package crunchrun
import (
+ "fmt"
"io/ioutil"
"os"
"os/exec"
"sort"
"syscall"
+ "time"
+ "git.arvados.org/arvados.git/sdk/go/arvados"
"golang.org/x/net/context"
)
}, nil
}
-func (e *singularityExecutor) ImageLoaded(string) bool {
- return false
+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 := collectionName + " " + time.Now().UTC().Format(time.RFC3339)
+ 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),
+ },
+ })
+ 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) {
+ 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
+ }
+
+ build := exec.Command("singularity", "build", 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 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
+ }
+ 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.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)
+
+ 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
}
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