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