package crunchrun
import (
+ "fmt"
+ "io"
"io/ioutil"
"os"
"os/exec"
+ "sort"
+ "strings"
"syscall"
+ "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
+ 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
}
func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
}, nil
}
-func (e *singularityExecutor) ImageLoaded(string) bool {
- return false
+func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string, create bool) (*arvados.Group, error) {
+ var gp arvados.GroupList
+ err := e.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
+ }
+ if !create {
+ return nil, nil
+ }
+ var rgroup arvados.Group
+ err = e.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) ImageLoaded(imageId string) bool {
+ // Check if docker image is cached in keep & if so set imageFilename
+
+ // Cache the image to keep
+ cacheGroup, err := e.getOrCreateProject(e.container.RuntimeUserUUID, ".cache", false)
+ if err != nil {
+ e.logf("error getting '.cache' project: %v", err)
+ return false
+ }
+ imageGroup, err := e.getOrCreateProject(cacheGroup.UUID, "auto-generated singularity images", false)
+ if err != nil {
+ e.logf("error getting 'auto-generated singularity images' project: %s", err)
+ return false
+ }
+
+ collectionName := fmt.Sprintf("singularity image for %v", imageId)
+ var cl arvados.CollectionList
+ err = e.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 {
+ 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
+ }
+
+ 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
}
// 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
+ }
+
e.logf("building singularity image")
// "singularity build" does not accept a
// docker-archive://... filename containing a ":" character,
if 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
+ }
+
+ parts := strings.Split(imageTarballPath, "/")
+ imageId := parts[len(parts)-1]
+ if strings.HasSuffix(imageId, ".tar") {
+ imageId = imageId[0 : len(imageId)-4]
+ }
+
+ fs, err := (&arvados.Collection{ManifestText: ""}).FileSystem(e.containerClient, e.keepClient)
+ if err != nil {
+ e.logf("error creating FileSystem: %s", err)
+ }
+
+ 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)
+ }
+
+ src, err := os.Open(e.imageFilename)
+ if err != nil {
+ dst.Close()
+ return nil
+ }
+ defer src.Close()
+ _, err = io.Copy(dst, src)
+ if err != nil {
+ dst.Close()
+ 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,
+ nil, map[string]interface{}{
+ "collection": map[string]string{
+ "owner_uuid": imageGroup.UUID,
+ "name": collectionName,
+ "manifest_text": manifestText,
+ },
+ })
+ if err != nil {
+ e.logf("error creating '%v' collection: %s", collectionName, err)
+ }
+
return nil
}
}
func (e *singularityExecutor) Start() error {
- args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv"}
+ args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv", "--pwd", e.spec.WorkingDir}
if !e.spec.EnableNetwork {
args = append(args, "--net", "--network=none")
}
false: "rw",
true: "ro",
}
- for path, mount := range e.spec.BindMounts {
+ 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]
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:
// 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 {
- env = append(env, "SINGULARITYENV_"+k+"="+v)
+ if k == "HOME" {
+ // $HOME is a special case
+ args = append(args, "--home="+v)
+ } else {
+ env = append(env, "SINGULARITYENV_"+k+"="+v)
+ }
}
+ args = append(args, e.imageFilename)
+ args = append(args, e.spec.Command...)
+
path, err := exec.LookPath(args[0])
if err != nil {
return err
e.logf("error removing temp dir: %s", err)
}
}
+
+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
+}
projects / arvados.git / blobdiff