lib/crunchrun/singularity.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package crunchrun
   6
   7 import (
   8         "fmt"
   9         "io/ioutil"
  10         "os"
  11         "os/exec"
  12         "sort"
  13         "syscall"
  14         "time"
  15
  16         "git.arvados.org/arvados.git/sdk/go/arvados"
  17         "golang.org/x/net/context"
  18 )
  19
  20 type singularityExecutor struct {
  21         logf          func(string, ...interface{})
  22         spec          containerSpec
  23         tmpdir        string
  24         child         *exec.Cmd
  25         imageFilename string // "sif" image
  26 }
  27
  28 func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
  29         tmpdir, err := ioutil.TempDir("", "crunch-run-singularity-")
  30         if err != nil {
  31                 return nil, err
  32         }
  33         return &singularityExecutor{
  34                 logf:   logf,
  35                 tmpdir: tmpdir,
  36         }, nil
  37 }
  38
  39 func (e *singularityExecutor) Runtime() string { return "singularity" }
  40
  41 func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string, containerClient *arvados.Client) (*arvados.Group, error) {
  42         var gp arvados.GroupList
  43         err := containerClient.RequestAndDecode(&gp,
  44                 arvados.EndpointGroupList.Method,
  45                 arvados.EndpointGroupList.Path,
  46                 nil, arvados.ListOptions{Filters: []arvados.Filter{
  47                         arvados.Filter{"owner_uuid", "=", ownerUuid},
  48                         arvados.Filter{"name", "=", name},
  49                         arvados.Filter{"group_class", "=", "project"},
  50                 },
  51                         Limit: 1})
  52         if err != nil {
  53                 return nil, err
  54         }
  55         if len(gp.Items) == 1 {
  56                 return &gp.Items[0], nil
  57         }
  58
  59         var rgroup arvados.Group
  60         err = containerClient.RequestAndDecode(&rgroup,
  61                 arvados.EndpointGroupCreate.Method,
  62                 arvados.EndpointGroupCreate.Path,
  63                 nil, map[string]interface{}{
  64                         "group": map[string]string{
  65                                 "owner_uuid":  ownerUuid,
  66                                 "name":        name,
  67                                 "group_class": "project",
  68                         },
  69                 })
  70         if err != nil {
  71                 return nil, err
  72         }
  73         return &rgroup, nil
  74 }
  75
  76 func (e *singularityExecutor) checkImageCache(dockerImageID string, container arvados.Container, arvMountPoint string,
  77         containerClient *arvados.Client) (collection *arvados.Collection, err error) {
  78
  79         // Cache the image to keep
  80         cacheGroup, err := e.getOrCreateProject(container.RuntimeUserUUID, ".cache", containerClient)
  81         if err != nil {
  82                 return nil, fmt.Errorf("error getting '.cache' project: %v", err)
  83         }
  84         imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", containerClient)
  85         if err != nil {
  86                 return nil, fmt.Errorf("error getting 'auto-generated singularity images' project: %s", err)
  87         }
  88
  89         collectionName := fmt.Sprintf("singularity image for %v", dockerImageID)
  90         var cl arvados.CollectionList
  91         err = containerClient.RequestAndDecode(&cl,
  92                 arvados.EndpointCollectionList.Method,
  93                 arvados.EndpointCollectionList.Path,
  94                 nil, arvados.ListOptions{Filters: []arvados.Filter{
  95                         arvados.Filter{"owner_uuid", "=", imageGroup.UUID},
  96                         arvados.Filter{"name", "=", collectionName},
  97                 },
  98                         Limit: 1})
  99         if err != nil {
 100                 return nil, fmt.Errorf("error querying for collection '%v': %v", collectionName, err)
 101         }
 102         var imageCollection arvados.Collection
 103         if len(cl.Items) == 1 {
 104                 imageCollection = cl.Items[0]
 105         } else {
 106                 collectionName := "converting " + collectionName
 107                 exp := time.Now().Add(24 * 7 * 2 * time.Hour)
 108                 err = containerClient.RequestAndDecode(&imageCollection,
 109                         arvados.EndpointCollectionCreate.Method,
 110                         arvados.EndpointCollectionCreate.Path,
 111                         nil, map[string]interface{}{
 112                                 "collection": map[string]string{
 113                                         "owner_uuid": imageGroup.UUID,
 114                                         "name":       collectionName,
 115                                         "trash_at":   exp.UTC().Format(time.RFC3339),
 116                                 },
 117                                 "ensure_unique_name": true,
 118                         })
 119                 if err != nil {
 120                         return nil, fmt.Errorf("error creating '%v' collection: %s", collectionName, err)
 121                 }
 122
 123         }
 124
 125         return &imageCollection, nil
 126 }
 127
 128 // LoadImage will satisfy ContainerExecuter interface transforming
 129 // containerImage into a sif file for later use.
 130 func (e *singularityExecutor) LoadImage(dockerImageID string, imageTarballPath string, container arvados.Container, arvMountPoint string,
 131         containerClient *arvados.Client) error {
 132
 133         var imageFilename string
 134         var sifCollection *arvados.Collection
 135         var err error
 136         if containerClient != nil {
 137                 sifCollection, err = e.checkImageCache(dockerImageID, container, arvMountPoint, containerClient)
 138                 if err != nil {
 139                         return err
 140                 }
 141                 imageFilename = fmt.Sprintf("%s/by_uuid/%s/image.sif", arvMountPoint, sifCollection.UUID)
 142         } else {
 143                 imageFilename = e.tmpdir + "/image.sif"
 144         }
 145
 146         if _, err := os.Stat(imageFilename); os.IsNotExist(err) {
 147                 // Make sure the docker image is readable, and error
 148                 // out if not.
 149                 if _, err := os.Stat(imageTarballPath); err != nil {
 150                         return err
 151                 }
 152
 153                 e.logf("building singularity image")
 154                 // "singularity build" does not accept a
 155                 // docker-archive://... filename containing a ":" character,
 156                 // as in "/path/to/sha256:abcd...1234.tar". Workaround: make a
 157                 // symlink that doesn't have ":" chars.
 158                 err := os.Symlink(imageTarballPath, e.tmpdir+"/image.tar")
 159                 if err != nil {
 160                         return err
 161                 }
 162
 163                 // Set up a cache and tmp dir for singularity build
 164                 err = os.Mkdir(e.tmpdir+"/cache", 0700)
 165                 if err != nil {
 166                         return err
 167                 }
 168                 defer os.RemoveAll(e.tmpdir + "/cache")
 169                 err = os.Mkdir(e.tmpdir+"/tmp", 0700)
 170                 if err != nil {
 171                         return err
 172                 }
 173                 defer os.RemoveAll(e.tmpdir + "/tmp")
 174
 175                 build := exec.Command("singularity", "build", imageFilename, "docker-archive://"+e.tmpdir+"/image.tar")
 176                 build.Env = os.Environ()
 177                 build.Env = append(build.Env, "SINGULARITY_CACHEDIR="+e.tmpdir+"/cache")
 178                 build.Env = append(build.Env, "SINGULARITY_TMPDIR="+e.tmpdir+"/tmp")
 179                 e.logf("%v", build.Args)
 180                 out, err := build.CombinedOutput()
 181                 // INFO:    Starting build...
 182                 // Getting image source signatures
 183                 // Copying blob ab15617702de done
 184                 // Copying config 651e02b8a2 done
 185                 // Writing manifest to image destination
 186                 // Storing signatures
 187                 // 2021/04/22 14:42:14  info unpack layer: sha256:21cbfd3a344c52b197b9fa36091e66d9cbe52232703ff78d44734f85abb7ccd3
 188                 // INFO:    Creating SIF file...
 189                 // INFO:    Build complete: arvados-jobs.latest.sif
 190                 e.logf("%s", out)
 191                 if err != nil {
 192                         return err
 193                 }
 194         }
 195
 196         if containerClient == nil {
 197                 e.imageFilename = imageFilename
 198                 return nil
 199         }
 200
 201         // update TTL to now + two weeks
 202         exp := time.Now().Add(24 * 7 * 2 * time.Hour)
 203
 204         uuidPath, err := containerClient.PathForUUID("update", sifCollection.UUID)
 205         if err != nil {
 206                 e.logf("error PathForUUID: %v", err)
 207                 return nil
 208         }
 209         var imageCollection arvados.Collection
 210         err = containerClient.RequestAndDecode(&imageCollection,
 211                 arvados.EndpointCollectionUpdate.Method,
 212                 uuidPath,
 213                 nil, map[string]interface{}{
 214                         "collection": map[string]string{
 215                                 "name":     fmt.Sprintf("singularity image for %v", dockerImageID),
 216                                 "trash_at": exp.UTC().Format(time.RFC3339),
 217                         },
 218                 })
 219         if err == nil {
 220                 // If we just wrote the image to the cache, the
 221                 // response also returns the updated PDH
 222                 e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, imageCollection.PortableDataHash)
 223                 return nil
 224         }
 225
 226         e.logf("error updating/renaming collection for cached sif image: %v", err)
 227         // Failed to update but maybe it lost a race and there is
 228         // another cached collection in the same place, so check the cache
 229         // again
 230         sifCollection, err = e.checkImageCache(dockerImageID, container, arvMountPoint, containerClient)
 231         if err != nil {
 232                 return err
 233         }
 234         e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, sifCollection.PortableDataHash)
 235
 236         return nil
 237 }
 238
 239 func (e *singularityExecutor) Create(spec containerSpec) error {
 240         e.spec = spec
 241         return nil
 242 }
 243
 244 func (e *singularityExecutor) Start() error {
 245         args := []string{"singularity", "exec", "--containall", "--cleanenv", "--pwd", e.spec.WorkingDir}
 246         if !e.spec.EnableNetwork {
 247                 args = append(args, "--net", "--network=none")
 248         }
 249         readonlyflag := map[bool]string{
 250                 false: "rw",
 251                 true:  "ro",
 252         }
 253         var binds []string
 254         for path, _ := range e.spec.BindMounts {
 255                 binds = append(binds, path)
 256         }
 257         sort.Strings(binds)
 258         for _, path := range binds {
 259                 mount := e.spec.BindMounts[path]
 260                 if path == e.spec.Env["HOME"] {
 261                         // Singularity treates $HOME as special case
 262                         args = append(args, "--home", mount.HostPath+":"+path)
 263                 } else {
 264                         args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly])
 265                 }
 266         }
 267
 268         // This is for singularity 3.5.2. There are some behaviors
 269         // that will change in singularity 3.6, please see:
 270         // https://sylabs.io/guides/3.7/user-guide/environment_and_metadata.html
 271         // https://sylabs.io/guides/3.5/user-guide/environment_and_metadata.html
 272         env := make([]string, 0, len(e.spec.Env))
 273         for k, v := range e.spec.Env {
 274                 if k == "HOME" {
 275                         // Singularity treates $HOME as special case, this is handled
 276                         // with --home above
 277                         continue
 278                 }
 279                 env = append(env, "SINGULARITYENV_"+k+"="+v)
 280         }
 281
 282         args = append(args, e.imageFilename)
 283         args = append(args, e.spec.Command...)
 284
 285         path, err := exec.LookPath(args[0])
 286         if err != nil {
 287                 return err
 288         }
 289         child := &exec.Cmd{
 290                 Path:   path,
 291                 Args:   args,
 292                 Env:    env,
 293                 Stdin:  e.spec.Stdin,
 294                 Stdout: e.spec.Stdout,
 295                 Stderr: e.spec.Stderr,
 296         }
 297         err = child.Start()
 298         if err != nil {
 299                 return err
 300         }
 301         e.child = child
 302         return nil
 303 }
 304
 305 func (e *singularityExecutor) CgroupID() string {
 306         return ""
 307 }
 308
 309 func (e *singularityExecutor) Stop() error {
 310         if err := e.child.Process.Signal(syscall.Signal(0)); err != nil {
 311                 // process already exited
 312                 return nil
 313         }
 314         return e.child.Process.Signal(syscall.SIGKILL)
 315 }
 316
 317 func (e *singularityExecutor) Wait(context.Context) (int, error) {
 318         err := e.child.Wait()
 319         if err, ok := err.(*exec.ExitError); ok {
 320                 return err.ProcessState.ExitCode(), nil
 321         }
 322         if err != nil {
 323                 return 0, err
 324         }
 325         return e.child.ProcessState.ExitCode(), nil
 326 }
 327
 328 func (e *singularityExecutor) Close() {
 329         err := os.RemoveAll(e.tmpdir)
 330         if err != nil {
 331                 e.logf("error removing temp dir: %s", err)
 332         }
 333 }