Merge branch '19081-singularity-no-eval'

[arvados.git] / lib / crunchrun / singularity.go

diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 681dbb6cc98803a2c9524a5987860b7f4ac9599b..1af0d420e4ca814c0da717b9f21ed1a432a59161 100644 (file)
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -10,6 +10,7 @@ import (
        "os"
        "os/exec"
        "sort"
+       "strings"
        "syscall"
        "time"
 
@@ -36,7 +37,13 @@ func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExec
        }, nil
 }
 
-func (e *singularityExecutor) Runtime() string { return "singularity" }
+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
@@ -160,15 +167,22 @@ 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...
@@ -234,11 +248,16 @@ func (e *singularityExecutor) Create(spec containerSpec) error {
        return nil
 }
 
-func (e *singularityExecutor) Start() error {
-       args := []string{"singularity", "exec", "--containall", "--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.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",
@@ -272,14 +291,27 @@ func (e *singularityExecutor) Start() error {
                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,
@@ -287,6 +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