X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2d43f3de749909c040ea17460ec828047e6db7c2..13f6d45704efc68ca8419e8917376aa44fdee1be:/lib/crunchrun/singularity.go

diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index be2d188715..1da401f859 100644
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -5,29 +5,32 @@
 package crunchrun
 
 import (
+	"bytes"
+	"errors"
 	"fmt"
-	"io"
 	"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{})
-	spec            containerSpec
-	tmpdir          string
-	child           *exec.Cmd
-	imageFilename   string // "sif" image
-	containerClient *arvados.Client
-	container       arvados.Container
-	keepClient      IKeepClient
-	keepMount       string
+	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
+	imageFilename string // "sif" image
 }
 
 func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
@@ -41,9 +44,17 @@ func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExec
 	}, nil
 }
 
-func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string, create bool) (*arvados.Group, error) {
+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 := e.containerClient.RequestAndDecode(&gp,
+	err := containerClient.RequestAndDecode(&gp,
 		arvados.EndpointGroupList.Method,
 		arvados.EndpointGroupList.Path,
 		nil, arvados.ListOptions{Filters: []arvados.Filter{
@@ -58,11 +69,9 @@ func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string,
 	if len(gp.Items) == 1 {
 		return &gp.Items[0], nil
 	}
-	if !create {
-		return nil, nil
-	}
+
 	var rgroup arvados.Group
-	err = e.containerClient.RequestAndDecode(&rgroup,
+	err = containerClient.RequestAndDecode(&rgroup,
 		arvados.EndpointGroupCreate.Method,
 		arvados.EndpointGroupCreate.Path,
 		nil, map[string]interface{}{
@@ -78,24 +87,22 @@ func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string,
 	return &rgroup, nil
 }
 
-func (e *singularityExecutor) ImageLoaded(imageId string) bool {
-	// Check if docker image is cached in keep & if so set imageFilename
+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(e.container.RuntimeUserUUID, ".cache", false)
+	cacheGroup, err := e.getOrCreateProject(container.RuntimeUserUUID, ".cache", containerClient)
 	if err != nil {
-		e.logf("error getting '.cache' project: %v", err)
-		return false
+		return nil, fmt.Errorf("error getting '.cache' project: %v", err)
 	}
-	imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", false)
+	imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", containerClient)
 	if err != nil {
-		e.logf("error getting 'auto-generated singularity images' project: %s", err)
-		return false
+		return nil, fmt.Errorf("error getting 'auto-generated singularity images' project: %s", err)
 	}
 
-	collectionName := fmt.Sprintf("singularity image for %v", imageId)
+	collectionName := fmt.Sprintf("singularity image for %v", dockerImageID)
 	var cl arvados.CollectionList
-	err = e.containerClient.RequestAndDecode(&cl,
+	err = containerClient.RequestAndDecode(&cl,
 		arvados.EndpointCollectionList.Method,
 		arvados.EndpointCollectionList.Path,
 		nil, arvados.ListOptions{Filters: []arvados.Filter{
@@ -104,121 +111,141 @@ func (e *singularityExecutor) ImageLoaded(imageId string) bool {
 		},
 			Limit: 1})
 	if err != nil {
-		e.logf("error getting collection '%v' project: %v", err)
-		return false
-	}
-	if len(cl.Items) == 0 {
-		e.logf("no cached image '%v' found", collectionName)
-		return false
+		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)
+		}
 
-	path := fmt.Sprintf("%s/by_id/%s/image.sif", e.keepMount, cl.Items[0].PortableDataHash)
-	e.logf("Looking for %v", path)
-	if _, err = os.Stat(path); os.IsNotExist(err) {
-		return false
 	}
-	e.imageFilename = path
 
-	return true
+	return &imageCollection, nil
 }
 
 // LoadImage will satisfy ContainerExecuter interface transforming
 // containerImage into a sif file for later use.
-func (e *singularityExecutor) LoadImage(imageTarballPath string) error {
-	if e.imageFilename != "" {
-		e.logf("using singularity image %v", e.imageFilename)
-
-		// was set by ImageLoaded
-		return nil
+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"
 	}
 
-	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
-	}
-	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)
-	if err != nil {
-		return err
-	}
+	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
+		}
 
-	// Cache the image to keep
-	cacheGroup, err := e.getOrCreateProject(e.container.RuntimeUserUUID, ".cache", true)
-	if err != nil {
-		e.logf("error getting '.cache' project: %v", err)
-		return nil
-	}
-	imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", true)
-	if err != nil {
-		e.logf("error getting 'auto-generated singularity images' project: %v", err)
-		return nil
-	}
+		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
+		}
 
-	parts := strings.Split(imageTarballPath, "/")
-	imageId := parts[len(parts)-1]
-	if strings.HasSuffix(imageId, ".tar") {
-		imageId = imageId[0 : len(imageId)-4]
+		// 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
+		}
 	}
 
-	fs, err := (&arvados.Collection{ManifestText: ""}).FileSystem(e.containerClient, e.keepClient)
-	if err != nil {
-		e.logf("error creating FileSystem: %s", err)
+	if containerClient == nil {
+		e.imageFilename = imageFilename
+		return nil
 	}
 
-	dst, err := fs.OpenFile("image.sif", os.O_CREATE|os.O_WRONLY, 0666)
-	if err != nil {
-		e.logf("error creating opening collection file for writing: %s", err)
-	}
+	// update TTL to now + two weeks
+	exp := time.Now().Add(24 * 7 * 2 * time.Hour)
 
-	src, err := os.Open(e.imageFilename)
-	if err != nil {
-		dst.Close()
-		return nil
-	}
-	defer src.Close()
-	_, err = io.Copy(dst, src)
+	uuidPath, err := containerClient.PathForUUID("update", sifCollection.UUID)
 	if err != nil {
-		dst.Close()
+		e.logf("error PathForUUID: %v", err)
 		return nil
 	}
-
-	manifestText, err := fs.MarshalManifest(".")
-	if err != nil {
-		e.logf("error creating manifest text: %s", err)
-	}
-
 	var imageCollection arvados.Collection
-	collectionName := fmt.Sprintf("singularity image for %s", imageId)
-	err = e.containerClient.RequestAndDecode(&imageCollection,
-		arvados.EndpointCollectionCreate.Method,
-		arvados.EndpointCollectionCreate.Path,
+	err = containerClient.RequestAndDecode(&imageCollection,
+		arvados.EndpointCollectionUpdate.Method,
+		uuidPath,
 		nil, map[string]interface{}{
 			"collection": map[string]string{
-				"owner_uuid":    imageGroup.UUID,
-				"name":          collectionName,
-				"manifest_text": manifestText,
+				"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 {
-		e.logf("error creating '%v' collection: %s", collectionName, err)
+		return err
 	}
+	e.imageFilename = fmt.Sprintf("%s/by_id/%s/image.sif", arvMountPoint, sifCollection.PortableDataHash)
 
 	return nil
 }
@@ -228,11 +255,27 @@ func (e *singularityExecutor) Create(spec containerSpec) error {
 	return nil
 }
 
-func (e *singularityExecutor) Start() error {
-	args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv", "--pwd", e.spec.WorkingDir}
+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",
@@ -244,7 +287,12 @@ func (e *singularityExecutor) Start() error {
 	sort.Strings(binds)
 	for _, path := range binds {
 		mount := e.spec.BindMounts[path]
-		args = append(args, "--bind", mount.HostPath+":"+path+":"+readonlyflag[mount.ReadOnly])
+		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])
+		}
 	}
 
 	// This is for singularity 3.5.2. There are some behaviors
@@ -254,21 +302,34 @@ func (e *singularityExecutor) Start() error {
 	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)
+			// Singularity treats $HOME as special case,
+			// this is handled with --home above
+			continue
 		}
-	}
+		env = append(env, "SINGULARITYENV_"+k+"="+v)
+	}
+
+	// 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)
+	}
+	// 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...)
 
-	path, err := exec.LookPath(args[0])
-	if err != nil {
-		return err
-	}
-	child := &exec.Cmd{
+	return &exec.Cmd{
 		Path:   path,
 		Args:   args,
 		Env:    env,
@@ -276,6 +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
@@ -314,9 +383,117 @@ func (e *singularityExecutor) Close() {
 	}
 }
 
-func (e *singularityExecutor) SetArvadoClient(containerClient *arvados.Client, keepClient IKeepClient, container arvados.Container, keepMount string) {
-	e.containerClient = containerClient
-	e.container = container
-	e.keepClient = keepClient
-	e.keepMount = keepMount
+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
 }