[ARVADOS] updated: 2.1.0-1077-ga2dcdbb41
Git user
git at public.arvados.org
Mon Jul 19 20:14:17 UTC 2021
Summary of changes:
lib/crunchrun/crunchrun.go | 8 ++--
lib/crunchrun/docker.go | 2 +-
lib/crunchrun/executor.go | 2 +-
lib/crunchrun/singularity.go | 100 ++++++++++++++++++++++++++++++++++++++-----
4 files changed, 96 insertions(+), 16 deletions(-)
via a2dcdbb414a73f4b4d4c395c823a07b929358aae (commit)
from 6766d1b04bd238d05890f3ec221c65e84920dde6 (commit)
Those revisions listed above that are new to this repository have
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revisions in full, below.
commit a2dcdbb414a73f4b4d4c395c823a07b929358aae
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Mon Jul 19 16:13:33 2021 -0400
17813: Upload .sif file to cache project & read it from keep
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go
index 59ef73e65..1937b8815 100644
--- a/lib/crunchrun/crunchrun.go
+++ b/lib/crunchrun/crunchrun.go
@@ -270,7 +270,7 @@ func (runner *ContainerRunner) LoadImage() (string, error) {
return "", err
}
} else {
- runner.CrunchLog.Print("Docker image is available")
+ runner.CrunchLog.Print("Container image is available")
}
return imageID, nil
}
@@ -1458,6 +1458,10 @@ func (runner *ContainerRunner) Run() (err error) {
return
}
+ // Communicate some additional configuration to the executor
+ runner.executor.SetArvadoClient(runner.containerClient, runner.ContainerKeepClient,
+ runner.Container, runner.ArvMountPoint)
+
// check for and/or load image
imageID, err := runner.LoadImage()
if err != nil {
@@ -1559,8 +1563,6 @@ func (runner *ContainerRunner) fetchContainerRecord() error {
}
runner.SecretMounts = sm.SecretMounts
- runner.executor.SetArvadoClient(runner.containerClient, runner.Container)
-
return nil
}
diff --git a/lib/crunchrun/docker.go b/lib/crunchrun/docker.go
index 05e540da8..4d3f7caf9 100644
--- a/lib/crunchrun/docker.go
+++ b/lib/crunchrun/docker.go
@@ -254,5 +254,5 @@ func (e *dockerExecutor) Close() {
e.dockerclient.ContainerRemove(context.TODO(), e.containerID, dockertypes.ContainerRemoveOptions{Force: true})
}
-func (e *dockerExecutor) SetArvadoClient(containerClient *arvados.Client, container arvados.Container) {
+func (e *dockerExecutor) SetArvadoClient(containerClient *arvados.Client, keepClient IKeepClient, container arvados.Container, keepMount string) {
}
diff --git a/lib/crunchrun/executor.go b/lib/crunchrun/executor.go
index 09258ed9d..05e9adefe 100644
--- a/lib/crunchrun/executor.go
+++ b/lib/crunchrun/executor.go
@@ -63,5 +63,5 @@ type containerExecutor interface {
Close()
// Give the executor access to arvados client & container info
- SetArvadoClient(containerClient *arvados.Client, container arvados.Container)
+ SetArvadoClient(containerClient *arvados.Client, keepClient IKeepClient, container arvados.Container, keepMount string)
}
diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
index 45926b065..cd03e32e5 100644
--- a/lib/crunchrun/singularity.go
+++ b/lib/crunchrun/singularity.go
@@ -6,6 +6,7 @@ package crunchrun
import (
"fmt"
+ "io"
"io/ioutil"
"os"
"os/exec"
@@ -25,6 +26,8 @@ type singularityExecutor struct {
imageFilename string // "sif" image
containerClient *arvados.Client
container arvados.Container
+ keepClient IKeepClient
+ keepMount string
}
func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
@@ -47,11 +50,12 @@ func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string,
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) > 0 {
+ if len(gp.Items) == 1 {
return &gp.Items[0], nil
}
if !create {
@@ -74,16 +78,56 @@ func (e *singularityExecutor) getOrCreateProject(ownerUuid string, name string,
return &rgroup, nil
}
-func (e *singularityExecutor) ImageLoaded(string) bool {
+func (e *singularityExecutor) ImageLoaded(imageId string) bool {
// Check if docker image is cached in keep & if so set imageFilename
- return false
+ // 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
}
@@ -118,30 +162,62 @@ func (e *singularityExecutor) LoadImage(imageTarballPath string) error {
// Cache the image to keep
cacheGroup, err := e.getOrCreateProject(e.container.RuntimeUserUUID, ".cache", true)
if err != nil {
- e.logf("error getting '.cache' project: %s", err)
+ 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: %s", err)
+ 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": fmt.Sprintf("singularity image for %s", imageId),
- }
+ "owner_uuid": imageGroup.UUID,
+ "name": collectionName,
+ "manifest_text": manifestText,
+ },
})
if err != nil {
- e.logf("error creating 'auto-generated singularity images' collection: %s", err)
+ e.logf("error creating '%v' collection: %s", collectionName, err)
}
return nil
@@ -232,7 +308,9 @@ func (e *singularityExecutor) Close() {
}
}
-func (e *singularityExecutor) SetArvadoClient(containerClient *arvados.Client, container arvados.Container) {
+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
}
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