// Copyright (C) The Arvados Authors. All rights reserved. // // SPDX-License-Identifier: AGPL-3.0 package crunchrun import ( "fmt" "io/ioutil" "os" "os/exec" "sort" "syscall" "time" "git.arvados.org/arvados.git/sdk/go/arvados" "golang.org/x/net/context" ) type singularityExecutor struct { logf func(string, ...interface{}) spec containerSpec tmpdir string child *exec.Cmd imageFilename string // "sif" image } func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) { tmpdir, err := ioutil.TempDir("", "crunch-run-singularity-") if err != nil { return nil, err } return &singularityExecutor{ logf: logf, tmpdir: tmpdir, }, nil } func (e *singularityExecutor) Runtime() string { return "singularity" } func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string, containerClient *arvados.Client) (*arvados.Group, error) { var gp arvados.GroupList err := containerClient.RequestAndDecode(&gp, arvados.EndpointGroupList.Method, arvados.EndpointGroupList.Path, nil, arvados.ListOptions{Filters: []arvados.Filter{ arvados.Filter{"owner_uuid", "=", ownerUuid}, arvados.Filter{"name", "=", name}, arvados.Filter{"group_class", "=", "project"}, }, Limit: 1}) if err != nil { return nil, err } if len(gp.Items) == 1 { return &gp.Items[0], nil } var rgroup arvados.Group err = containerClient.RequestAndDecode(&rgroup, arvados.EndpointGroupCreate.Method, arvados.EndpointGroupCreate.Path, nil, map[string]interface{}{ "group": map[string]string{ "owner_uuid": ownerUuid, "name": name, "group_class": "project", }, }) if err != nil { return nil, err } return &rgroup, nil } func (e *singularityExecutor) checkImageCache(dockerImageID string, container arvados.Container, arvMountPoint string, containerClient *arvados.Client) (collection *arvados.Collection, err error) { // Cache the image to keep cacheGroup, err := e.getOrCreateProject(container.RuntimeUserUUID, ".cache", containerClient) if err != nil { return nil, fmt.Errorf("error getting '.cache' project: %v", err) } imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", containerClient) if err != nil { return nil, fmt.Errorf("error getting 'auto-generated singularity images' project: %s", err) } collectionName := fmt.Sprintf("singularity image for %v", dockerImageID) var cl arvados.CollectionList err = containerClient.RequestAndDecode(&cl, arvados.EndpointCollectionList.Method, arvados.EndpointCollectionList.Path, nil, arvados.ListOptions{Filters: []arvados.Filter{ arvados.Filter{"owner_uuid", "=", imageGroup.UUID}, arvados.Filter{"name", "=", collectionName}, }, Limit: 1}) if err != nil { return nil, fmt.Errorf("error querying for collection '%v': %v", collectionName, err) } var imageCollection arvados.Collection if len(cl.Items) == 1 { imageCollection = cl.Items[0] } else { collectionName := "converting " + collectionName exp := time.Now().Add(24 * 7 * 2 * time.Hour) err = containerClient.RequestAndDecode(&imageCollection, arvados.EndpointCollectionCreate.Method, arvados.EndpointCollectionCreate.Path, nil, map[string]interface{}{ "collection": map[string]string{ "owner_uuid": imageGroup.UUID, "name": collectionName, "trash_at": exp.UTC().Format(time.RFC3339), }, "ensure_unique_name": true, }) if err != nil { return nil, fmt.Errorf("error creating '%v' collection: %s", collectionName, err) } } return &imageCollection, nil } // LoadImage will satisfy ContainerExecuter interface transforming // containerImage into a sif file for later use. func (e *singularityExecutor) LoadImage(dockerImageID string, imageTarballPath string, container arvados.Container, arvMountPoint string, containerClient *arvados.Client) error { var imageFilename string var sifCollection *arvados.Collection var err error if containerClient != nil { sifCollection, err = e.checkImageCache(dockerImageID, container, arvMountPoint, containerClient) if err != nil { return err } imageFilename = fmt.Sprintf("%s/by_uuid/%s/image.sif", arvMountPoint, sifCollection.UUID) } else { imageFilename = e.tmpdir + "/image.sif" } if _, err := os.Stat(imageFilename); os.IsNotExist(err) { // Make sure the docker image is readable, and error // out if not. if _, err := os.Stat(imageTarballPath); err != nil { return err } e.logf("building singularity image") // "singularity build" does not accept a // docker-archive://... filename containing a ":" character, // as in "/path/to/sha256:abcd...1234.tar". Workaround: make a // symlink that doesn't have ":" chars. err := os.Symlink(imageTarballPath, e.tmpdir+"/image.tar") if err != nil { return err } build := exec.Command("singularity", "build", imageFilename, "docker-archive://"+e.tmpdir+"/image.tar") e.logf("%v", build.Args) out, err := build.CombinedOutput() // INFO: Starting build... // Getting image source signatures // Copying blob ab15617702de done // Copying config 651e02b8a2 done // Writing manifest to image destination // Storing signatures // 2021/04/22 14:42:14 info unpack layer: sha256:21cbfd3a344c52b197b9fa36091e66d9cbe52232703ff78d44734f85abb7ccd3 // INFO: Creating SIF file... // INFO: Build complete: arvados-jobs.latest.sif e.logf("%s", out) if err != nil { return err } } if containerClient == nil { e.imageFilename = imageFilename return nil } // update TTL to now + two weeks exp := time.Now().Add(24 * 7 * 2 * time.Hour) uuidPath, err := containerClient.PathForUUID("update", sifCollection.UUID) if err != nil { e.logf("error PathForUUID: %v", err) return nil } var imageCollection arvados.Collection err = containerClient.RequestAndDecode(&imageCollection, arvados.EndpointCollectionUpdate.Method, uuidPath, nil, map[string]interface{}{ "collection": map[string]string{ "name": fmt.Sprintf("singularity image for %v", dockerImageID), "trash_at": exp.UTC().Format(time.RFC3339), }, }) if err == nil { // If we just wrote the image to the cache, the // response also returns the updated PDH e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, imageCollection.PortableDataHash) return nil } e.logf("error updating/renaming collection for cached sif image: %v", err) // Failed to update but maybe it lost a race and there is // another cached collection in the same place, so check the cache // again sifCollection, err = e.checkImageCache(dockerImageID, container, arvMountPoint, containerClient) if err != nil { return err } e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, sifCollection.PortableDataHash) return nil } func (e *singularityExecutor) Create(spec containerSpec) error { e.spec = spec return nil } func (e *singularityExecutor) Start() error { args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv", "--pwd", e.spec.WorkingDir} if !e.spec.EnableNetwork { args = append(args, "--net", "--network=none") } readonlyflag := map[bool]string{ false: "rw", true: "ro", } var binds []string for path, _ := range e.spec.BindMounts { binds = append(binds, path) } sort.Strings(binds) for _, path := range binds { mount := e.spec.BindMounts[path] args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly]) } // This is for singularity 3.5.2. There are some behaviors // that will change in singularity 3.6, please see: // https://sylabs.io/guides/3.7/user-guide/environment_and_metadata.html // https://sylabs.io/guides/3.5/user-guide/environment_and_metadata.html env := make([]string, 0, len(e.spec.Env)) for k, v := range e.spec.Env { if k == "HOME" { // $HOME is a special case args = append(args, "--home="+v) } else { env = append(env, "SINGULARITYENV_"+k+"="+v) } } args = append(args, e.imageFilename) args = append(args, e.spec.Command...) path, err := exec.LookPath(args[0]) if err != nil { return err } child := &exec.Cmd{ Path: path, Args: args, Env: env, Stdin: e.spec.Stdin, Stdout: e.spec.Stdout, Stderr: e.spec.Stderr, } err = child.Start() if err != nil { return err } e.child = child return nil } func (e *singularityExecutor) CgroupID() string { return "" } func (e *singularityExecutor) Stop() error { if err := e.child.Process.Signal(syscall.Signal(0)); err != nil { // process already exited return nil } return e.child.Process.Signal(syscall.SIGKILL) } func (e *singularityExecutor) Wait(context.Context) (int, error) { err := e.child.Wait() if err, ok := err.(*exec.ExitError); ok { return err.ProcessState.ExitCode(), nil } if err != nil { return 0, err } return e.child.ProcessState.ExitCode(), nil } func (e *singularityExecutor) Close() { err := os.RemoveAll(e.tmpdir) if err != nil { e.logf("error removing temp dir: %s", err) } }