1 // Copyright (C) The Arvados Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
16 "git.arvados.org/arvados.git/sdk/go/arvados"
17 "golang.org/x/net/context"
20 type singularityExecutor struct {
21 logf func(string, ...interface{})
25 imageFilename string // "sif" image
28 func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
29 tmpdir, err := ioutil.TempDir("", "crunch-run-singularity-")
33 return &singularityExecutor{
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"},
53 if len(gp.Items) == 1 {
54 return &gp.Items[0], nil
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,
65 "group_class": "project",
74 func (e *singularityExecutor) checkImageCache(dockerImageID string, container arvados.Container, arvMountPoint string,
75 containerClient *arvados.Client, keepClient IKeepClient) (collectionUuid string, err error) {
77 // Cache the image to keep
78 cacheGroup, err := e.getOrCreateProject(container.RuntimeUserUUID, ".cache", containerClient)
80 return "", fmt.Errorf("error getting '.cache' project: %v", err)
82 imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", containerClient)
84 return "", fmt.Errorf("error getting 'auto-generated singularity images' project: %s", err)
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},
98 return "", fmt.Errorf("error querying for collection '%v': %v", err)
100 var imageCollection arvados.Collection
101 if len(cl.Items) == 1 {
102 imageCollection = cl.Items[0]
104 collectionName := collectionName + " " + time.Now().UTC().Format(time.RFC3339)
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,
116 e.logf("error creating '%v' collection: %s", collectionName, err)
121 return imageCollection.UUID, nil
124 // LoadImage will satisfy ContainerExecuter interface transforming
125 // containerImage into a sif file for later use.
126 func (e *singularityExecutor) LoadImage(dockerImageID string, container arvados.Container, arvMountPoint string,
127 containerClient *arvados.Client, keepClient IKeepClient) error {
129 sifCollectionUUID, err := e.checkImageCache(dockerImageID, container, arvMountPoint, containerClient, keepClient)
134 imageTarballPath := arvMountPoint + "/by_id/" + container.ContainerImage + "/" + dockerImageID + ".tar"
136 imageFilename := fmt.Sprintf("%s/by_uuid/%s/image.sif", arvMountPoint, sifCollectionUUID)
138 if _, err = os.Stat(imageFilename); os.IsNotExist(err) {
139 exec.Command("find", arvMountPoint+"/by_id/").Run()
141 e.logf("building singularity image")
142 // "singularity build" does not accept a
143 // docker-archive://... filename containing a ":" character,
144 // as in "/path/to/sha256:abcd...1234.tar". Workaround: make a
145 // symlink that doesn't have ":" chars.
146 err := os.Symlink(imageTarballPath, e.tmpdir+"/image.tar")
151 build := exec.Command("singularity", "build", imageFilename, "docker-archive://"+e.tmpdir+"/image.tar")
152 e.logf("%v", build.Args)
153 out, err := build.CombinedOutput()
154 // INFO: Starting build...
155 // Getting image source signatures
156 // Copying blob ab15617702de done
157 // Copying config 651e02b8a2 done
158 // Writing manifest to image destination
159 // Storing signatures
160 // 2021/04/22 14:42:14 info unpack layer: sha256:21cbfd3a344c52b197b9fa36091e66d9cbe52232703ff78d44734f85abb7ccd3
161 // INFO: Creating SIF file...
162 // INFO: Build complete: arvados-jobs.latest.sif
169 // update TTL to now + two weeks
170 exp := time.Now().Add(24 * 7 * 2 * time.Hour)
172 uuidPath, err := containerClient.PathForUUID("update", sifCollectionUUID)
174 e.logf("error PathForUUID: %v", err)
177 var imageCollection arvados.Collection
178 err = containerClient.RequestAndDecode(&imageCollection,
179 arvados.EndpointCollectionUpdate.Method,
181 nil, map[string]interface{}{
182 "collection": map[string]string{
183 "name": fmt.Sprintf("singularity image for %v", dockerImageID),
184 "trash_at": exp.UTC().Format(time.RFC3339),
188 e.logf("error updating collection trash_at: %v", err)
190 e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, imageCollection.PortableDataHash)
195 func (e *singularityExecutor) Create(spec containerSpec) error {
200 func (e *singularityExecutor) Start() error {
201 args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv", "--pwd", e.spec.WorkingDir}
202 if !e.spec.EnableNetwork {
203 args = append(args, "--net", "--network=none")
205 readonlyflag := map[bool]string{
210 for path, _ := range e.spec.BindMounts {
211 binds = append(binds, path)
214 for _, path := range binds {
215 mount := e.spec.BindMounts[path]
216 args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly])
219 // This is for singularity 3.5.2. There are some behaviors
220 // that will change in singularity 3.6, please see:
221 // https://sylabs.io/guides/3.7/user-guide/environment_and_metadata.html
222 // https://sylabs.io/guides/3.5/user-guide/environment_and_metadata.html
223 env := make([]string, 0, len(e.spec.Env))
224 for k, v := range e.spec.Env {
226 // $HOME is a special case
227 args = append(args, "--home="+v)
229 env = append(env, "SINGULARITYENV_"+k+"="+v)
233 args = append(args, e.imageFilename)
234 args = append(args, e.spec.Command...)
236 path, err := exec.LookPath(args[0])
245 Stdout: e.spec.Stdout,
246 Stderr: e.spec.Stderr,
256 func (e *singularityExecutor) CgroupID() string {
260 func (e *singularityExecutor) Stop() error {
261 if err := e.child.Process.Signal(syscall.Signal(0)); err != nil {
262 // process already exited
265 return e.child.Process.Signal(syscall.SIGKILL)
268 func (e *singularityExecutor) Wait(context.Context) (int, error) {
269 err := e.child.Wait()
270 if err, ok := err.(*exec.ExitError); ok {
271 return err.ProcessState.ExitCode(), nil
276 return e.child.ProcessState.ExitCode(), nil
279 func (e *singularityExecutor) Close() {
280 err := os.RemoveAll(e.tmpdir)
282 e.logf("error removing temp dir: %s", err)