X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/bcab6c50f54f155f14d1dd635becd85a5e91289d..469ea187586ea8017e26874c2d80414ce7571fae:/lib/crunchrun/singularity.go diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go index 4bec8c3ebe..1da401f859 100644 --- a/lib/crunchrun/singularity.go +++ b/lib/crunchrun/singularity.go @@ -5,16 +5,28 @@ package crunchrun import ( + "bytes" + "errors" + "fmt" "io/ioutil" + "net" "os" "os/exec" + "os/user" + "regexp" + "sort" + "strconv" + "strings" "syscall" + "time" + "git.arvados.org/arvados.git/sdk/go/arvados" "golang.org/x/net/context" ) type singularityExecutor struct { logf func(string, ...interface{}) + fakeroot bool // use --fakeroot flag, allow --network=bridge when non-root (currently only used by tests) spec containerSpec tmpdir string child *exec.Cmd @@ -32,39 +44,209 @@ 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 +255,45 @@ 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.fakeroot { + args = append(args, "--fakeroot") + } if !e.spec.EnableNetwork { args = append(args, "--net", "--network=none") + } else if u, err := user.Current(); err == nil && u.Uid == "0" || e.fakeroot { + // Specifying --network=bridge fails unless (a) we are + // root, (b) we are using --fakeroot, or (c) + // singularity has been configured to allow our + // uid/gid to use it like so: + // + // singularity config global --set 'allow net networks' bridge + // singularity config global --set 'allow net groups' mygroup + args = append(args, "--net", "--network=bridge") } + 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 treats $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 +301,35 @@ 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 treats $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 +337,14 @@ 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 @@ -146,3 +382,118 @@ func (e *singularityExecutor) Close() { e.logf("error removing temp dir: %s", err) } } + +func (e *singularityExecutor) InjectCommand(ctx context.Context, detachKeys, username string, usingTTY bool, injectcmd []string) (*exec.Cmd, error) { + target, err := e.containedProcess() + if err != nil { + return nil, err + } + return exec.CommandContext(ctx, "nsenter", append([]string{fmt.Sprintf("--target=%d", target), "--all"}, injectcmd...)...), nil +} + +var ( + errContainerHasNoIPAddress = errors.New("container has no IP address distinct from host") +) + +func (e *singularityExecutor) IPAddress() (string, error) { + target, err := e.containedProcess() + if err != nil { + return "", err + } + targetIPs, err := processIPs(target) + if err != nil { + return "", err + } + selfIPs, err := processIPs(os.Getpid()) + if err != nil { + return "", err + } + for ip := range targetIPs { + if !selfIPs[ip] { + return ip, nil + } + } + return "", errContainerHasNoIPAddress +} + +func processIPs(pid int) (map[string]bool, error) { + fibtrie, err := os.ReadFile(fmt.Sprintf("/proc/%d/net/fib_trie", pid)) + if err != nil { + return nil, err + } + + addrs := map[string]bool{} + // When we see a pair of lines like this: + // + // |-- 10.1.2.3 + // /32 host LOCAL + // + // ...we set addrs["10.1.2.3"] = true + lines := bytes.Split(fibtrie, []byte{'\n'}) + for linenumber, line := range lines { + if !bytes.HasSuffix(line, []byte("/32 host LOCAL")) { + continue + } + if linenumber < 1 { + continue + } + i := bytes.LastIndexByte(lines[linenumber-1], ' ') + if i < 0 || i >= len(line)-7 { + continue + } + addr := string(lines[linenumber-1][i+1:]) + if net.ParseIP(addr).To4() != nil { + addrs[addr] = true + } + } + return addrs, nil +} + +var ( + errContainerNotStarted = errors.New("container has not started yet") + errCannotFindChild = errors.New("failed to find any process inside the container") + reProcStatusPPid = regexp.MustCompile(`\nPPid:\t(\d+)\n`) +) + +// Return the PID of a process that is inside the container (not +// necessarily the topmost/pid=1 process in the container). +func (e *singularityExecutor) containedProcess() (int, error) { + if e.child == nil || e.child.Process == nil { + return 0, errContainerNotStarted + } + lsns, err := exec.Command("lsns").CombinedOutput() + if err != nil { + return 0, fmt.Errorf("lsns: %w", err) + } + for _, line := range bytes.Split(lsns, []byte{'\n'}) { + fields := bytes.Fields(line) + if len(fields) < 4 { + continue + } + if !bytes.Equal(fields[1], []byte("pid")) { + continue + } + pid, err := strconv.ParseInt(string(fields[3]), 10, 64) + if err != nil { + return 0, fmt.Errorf("error parsing PID field in lsns output: %q", fields[3]) + } + for parent := pid; ; { + procstatus, err := os.ReadFile(fmt.Sprintf("/proc/%d/status", parent)) + if err != nil { + break + } + m := reProcStatusPPid.FindSubmatch(procstatus) + if m == nil { + break + } + parent, err = strconv.ParseInt(string(m[1]), 10, 64) + if err != nil { + break + } + if int(parent) == e.child.Process.Pid { + return int(pid), nil + } + } + } + return 0, errCannotFindChild +}