X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/64c516079154f73da3f2a33a957fa8ae8eb23749..844ff7cc1dc1c93a29b7ad8eca2987b987cf89e6:/lib/crunchrun/singularity.go diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go index 4bec8c3ebe..1af0d420e4 100644 --- a/lib/crunchrun/singularity.go +++ b/lib/crunchrun/singularity.go @@ -5,11 +5,16 @@ package crunchrun import ( + "fmt" "io/ioutil" "os" "os/exec" + "sort" + "strings" "syscall" + "time" + "git.arvados.org/arvados.git/sdk/go/arvados" "golang.org/x/net/context" ) @@ -32,39 +37,209 @@ func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExec }, nil } -func (e *singularityExecutor) ImageLoaded(string) bool { - return false +func (e *singularityExecutor) Runtime() string { + buf, err := exec.Command("singularity", "--version").CombinedOutput() + if err != nil { + return "singularity (unknown version)" + } + return strings.TrimSuffix(string(buf), "\n") +} + +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(imageTarballPath string) error { - 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") +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 + } + + // Set up a cache and tmp dir for singularity build + err = os.Mkdir(e.tmpdir+"/cache", 0700) + if err != nil { + return err + } + defer os.RemoveAll(e.tmpdir + "/cache") + err = os.Mkdir(e.tmpdir+"/tmp", 0700) + if err != nil { + return err + } + defer os.RemoveAll(e.tmpdir + "/tmp") + + build := exec.Command("singularity", "build", imageFilename, "docker-archive://"+e.tmpdir+"/image.tar") + build.Env = os.Environ() + build.Env = append(build.Env, "SINGULARITY_CACHEDIR="+e.tmpdir+"/cache") + build.Env = append(build.Env, "SINGULARITY_TMPDIR="+e.tmpdir+"/tmp") + 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 { - return err + e.logf("error PathForUUID: %v", err) + return nil } - e.imageFilename = e.tmpdir + "/image.sif" - build := exec.Command("singularity", "build", e.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) + 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 } @@ -73,20 +248,34 @@ func (e *singularityExecutor) Create(spec containerSpec) error { return nil } -func (e *singularityExecutor) Start() error { - args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv"} +func (e *singularityExecutor) execCmd(path string) *exec.Cmd { + args := []string{path, "exec", "--containall", "--cleanenv", "--pwd", e.spec.WorkingDir} if !e.spec.EnableNetwork { args = append(args, "--net", "--network=none") } + + if e.spec.CUDADeviceCount != 0 { + args = append(args, "--nv") + } + readonlyflag := map[bool]string{ false: "rw", true: "ro", } - for path, mount := range e.spec.BindMounts { - args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly]) + 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] + if path == e.spec.Env["HOME"] { + // Singularity treates $HOME as special case + args = append(args, "--home", mount.HostPath+":"+path) + } else { + args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly]) + } } - args = append(args, e.imageFilename) - args = append(args, e.spec.Command...) // This is for singularity 3.5.2. There are some behaviors // that will change in singularity 3.6, please see: @@ -94,14 +283,35 @@ func (e *singularityExecutor) Start() error { // 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" { + // Singularity treates $HOME as special case, this is handled + // with --home above + continue + } env = append(env, "SINGULARITYENV_"+k+"="+v) } - path, err := exec.LookPath(args[0]) - if err != nil { - return err + // Singularity always makes all nvidia devices visible to the + // container. If a resource manager such as slurm or LSF told + // us to select specific devices we need to propagate that. + if cudaVisibleDevices := os.Getenv("CUDA_VISIBLE_DEVICES"); cudaVisibleDevices != "" { + // If a resource manager such as slurm or LSF told + // us to select specific devices we need to propagate that. + env = append(env, "SINGULARITYENV_CUDA_VISIBLE_DEVICES="+cudaVisibleDevices) } - child := &exec.Cmd{ + // Singularity's default behavior is to evaluate each + // SINGULARITYENV_* env var with a shell as a double-quoted + // string and pass the result to the contained + // process. Singularity 3.10+ has an option to pass env vars + // through literally without evaluating, which is what we + // want. See https://github.com/sylabs/singularity/pull/704 + // and https://dev.arvados.org/issues/19081 + env = append(env, "SINGULARITY_NO_EVAL=1") + + args = append(args, e.imageFilename) + args = append(args, e.spec.Command...) + + return &exec.Cmd{ Path: path, Args: args, Env: env, @@ -109,6 +319,14 @@ func (e *singularityExecutor) Start() error { Stdout: e.spec.Stdout, Stderr: e.spec.Stderr, } +} + +func (e *singularityExecutor) Start() error { + path, err := exec.LookPath("singularity") + if err != nil { + return err + } + child := e.execCmd(path) err = child.Start() if err != nil { return err