X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d59079ca2a8e1afb3cf02bd9908c2cfe4c025d4f..13f6d45704efc68ca8419e8917376aa44fdee1be:/lib/crunchrun/singularity.go

diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 61fecad0a1..1da401f859 100644
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -5,11 +5,18 @@
 package crunchrun
 
 import (
+	"bytes"
+	"errors"
 	"fmt"
 	"io/ioutil"
+	"net"
 	"os"
 	"os/exec"
+	"os/user"
+	"regexp"
 	"sort"
+	"strconv"
+	"strings"
 	"syscall"
 	"time"
 
@@ -19,6 +26,7 @@ import (
 
 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
@@ -36,6 +44,14 @@ func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExec
 	}, nil
 }
 
+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,
@@ -158,7 +174,22 @@ func (e *singularityExecutor) LoadImage(dockerImageID string, imageTarballPath s
 			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...
@@ -224,11 +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",
@@ -240,7 +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
@@ -250,21 +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,
@@ -272,6 +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
@@ -309,3 +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
+}