec.UseNumber()
1556         err = dec.Decode(&runner.Container)
1557         if err != nil {
1558                 return fmt.Errorf("error decoding container record: %v", err)
1559         }
1560
1561         var sm struct {
1562                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
1563         }
1564
1565         containerToken, err := runner.ContainerToken()
1566         if err != nil {
1567                 return fmt.Errorf("error getting container token: %v", err)
1568         }
1569
1570         containerClient, err := runner.MkArvClient(containerToken)
1571         if err != nil {
1572                 return fmt.Errorf("error creating container API client: %v", err)
1573         }
1574
1575         err = containerClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
1576         if err != nil {
1577                 if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
1578                         return fmt.Errorf("error fetching secret_mounts: %v", err)
1579                 }
1580                 // ok && apierr.HttpStatusCode == 404, which means
1581                 // secret_mounts isn't supported by this API server.
1582         }
1583         runner.SecretMounts = sm.SecretMounts
1584
1585         return nil
1586 }
1587
1588 // NewContainerRunner creates a new container runner.
1589 func NewContainerRunner(client *arvados.Client, api IArvadosClient, kc IKeepClient, docker ThinDockerClient, containerUUID string) (*ContainerRunner, error) {
1590         cr := &ContainerRunner{
1591                 client:    client,
1592                 ArvClient: api,
1593                 Kc:        kc,
1594                 Docker:    docker,
1595         }
1596         cr.NewLogWriter = cr.NewArvLogWriter
1597         cr.RunArvMount = cr.ArvMountCmd
1598         cr.MkTempDir = ioutil.TempDir
1599         cr.ListProcesses = func() ([]PsProcess, error) {
1600                 pr, err := process.Processes()
1601                 if err != nil {
1602                         return nil, err
1603                 }
1604                 ps := make([]PsProcess, len(pr))
1605                 for i, j := range pr {
1606                         ps[i] = j
1607                 }
1608                 return ps, nil
1609         }
1610         cr.MkArvClient = func(token string) (IArvadosClient, error) {
1611                 cl, err := arvadosclient.MakeArvadosClient()
1612                 if err != nil {
1613                         return nil, err
1614                 }
1615                 cl.ApiToken = token
1616                 return cl, nil
1617         }
1618         var err error
1619         cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.client, cr.Kc)
1620         if err != nil {
1621                 return nil, err
1622         }
1623         cr.Container.UUID = containerUUID
1624         w, err := cr.NewLogWriter("crunch-run")
1625         if err != nil {
1626                 return nil, err
1627         }
1628         cr.CrunchLog = NewThrottledLogger(w)
1629         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
1630
1631         loadLogThrottleParams(api)
1632
1633         return cr, nil
1634 }
1635
1636 func main() {
1637         statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
1638         cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
1639         cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
1640         cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
1641         caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
1642         enableNetwork := flag.String("container-enable-networking", "default",
1643                 `Specify if networking should be enabled for container.  One of 'default', 'always':
1644         default: only enable networking if container requests it.
1645         always:  containers always have networking enabled
1646         `)
1647         networkMode := flag.String("container-network-mode", "default",
1648                 `Set networking mode for container.  Corresponds to Docker network mode (--net).
1649         `)
1650         memprofile := flag.String("memprofile", "", "write memory profile to `file` after running container")
1651         getVersion := flag.Bool("version", false, "Print version information and exit.")
1652         checkContainerd := flag.Duration("check-containerd", 60*time.Second, "Periodic check if (docker-)containerd is running, period in seconds.")
1653         flag.Parse()
1654
1655         // Print version information if requested
1656         if *getVersion {
1657                 fmt.Printf("crunch-run %s\n", version)
1658                 return
1659         }
1660
1661         log.Printf("crunch-run %s started", version)
1662
1663         containerId := flag.Arg(0)
1664
1665         if *caCertsPath != "" {
1666                 arvadosclient.CertFiles = []string{*caCertsPath}
1667         }
1668
1669         api, err := arvadosclient.MakeArvadosClient()
1670         if err != nil {
1671                 log.Fatalf("%s: %v", containerId, err)
1672         }
1673         api.Retries = 8
1674
1675         kc, kcerr := keepclient.MakeKeepClient(api)
1676         if kcerr != nil {
1677                 log.Fatalf("%s: %v", containerId, kcerr)
1678         }
1679         kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
1680         kc.Retries = 4
1681
1682         // API version 1.21 corresponds to Docker 1.9, which is currently the
1683         // minimum version we want to support.
1684         docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
1685
1686         cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, docker, containerId)
1687         if err != nil {
1688                 log.Fatal(err)
1689         }
1690         if dockererr != nil {
1691                 cr.CrunchLog.Printf("%s: %v", containerId, dockererr)
1692                 cr.checkBrokenNode(dockererr)
1693                 cr.CrunchLog.Close()
1694                 os.Exit(1)
1695         }
1696
1697         parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerId+".")
1698         if tmperr != nil {
1699                 log.Fatalf("%s: %v", containerId, tmperr)
1700         }
1701
1702         cr.parentTemp = parentTemp
1703         cr.statInterval = *statInterval
1704         cr.cgroupRoot = *cgroupRoot
1705         cr.expectCgroupParent = *cgroupParent
1706         cr.enableNetwork = *enableNetwork
1707         cr.networkMode = *networkMode
1708         cr.checkContainerd = *checkContainerd
1709         if *cgroupParentSubsystem != "" {
1710                 p := findCgroup(*cgroupParentSubsystem)
1711                 cr.setCgroupParent = p
1712                 cr.expectCgroupParent = p
1713         }
1714
1715         runerr := cr.Run()
1716
1717         if *memprofile != "" {
1718                 f, err := os.Create(*memprofile)
1719                 if err != nil {
1720                         log.Printf("could not create memory profile: %s", err)
1721                 }
1722                 runtime.GC() // get up-to-date statistics
1723                 if err := pprof.WriteHeapProfile(f); err != nil {
1724                         log.Printf("could not write memory profile: %s", err)
1725                 }
1726                 closeerr := f.Close()
1727                 if closeerr != nil {
1728                         log.Printf("closing memprofile file: %s", err)
1729                 }
1730         }
1731
1732         if runerr != nil {
1733                 log.Fatalf("%s: %v", containerId, runerr)
1734         }
1735 }