[ARVADOS] created: 2.1.0-799-g83d6cc94a
Git user
git at public.arvados.org
Mon May 17 21:06:55 UTC 2021
at 83d6cc94a72c1be8a371976ca6198abfb8bfc5a9 (commit)
commit 83d6cc94a72c1be8a371976ca6198abfb8bfc5a9
Author: Tom Clegg <tom at curii.com>
Date: Mon May 17 17:06:41 2021 -0400
17296: Disentangle docker-specific code, add singularity option.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>
diff --git a/lib/config/config.default.yml b/lib/config/config.default.yml
index 50a965a9a..c94b4ee9a 100644
--- a/lib/config/config.default.yml
+++ b/lib/config/config.default.yml
@@ -862,6 +862,9 @@ Clusters:
# Minimum time between two attempts to run the same container
MinRetryPeriod: 0s
+ # Container runtime: "docker" (default) or "singularity" (experimental)
+ RuntimeEngine: docker
+
Logging:
# When you run the db:delete_old_container_logs task, it will find
# containers that have been finished for at least this many seconds,
diff --git a/lib/config/generated_config.go b/lib/config/generated_config.go
index 5216f8161..e344d2266 100644
--- a/lib/config/generated_config.go
+++ b/lib/config/generated_config.go
@@ -868,6 +868,9 @@ Clusters:
# Minimum time between two attempts to run the same container
MinRetryPeriod: 0s
+ # Container runtime: "docker" (default) or "singularity" (experimental)
+ RuntimeEngine: docker
+
Logging:
# When you run the db:delete_old_container_logs task, it will find
# containers that have been finished for at least this many seconds,
diff --git a/lib/crunchrun/copier.go b/lib/crunchrun/copier.go
index 1b0f168b8..78e5f4faa 100644
--- a/lib/crunchrun/copier.go
+++ b/lib/crunchrun/copier.go
@@ -55,7 +55,7 @@ type copier struct {
keepClient IKeepClient
hostOutputDir string
ctrOutputDir string
- binds []string
+ bindmounts map[string]bindmount
mounts map[string]arvados.Mount
secretMounts map[string]arvados.Mount
logger printfer
@@ -341,11 +341,8 @@ func (cp *copier) hostRoot(ctrRoot string) (string, error) {
if ctrRoot == cp.ctrOutputDir {
return cp.hostOutputDir, nil
}
- for _, bind := range cp.binds {
- tokens := strings.Split(bind, ":")
- if len(tokens) >= 2 && tokens[1] == ctrRoot {
- return tokens[0], nil
- }
+ if mnt, ok := cp.bindmounts[ctrRoot]; ok {
+ return mnt.HostPath, nil
}
return "", fmt.Errorf("not bind-mounted: %q", ctrRoot)
}
diff --git a/lib/crunchrun/copier_test.go b/lib/crunchrun/copier_test.go
index 777b715d7..9135bcaa1 100644
--- a/lib/crunchrun/copier_test.go
+++ b/lib/crunchrun/copier_test.go
@@ -128,7 +128,9 @@ func (s *copierSuite) TestSymlinkToMountedCollection(c *check.C) {
PortableDataHash: arvadostest.FooCollectionPDH,
Writable: true,
}
- s.cp.binds = append(s.cp.binds, bindtmp+":/mnt-w")
+ s.cp.bindmounts = map[string]bindmount{
+ "/mnt-w": bindmount{HostPath: bindtmp, ReadOnly: false},
+ }
c.Assert(os.Symlink("../../mnt", s.cp.hostOutputDir+"/l_dir"), check.IsNil)
c.Assert(os.Symlink("/mnt/foo", s.cp.hostOutputDir+"/l_file"), check.IsNil)
diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go
index 88c137277..4bdaca4d6 100644
--- a/lib/crunchrun/crunchrun.go
+++ b/lib/crunchrun/crunchrun.go
@@ -34,11 +34,6 @@ import (
"git.arvados.org/arvados.git/sdk/go/keepclient"
"git.arvados.org/arvados.git/sdk/go/manifest"
"golang.org/x/net/context"
-
- dockertypes "github.com/docker/docker/api/types"
- dockercontainer "github.com/docker/docker/api/types/container"
- dockernetwork "github.com/docker/docker/api/types/network"
- dockerclient "github.com/docker/docker/client"
)
type command struct{}
@@ -74,20 +69,6 @@ type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
type MkTempDir func(string, string) (string, error)
-// ThinDockerClient is the minimal Docker client interface used by crunch-run.
-type ThinDockerClient interface {
- ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error)
- ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig,
- networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error)
- ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error
- ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error
- ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error)
- ContainerInspect(ctx context.Context, id string) (dockertypes.ContainerJSON, error)
- ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error)
- ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error)
- ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error)
-}
-
type PsProcess interface {
CmdlineSlice() ([]string, error)
}
@@ -95,7 +76,7 @@ type PsProcess interface {
// ContainerRunner is the main stateful struct used for a single execution of a
// container.
type ContainerRunner struct {
- Docker ThinDockerClient
+ executor containerExecutor
// Dispatcher client is initialized with the Dispatcher token.
// This is a privileged token used to manage container status
@@ -119,35 +100,30 @@ type ContainerRunner struct {
ContainerArvClient IArvadosClient
ContainerKeepClient IKeepClient
- Container arvados.Container
- ContainerConfig dockercontainer.Config
- HostConfig dockercontainer.HostConfig
- token string
- ContainerID string
- ExitCode *int
- NewLogWriter NewLogWriter
- loggingDone chan bool
- CrunchLog *ThrottledLogger
- Stdout io.WriteCloser
- Stderr io.WriteCloser
- logUUID string
- logMtx sync.Mutex
- LogCollection arvados.CollectionFileSystem
- LogsPDH *string
- RunArvMount RunArvMount
- MkTempDir MkTempDir
- ArvMount *exec.Cmd
- ArvMountPoint string
- HostOutputDir string
- Binds []string
- Volumes map[string]struct{}
- OutputPDH *string
- SigChan chan os.Signal
- ArvMountExit chan error
- SecretMounts map[string]arvados.Mount
- MkArvClient func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
- finalState string
- parentTemp string
+ Container arvados.Container
+ token string
+ ExitCode *int
+ NewLogWriter NewLogWriter
+ CrunchLog *ThrottledLogger
+ Stdout io.WriteCloser
+ Stderr io.WriteCloser
+ logUUID string
+ logMtx sync.Mutex
+ LogCollection arvados.CollectionFileSystem
+ LogsPDH *string
+ RunArvMount RunArvMount
+ MkTempDir MkTempDir
+ ArvMount *exec.Cmd
+ ArvMountPoint string
+ HostOutputDir string
+ Volumes map[string]struct{}
+ OutputPDH *string
+ SigChan chan os.Signal
+ ArvMountExit chan error
+ SecretMounts map[string]arvados.Mount
+ MkArvClient func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
+ finalState string
+ parentTemp string
statLogger io.WriteCloser
statReporter *crunchstat.Reporter
@@ -171,10 +147,9 @@ type ContainerRunner struct {
cStateLock sync.Mutex
cCancelled bool // StopContainer() invoked
- cRemoved bool // docker confirmed the container no longer exists
enableNetwork string // one of "default" or "always"
- networkMode string // passed through to HostConfig.NetworkMode
+ networkMode string // "none", "host", or "" -- passed through to executor
arvMountLog *ThrottledLogger
containerWatchdogInterval time.Duration
@@ -182,8 +157,9 @@ type ContainerRunner struct {
gateway Gateway
}
-// setupSignals sets up signal handling to gracefully terminate the underlying
-// Docker container and update state when receiving a TERM, INT or QUIT signal.
+// setupSignals sets up signal handling to gracefully terminate the
+// underlying container and update state when receiving a TERM, INT or
+// QUIT signal.
func (runner *ContainerRunner) setupSignals() {
runner.SigChan = make(chan os.Signal, 1)
signal.Notify(runner.SigChan, syscall.SIGTERM)
@@ -197,24 +173,18 @@ func (runner *ContainerRunner) setupSignals() {
}(runner.SigChan)
}
-// stop the underlying Docker container.
+// stop the underlying container.
func (runner *ContainerRunner) stop(sig os.Signal) {
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if sig != nil {
runner.CrunchLog.Printf("caught signal: %v", sig)
}
- if runner.ContainerID == "" {
- return
- }
runner.cCancelled = true
- runner.CrunchLog.Printf("removing container")
- err := runner.Docker.ContainerRemove(context.TODO(), runner.ContainerID, dockertypes.ContainerRemoveOptions{Force: true})
+ runner.CrunchLog.Printf("stopping container")
+ err := runner.executor.Stop()
if err != nil {
- runner.CrunchLog.Printf("error removing container: %s", err)
- }
- if err == nil || strings.Contains(err.Error(), "No such container: "+runner.ContainerID) {
- runner.cRemoved = true
+ runner.CrunchLog.Printf("error stopping container: %s", err)
}
}
@@ -262,57 +232,44 @@ func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
// LoadImage determines the docker image id from the container record and
// checks if it is available in the local Docker image store. If not, it loads
// the image from Keep.
-func (runner *ContainerRunner) LoadImage() (err error) {
-
+func (runner *ContainerRunner) LoadImage() (string, error) {
runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
- var collection arvados.Collection
- err = runner.ContainerArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
+ d, err := os.Open(runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage)
+ if err != nil {
+ return "", err
+ }
+ defer d.Close()
+ allfiles, err := d.Readdirnames(-1)
if err != nil {
- return fmt.Errorf("While getting container image collection: %v", err)
+ return "", err
}
- manifest := manifest.Manifest{Text: collection.ManifestText}
- var img, imageID string
- for ms := range manifest.StreamIter() {
- img = ms.FileStreamSegments[0].Name
- if !strings.HasSuffix(img, ".tar") {
- return fmt.Errorf("First file in the container image collection does not end in .tar")
+ var tarfiles []string
+ for _, fnm := range allfiles {
+ if strings.HasSuffix(fnm, ".tar") {
+ tarfiles = append(tarfiles, fnm)
}
- imageID = img[:len(img)-4]
}
+ if len(tarfiles) == 0 {
+ return "", fmt.Errorf("image collection does not include a .tar image file")
+ }
+ if len(tarfiles) > 1 {
+ return "", fmt.Errorf("cannot choose from multiple tar files in image collection: %v", tarfiles)
+ }
+ imageID := tarfiles[0][:len(tarfiles[0])-4]
+ imageFile := runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage + "/" + tarfiles[0]
+ runner.CrunchLog.Printf("Using Docker image id %q", imageID)
- runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
-
- _, _, err = runner.Docker.ImageInspectWithRaw(context.TODO(), imageID)
- if err != nil {
+ if !runner.executor.ImageLoaded(imageID) {
runner.CrunchLog.Print("Loading Docker image from keep")
-
- var readCloser io.ReadCloser
- readCloser, err = runner.ContainerKeepClient.ManifestFileReader(manifest, img)
+ err = runner.executor.LoadImage(imageFile)
if err != nil {
- return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
+ return "", err
}
-
- response, err := runner.Docker.ImageLoad(context.TODO(), readCloser, true)
- if err != nil {
- return fmt.Errorf("While loading container image into Docker: %v", err)
- }
-
- defer response.Body.Close()
- rbody, err := ioutil.ReadAll(response.Body)
- if err != nil {
- return fmt.Errorf("Reading response to image load: %v", err)
- }
- runner.CrunchLog.Printf("Docker response: %s", rbody)
} else {
runner.CrunchLog.Print("Docker image is available")
}
-
- runner.ContainerConfig.Image = imageID
-
- runner.ContainerKeepClient.ClearBlockCache()
-
- return nil
+ return imageID, nil
}
func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
@@ -418,15 +375,16 @@ func copyfile(src string, dst string) (err error) {
return nil
}
-func (runner *ContainerRunner) SetupMounts() (err error) {
- err = runner.SetupArvMountPoint("keep")
+func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
+ bindmounts := map[string]bindmount{}
+ err := runner.SetupArvMountPoint("keep")
if err != nil {
- return fmt.Errorf("While creating keep mount temp dir: %v", err)
+ return nil, fmt.Errorf("While creating keep mount temp dir: %v", err)
}
token, err := runner.ContainerToken()
if err != nil {
- return fmt.Errorf("could not get container token: %s", err)
+ return nil, fmt.Errorf("could not get container token: %s", err)
}
pdhOnly := true
@@ -442,8 +400,6 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
}
collectionPaths := []string{}
- runner.Binds = nil
- runner.Volumes = make(map[string]struct{})
needCertMount := true
type copyFile struct {
src string
@@ -457,11 +413,11 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
}
for bind := range runner.SecretMounts {
if _, ok := runner.Container.Mounts[bind]; ok {
- return fmt.Errorf("secret mount %q conflicts with regular mount", bind)
+ return nil, fmt.Errorf("secret mount %q conflicts with regular mount", bind)
}
if runner.SecretMounts[bind].Kind != "json" &&
runner.SecretMounts[bind].Kind != "text" {
- return fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
+ return nil, fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
bind, runner.SecretMounts[bind].Kind)
}
binds = append(binds, bind)
@@ -476,7 +432,7 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
if bind == "stdout" || bind == "stderr" {
// Is it a "file" mount kind?
if mnt.Kind != "file" {
- return fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
+ return nil, fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
}
// Does path start with OutputPath?
@@ -485,14 +441,14 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
prefix += "/"
}
if !strings.HasPrefix(mnt.Path, prefix) {
- return fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
+ return nil, fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
}
}
if bind == "stdin" {
// Is it a "collection" mount kind?
if mnt.Kind != "collection" && mnt.Kind != "json" {
- return fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
+ return nil, fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
}
}
@@ -502,7 +458,7 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
- return fmt.Errorf("only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
+ return nil, fmt.Errorf("only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
}
}
@@ -510,17 +466,17 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
case mnt.Kind == "collection" && bind != "stdin":
var src string
if mnt.UUID != "" && mnt.PortableDataHash != "" {
- return fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
+ return nil, fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
}
if mnt.UUID != "" {
if mnt.Writable {
- return fmt.Errorf("writing to existing collections currently not permitted")
+ return nil, fmt.Errorf("writing to existing collections currently not permitted")
}
pdhOnly = false
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
} else if mnt.PortableDataHash != "" {
if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
- return fmt.Errorf("can never write to a collection specified by portable data hash")
+ return nil, fmt.Errorf("can never write to a collection specified by portable data hash")
}
idx := strings.Index(mnt.PortableDataHash, "/")
if idx > 0 {
@@ -546,14 +502,14 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
if mnt.Writable {
if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
+ bindmounts[bind] = bindmount{HostPath: src}
} else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
+ bindmounts[bind] = bindmount{HostPath: src}
}
} else {
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
+ bindmounts[bind] = bindmount{HostPath: src, ReadOnly: true}
}
collectionPaths = append(collectionPaths, src)
@@ -561,17 +517,17 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
var tmpdir string
tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
if err != nil {
- return fmt.Errorf("while creating mount temp dir: %v", err)
+ return nil, fmt.Errorf("while creating mount temp dir: %v", err)
}
st, staterr := os.Stat(tmpdir)
if staterr != nil {
- return fmt.Errorf("while Stat on temp dir: %v", staterr)
+ return nil, fmt.Errorf("while Stat on temp dir: %v", staterr)
}
err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
if staterr != nil {
- return fmt.Errorf("while Chmod temp dir: %v", err)
+ return nil, fmt.Errorf("while Chmod temp dir: %v", err)
}
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
+ bindmounts[bind] = bindmount{HostPath: tmpdir}
if bind == runner.Container.OutputPath {
runner.HostOutputDir = tmpdir
}
@@ -581,53 +537,53 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
if mnt.Kind == "json" {
filedata, err = json.Marshal(mnt.Content)
if err != nil {
- return fmt.Errorf("encoding json data: %v", err)
+ return nil, fmt.Errorf("encoding json data: %v", err)
}
} else {
text, ok := mnt.Content.(string)
if !ok {
- return fmt.Errorf("content for mount %q must be a string", bind)
+ return nil, fmt.Errorf("content for mount %q must be a string", bind)
}
filedata = []byte(text)
}
tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
if err != nil {
- return fmt.Errorf("creating temp dir: %v", err)
+ return nil, fmt.Errorf("creating temp dir: %v", err)
}
tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
err = ioutil.WriteFile(tmpfn, filedata, 0444)
if err != nil {
- return fmt.Errorf("writing temp file: %v", err)
+ return nil, fmt.Errorf("writing temp file: %v", err)
}
if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
+ bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
}
case mnt.Kind == "git_tree":
tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
if err != nil {
- return fmt.Errorf("creating temp dir: %v", err)
+ return nil, fmt.Errorf("creating temp dir: %v", err)
}
err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
if err != nil {
- return err
+ return nil, err
}
- runner.Binds = append(runner.Binds, tmpdir+":"+bind+":ro")
+ bindmounts[bind] = bindmount{HostPath: tmpdir, ReadOnly: true}
}
}
if runner.HostOutputDir == "" {
- return fmt.Errorf("output path does not correspond to a writable mount point")
+ return nil, fmt.Errorf("output path does not correspond to a writable mount point")
}
if needCertMount && runner.Container.RuntimeConstraints.API {
for _, certfile := range arvadosclient.CertFiles {
_, err := os.Stat(certfile)
if err == nil {
- runner.Binds = append(runner.Binds, fmt.Sprintf("%s:/etc/arvados/ca-certificates.crt:ro", certfile))
+ bindmounts["/etc/arvados/ca-certificates.crt"] = bindmount{HostPath: certfile, ReadOnly: true}
break
}
}
@@ -642,20 +598,20 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
if err != nil {
- return fmt.Errorf("while trying to start arv-mount: %v", err)
+ return nil, fmt.Errorf("while trying to start arv-mount: %v", err)
}
for _, p := range collectionPaths {
_, err = os.Stat(p)
if err != nil {
- return fmt.Errorf("while checking that input files exist: %v", err)
+ return nil, fmt.Errorf("while checking that input files exist: %v", err)
}
}
for _, cp := range copyFiles {
st, err := os.Stat(cp.src)
if err != nil {
- return fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
+ return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
if st.IsDir() {
err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
@@ -686,59 +642,11 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
}
}
if err != nil {
- return fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
+ return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
}
- return nil
-}
-
-func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
- // Handle docker log protocol
- // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
- defer close(runner.loggingDone)
-
- header := make([]byte, 8)
- var err error
- for err == nil {
- _, err = io.ReadAtLeast(containerReader, header, 8)
- if err != nil {
- if err == io.EOF {
- err = nil
- }
- break
- }
- readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
- if header[0] == 1 {
- // stdout
- _, err = io.CopyN(runner.Stdout, containerReader, readsize)
- } else {
- // stderr
- _, err = io.CopyN(runner.Stderr, containerReader, readsize)
- }
- }
-
- if err != nil {
- runner.CrunchLog.Printf("error reading docker logs: %v", err)
- }
-
- err = runner.Stdout.Close()
- if err != nil {
- runner.CrunchLog.Printf("error closing stdout logs: %v", err)
- }
-
- err = runner.Stderr.Close()
- if err != nil {
- runner.CrunchLog.Printf("error closing stderr logs: %v", err)
- }
-
- if runner.statReporter != nil {
- runner.statReporter.Stop()
- err = runner.statLogger.Close()
- if err != nil {
- runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
- }
- }
+ return bindmounts, nil
}
func (runner *ContainerRunner) stopHoststat() error {
@@ -775,7 +683,7 @@ func (runner *ContainerRunner) startCrunchstat() error {
}
runner.statLogger = NewThrottledLogger(w)
runner.statReporter = &crunchstat.Reporter{
- CID: runner.ContainerID,
+ CID: runner.executor.CgroupID(),
Logger: log.New(runner.statLogger, "", 0),
CgroupParent: runner.expectCgroupParent,
CgroupRoot: runner.cgroupRoot,
@@ -938,102 +846,6 @@ func (runner *ContainerRunner) logAPIResponse(label, path string, params map[str
return true, nil
}
-// AttachStreams connects the docker container stdin, stdout and stderr logs
-// to the Arvados logger which logs to Keep and the API server logs table.
-func (runner *ContainerRunner) AttachStreams() (err error) {
-
- runner.CrunchLog.Print("Attaching container streams")
-
- // If stdin mount is provided, attach it to the docker container
- var stdinRdr arvados.File
- var stdinJSON []byte
- if stdinMnt, ok := runner.Container.Mounts["stdin"]; ok {
- if stdinMnt.Kind == "collection" {
- var stdinColl arvados.Collection
- collID := stdinMnt.UUID
- if collID == "" {
- collID = stdinMnt.PortableDataHash
- }
- err = runner.ContainerArvClient.Get("collections", collID, nil, &stdinColl)
- if err != nil {
- return fmt.Errorf("While getting stdin collection: %v", err)
- }
-
- stdinRdr, err = runner.ContainerKeepClient.ManifestFileReader(
- manifest.Manifest{Text: stdinColl.ManifestText},
- stdinMnt.Path)
- if os.IsNotExist(err) {
- return fmt.Errorf("stdin collection path not found: %v", stdinMnt.Path)
- } else if err != nil {
- return fmt.Errorf("While getting stdin collection path %v: %v", stdinMnt.Path, err)
- }
- } else if stdinMnt.Kind == "json" {
- stdinJSON, err = json.Marshal(stdinMnt.Content)
- if err != nil {
- return fmt.Errorf("While encoding stdin json data: %v", err)
- }
- }
- }
-
- stdinUsed := stdinRdr != nil || len(stdinJSON) != 0
- response, err := runner.Docker.ContainerAttach(context.TODO(), runner.ContainerID,
- dockertypes.ContainerAttachOptions{Stream: true, Stdin: stdinUsed, Stdout: true, Stderr: true})
- if err != nil {
- return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
- }
-
- runner.loggingDone = make(chan bool)
-
- if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
- stdoutFile, err := runner.getStdoutFile(stdoutMnt.Path)
- if err != nil {
- return err
- }
- runner.Stdout = stdoutFile
- } else if w, err := runner.NewLogWriter("stdout"); err != nil {
- return err
- } else {
- runner.Stdout = NewThrottledLogger(w)
- }
-
- if stderrMnt, ok := runner.Container.Mounts["stderr"]; ok {
- stderrFile, err := runner.getStdoutFile(stderrMnt.Path)
- if err != nil {
- return err
- }
- runner.Stderr = stderrFile
- } else if w, err := runner.NewLogWriter("stderr"); err != nil {
- return err
- } else {
- runner.Stderr = NewThrottledLogger(w)
- }
-
- if stdinRdr != nil {
- go func() {
- _, err := io.Copy(response.Conn, stdinRdr)
- if err != nil {
- runner.CrunchLog.Printf("While writing stdin collection to docker container: %v", err)
- runner.stop(nil)
- }
- stdinRdr.Close()
- response.CloseWrite()
- }()
- } else if len(stdinJSON) != 0 {
- go func() {
- _, err := io.Copy(response.Conn, bytes.NewReader(stdinJSON))
- if err != nil {
- runner.CrunchLog.Printf("While writing stdin json to docker container: %v", err)
- runner.stop(nil)
- }
- response.CloseWrite()
- }()
- }
-
- go runner.ProcessDockerAttach(response.Reader)
-
- return nil
-}
-
func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
stdoutPath := mntPath[len(runner.Container.OutputPath):]
index := strings.LastIndex(stdoutPath, "/")
@@ -1060,86 +872,107 @@ func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
}
// CreateContainer creates the docker container.
-func (runner *ContainerRunner) CreateContainer() error {
- runner.CrunchLog.Print("Creating Docker container")
-
- runner.ContainerConfig.Cmd = runner.Container.Command
- if runner.Container.Cwd != "." {
- runner.ContainerConfig.WorkingDir = runner.Container.Cwd
+func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[string]bindmount) error {
+ var stdin io.ReadCloser
+ if mnt, ok := runner.Container.Mounts["stdin"]; ok {
+ switch mnt.Kind {
+ case "collection":
+ var collID string
+ if mnt.UUID != "" {
+ collID = mnt.UUID
+ } else {
+ collID = mnt.PortableDataHash
+ }
+ path := runner.ArvMountPoint + "/by_id/" + collID + "/" + mnt.Path
+ f, err := os.Open(path)
+ if err != nil {
+ return err
+ }
+ stdin = f
+ case "json":
+ j, err := json.Marshal(mnt.Content)
+ if err != nil {
+ return fmt.Errorf("error encoding stdin json data: %v", err)
+ }
+ stdin = ioutil.NopCloser(bytes.NewReader(j))
+ default:
+ return fmt.Errorf("stdin mount has unsupported kind %q", mnt.Kind)
+ }
}
- for k, v := range runner.Container.Environment {
- runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
+ var stdout, stderr io.WriteCloser
+ if mnt, ok := runner.Container.Mounts["stdout"]; ok {
+ f, err := runner.getStdoutFile(mnt.Path)
+ if err != nil {
+ return err
+ }
+ stdout = f
+ } else if w, err := runner.NewLogWriter("stdout"); err != nil {
+ return err
+ } else {
+ stdout = NewThrottledLogger(w)
}
- runner.ContainerConfig.Volumes = runner.Volumes
-
- maxRAM := int64(runner.Container.RuntimeConstraints.RAM)
- minDockerRAM := int64(16)
- if maxRAM < minDockerRAM*1024*1024 {
- // Docker daemon won't let you set a limit less than ~10 MiB
- maxRAM = minDockerRAM * 1024 * 1024
- }
- runner.HostConfig = dockercontainer.HostConfig{
- Binds: runner.Binds,
- LogConfig: dockercontainer.LogConfig{
- Type: "none",
- },
- Resources: dockercontainer.Resources{
- CgroupParent: runner.setCgroupParent,
- NanoCPUs: int64(runner.Container.RuntimeConstraints.VCPUs) * 1000000000,
- Memory: maxRAM, // RAM
- MemorySwap: maxRAM, // RAM+swap
- KernelMemory: maxRAM, // kernel portion
- },
+ if mnt, ok := runner.Container.Mounts["stderr"]; ok {
+ f, err := runner.getStdoutFile(mnt.Path)
+ if err != nil {
+ return err
+ }
+ stderr = f
+ } else if w, err := runner.NewLogWriter("stderr"); err != nil {
+ return err
+ } else {
+ stderr = NewThrottledLogger(w)
}
+ env := runner.Container.Environment
+ enableNetwork := runner.enableNetwork == "always"
if runner.Container.RuntimeConstraints.API {
+ enableNetwork = true
tok, err := runner.ContainerToken()
if err != nil {
return err
}
- runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
- "ARVADOS_API_TOKEN="+tok,
- "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
- "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
- )
- runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
- } else {
- if runner.enableNetwork == "always" {
- runner.HostConfig.NetworkMode = dockercontainer.NetworkMode(runner.networkMode)
- } else {
- runner.HostConfig.NetworkMode = dockercontainer.NetworkMode("none")
- }
- }
-
- _, stdinUsed := runner.Container.Mounts["stdin"]
- runner.ContainerConfig.OpenStdin = stdinUsed
- runner.ContainerConfig.StdinOnce = stdinUsed
- runner.ContainerConfig.AttachStdin = stdinUsed
- runner.ContainerConfig.AttachStdout = true
- runner.ContainerConfig.AttachStderr = true
-
- createdBody, err := runner.Docker.ContainerCreate(context.TODO(), &runner.ContainerConfig, &runner.HostConfig, nil, runner.Container.UUID)
- if err != nil {
- return fmt.Errorf("While creating container: %v", err)
- }
-
- runner.ContainerID = createdBody.ID
-
- return runner.AttachStreams()
+ env = map[string]string{}
+ for k, v := range runner.Container.Environment {
+ env[k] = v
+ }
+ env["ARVADOS_API_TOKEN"] = tok
+ env["ARVADOS_API_HOST"] = os.Getenv("ARVADOS_API_HOST")
+ env["ARVADOS_API_HOST_INSECURE"] = os.Getenv("ARVADOS_API_HOST_INSECURE")
+ }
+ workdir := runner.Container.Cwd
+ if workdir == "." {
+ // both "" and "." mean default
+ workdir = ""
+ }
+
+ return runner.executor.Create(containerSpec{
+ Image: imageID,
+ VCPUs: runner.Container.RuntimeConstraints.VCPUs,
+ RAM: runner.Container.RuntimeConstraints.RAM,
+ WorkingDir: workdir,
+ Env: env,
+ BindMounts: bindmounts,
+ Command: runner.Container.Command,
+ EnableNetwork: enableNetwork,
+ NetworkMode: runner.networkMode,
+ CgroupParent: runner.setCgroupParent,
+ Stdin: stdin,
+ Stdout: stdout,
+ Stderr: stderr,
+ })
}
// StartContainer starts the docker container created by CreateContainer.
func (runner *ContainerRunner) StartContainer() error {
- runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
+ runner.CrunchLog.Printf("Starting container")
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if runner.cCancelled {
return ErrCancelled
}
- err := runner.Docker.ContainerStart(context.TODO(), runner.ContainerID,
- dockertypes.ContainerStartOptions{})
+ err := runner.executor.Start()
if err != nil {
var advice string
if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
@@ -1153,71 +986,39 @@ func (runner *ContainerRunner) StartContainer() error {
// WaitFinish waits for the container to terminate, capture the exit code, and
// close the stdout/stderr logging.
func (runner *ContainerRunner) WaitFinish() error {
- var runTimeExceeded <-chan time.Time
runner.CrunchLog.Print("Waiting for container to finish")
-
- waitOk, waitErr := runner.Docker.ContainerWait(context.TODO(), runner.ContainerID, dockercontainer.WaitConditionNotRunning)
- arvMountExit := runner.ArvMountExit
- if timeout := runner.Container.SchedulingParameters.MaxRunTime; timeout > 0 {
- runTimeExceeded = time.After(time.Duration(timeout) * time.Second)
+ var timeout <-chan time.Time
+ if s := runner.Container.SchedulingParameters.MaxRunTime; s > 0 {
+ timeout = time.After(time.Duration(s) * time.Second)
}
-
- containerGone := make(chan struct{})
+ ctx, cancel := context.WithCancel(context.Background())
+ defer cancel()
go func() {
- defer close(containerGone)
- if runner.containerWatchdogInterval < 1 {
- runner.containerWatchdogInterval = time.Minute
- }
- for range time.NewTicker(runner.containerWatchdogInterval).C {
- ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(runner.containerWatchdogInterval))
- ctr, err := runner.Docker.ContainerInspect(ctx, runner.ContainerID)
- cancel()
- runner.cStateLock.Lock()
- done := runner.cRemoved || runner.ExitCode != nil
- runner.cStateLock.Unlock()
- if done {
- return
- } else if err != nil {
- runner.CrunchLog.Printf("Error inspecting container: %s", err)
- runner.checkBrokenNode(err)
- return
- } else if ctr.State == nil || !(ctr.State.Running || ctr.State.Status == "created") {
- runner.CrunchLog.Printf("Container is not running: State=%v", ctr.State)
- return
- }
- }
- }()
-
- for {
select {
- case waitBody := <-waitOk:
- runner.CrunchLog.Printf("Container exited with code: %v", waitBody.StatusCode)
- code := int(waitBody.StatusCode)
- runner.ExitCode = &code
-
- // wait for stdout/stderr to complete
- <-runner.loggingDone
- return nil
-
- case err := <-waitErr:
- return fmt.Errorf("container wait: %v", err)
-
- case <-arvMountExit:
- runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
- runner.stop(nil)
- // arvMountExit will always be ready now that
- // it's closed, but that doesn't interest us.
- arvMountExit = nil
-
- case <-runTimeExceeded:
+ case <-timeout:
runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
runner.stop(nil)
- runTimeExceeded = nil
+ case <-runner.ArvMountExit:
+ runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
+ runner.stop(nil)
+ case <-ctx.Done():
+ }
+ }()
+ exitcode, err := runner.executor.Wait(ctx)
+ if err != nil {
+ runner.checkBrokenNode(err)
+ return err
+ }
+ runner.ExitCode = &exitcode
- case <-containerGone:
- return errors.New("docker client never returned status")
+ if runner.statReporter != nil {
+ runner.statReporter.Stop()
+ err = runner.statLogger.Close()
+ if err != nil {
+ runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
}
}
+ return nil
}
func (runner *ContainerRunner) updateLogs() {
@@ -1270,7 +1071,7 @@ func (runner *ContainerRunner) updateLogs() {
// CaptureOutput saves data from the container's output directory if
// needed, and updates the container output accordingly.
-func (runner *ContainerRunner) CaptureOutput() error {
+func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) error {
if runner.Container.RuntimeConstraints.API {
// Output may have been set directly by the container, so
// refresh the container record to check.
@@ -1292,7 +1093,7 @@ func (runner *ContainerRunner) CaptureOutput() error {
keepClient: runner.ContainerKeepClient,
hostOutputDir: runner.HostOutputDir,
ctrOutputDir: runner.Container.OutputPath,
- binds: runner.Binds,
+ bindmounts: bindmounts,
mounts: runner.Container.Mounts,
secretMounts: runner.SecretMounts,
logger: runner.CrunchLog,
@@ -1568,6 +1369,7 @@ func (runner *ContainerRunner) Run() (err error) {
return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
}
+ var bindmounts map[string]bindmount
defer func() {
// checkErr prints e (unless it's nil) and sets err to
// e (unless err is already non-nil). Thus, if err
@@ -1602,7 +1404,9 @@ func (runner *ContainerRunner) Run() (err error) {
// capture partial output and write logs
}
- checkErr("CaptureOutput", runner.CaptureOutput())
+ if bindmounts != nil {
+ checkErr("CaptureOutput", runner.CaptureOutput(bindmounts))
+ }
checkErr("stopHoststat", runner.stopHoststat())
checkErr("CommitLogs", runner.CommitLogs())
checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
@@ -1614,8 +1418,16 @@ func (runner *ContainerRunner) Run() (err error) {
return
}
+ // set up FUSE mount and binds
+ bindmounts, err = runner.SetupMounts()
+ if err != nil {
+ runner.finalState = "Cancelled"
+ err = fmt.Errorf("While setting up mounts: %v", err)
+ return
+ }
+
// check for and/or load image
- err = runner.LoadImage()
+ imageID, err := runner.LoadImage()
if err != nil {
if !runner.checkBrokenNode(err) {
// Failed to load image but not due to a "broken node"
@@ -1626,15 +1438,7 @@ func (runner *ContainerRunner) Run() (err error) {
return
}
- // set up FUSE mount and binds
- err = runner.SetupMounts()
- if err != nil {
- runner.finalState = "Cancelled"
- err = fmt.Errorf("While setting up mounts: %v", err)
- return
- }
-
- err = runner.CreateContainer()
+ err = runner.CreateContainer(imageID, bindmounts)
if err != nil {
return
}
@@ -1727,14 +1531,12 @@ func (runner *ContainerRunner) fetchContainerRecord() error {
func NewContainerRunner(dispatcherClient *arvados.Client,
dispatcherArvClient IArvadosClient,
dispatcherKeepClient IKeepClient,
- docker ThinDockerClient,
containerUUID string) (*ContainerRunner, error) {
cr := &ContainerRunner{
dispatcherClient: dispatcherClient,
DispatcherArvClient: dispatcherArvClient,
DispatcherKeepClient: dispatcherKeepClient,
- Docker: docker,
}
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
@@ -1784,15 +1586,10 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
- enableNetwork := flags.String("container-enable-networking", "default",
- `Specify if networking should be enabled for container. One of 'default', 'always':
- default: only enable networking if container requests it.
- always: containers always have networking enabled
- `)
- networkMode := flags.String("container-network-mode", "default",
- `Set networking mode for container. Corresponds to Docker network mode (--net).
- `)
+ enableNetwork := flags.String("container-enable-networking", "default", "enable networking \"always\" (for all containers) or \"default\" (for containers that request it)")
+ networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
+ runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
ignoreDetachFlag := false
@@ -1825,18 +1622,18 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
}
}
- containerID := flags.Arg(0)
+ containerUUID := flags.Arg(0)
switch {
case *detach && !ignoreDetachFlag:
- return Detach(containerID, prog, args, os.Stdout, os.Stderr)
+ return Detach(containerUUID, prog, args, os.Stdout, os.Stderr)
case *kill >= 0:
- return KillProcess(containerID, syscall.Signal(*kill), os.Stdout, os.Stderr)
+ return KillProcess(containerUUID, syscall.Signal(*kill), os.Stdout, os.Stderr)
case *list:
return ListProcesses(os.Stdout, os.Stderr)
}
- if containerID == "" {
+ if containerUUID == "" {
log.Printf("usage: %s [options] UUID", prog)
return 1
}
@@ -1850,45 +1647,60 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
- log.Printf("%s: %v", containerID, err)
+ log.Printf("%s: %v", containerUUID, err)
return 1
}
api.Retries = 8
kc, kcerr := keepclient.MakeKeepClient(api)
if kcerr != nil {
- log.Printf("%s: %v", containerID, kcerr)
+ log.Printf("%s: %v", containerUUID, kcerr)
return 1
}
kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
kc.Retries = 4
- // API version 1.21 corresponds to Docker 1.9, which is currently the
- // minimum version we want to support.
- docker, dockererr := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
-
- cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, docker, containerID)
+ cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, containerUUID)
if err != nil {
log.Print(err)
return 1
}
- if dockererr != nil {
- cr.CrunchLog.Printf("%s: %v", containerID, dockererr)
- cr.checkBrokenNode(dockererr)
+
+ switch *runtimeEngine {
+ case "docker":
+ cr.executor, err = newDockerExecutor(containerUUID, cr.CrunchLog.Printf, cr.containerWatchdogInterval)
+ case "singularity":
+ cr.executor, err = newSingularityExecutor(cr.CrunchLog.Printf)
+ default:
+ cr.CrunchLog.Printf("%s: unsupported RuntimeEngine %q", containerUUID, *runtimeEngine)
cr.CrunchLog.Close()
return 1
}
-
- cr.gateway = Gateway{
- Address: os.Getenv("GatewayAddress"),
- AuthSecret: os.Getenv("GatewayAuthSecret"),
- ContainerUUID: containerID,
- DockerContainerID: &cr.ContainerID,
- Log: cr.CrunchLog,
- ContainerIPAddress: dockerContainerIPAddress(&cr.ContainerID),
+ if err != nil {
+ cr.CrunchLog.Printf("%s: %v", containerUUID, err)
+ cr.checkBrokenNode(err)
+ cr.CrunchLog.Close()
+ return 1
}
+ defer cr.executor.Close()
+
+ gwAuthSecret := os.Getenv("GatewayAuthSecret")
os.Unsetenv("GatewayAuthSecret")
- if cr.gateway.Address != "" {
+ if gwAuthSecret == "" {
+ // not safe to run a gateway service without an auth
+ // secret
+ } else if gwListen := os.Getenv("GatewayAddress"); gwListen == "" {
+ // dispatcher did not tell us which external IP
+ // address to advertise --> no gateway service
+ } else if de, ok := cr.executor.(*dockerExecutor); ok {
+ cr.gateway = Gateway{
+ Address: gwListen,
+ AuthSecret: gwAuthSecret,
+ ContainerUUID: containerUUID,
+ DockerContainerID: &de.containerID,
+ Log: cr.CrunchLog,
+ ContainerIPAddress: dockerContainerIPAddress(&de.containerID),
+ }
err = cr.gateway.Start()
if err != nil {
log.Printf("error starting gateway server: %s", err)
@@ -1896,9 +1708,9 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
}
}
- parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerID+".")
+ parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerUUID+".")
if tmperr != nil {
- log.Printf("%s: %v", containerID, tmperr)
+ log.Printf("%s: %v", containerUUID, tmperr)
return 1
}
@@ -1932,7 +1744,7 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
}
if runerr != nil {
- log.Printf("%s: %v", containerID, runerr)
+ log.Printf("%s: %v", containerUUID, runerr)
return 1
}
return 0
diff --git a/lib/crunchrun/crunchrun_test.go b/lib/crunchrun/crunchrun_test.go
index dbdaa6293..249d7f1bd 100644
--- a/lib/crunchrun/crunchrun_test.go
+++ b/lib/crunchrun/crunchrun_test.go
@@ -5,7 +5,6 @@
package crunchrun
import (
- "bufio"
"bytes"
"crypto/md5"
"encoding/json"
@@ -13,11 +12,10 @@ import (
"fmt"
"io"
"io/ioutil"
- "net"
"os"
"os/exec"
+ "regexp"
"runtime/pprof"
- "sort"
"strings"
"sync"
"syscall"
@@ -30,9 +28,6 @@ import (
"git.arvados.org/arvados.git/sdk/go/manifest"
"golang.org/x/net/context"
- dockertypes "github.com/docker/docker/api/types"
- dockercontainer "github.com/docker/docker/api/types/container"
- dockernetwork "github.com/docker/docker/api/types/network"
. "gopkg.in/check.v1"
)
@@ -41,18 +36,43 @@ func TestCrunchExec(t *testing.T) {
TestingT(t)
}
-// Gocheck boilerplate
var _ = Suite(&TestSuite{})
type TestSuite struct {
- client *arvados.Client
- docker *TestDockerClient
- runner *ContainerRunner
+ client *arvados.Client
+ api *ArvTestClient
+ runner *ContainerRunner
+ executor *stubExecutor
+ keepmount string
}
func (s *TestSuite) SetUpTest(c *C) {
+ *brokenNodeHook = ""
s.client = arvados.NewClientFromEnv()
- s.docker = NewTestDockerClient()
+ s.executor = &stubExecutor{}
+ var err error
+ s.api = &ArvTestClient{}
+ s.runner, err = NewContainerRunner(s.client, s.api, &KeepTestClient{}, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ c.Assert(err, IsNil)
+ s.runner.executor = s.executor
+ s.runner.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
+ return s.api, &KeepTestClient{}, s.client, nil
+ }
+ s.runner.RunArvMount = func(cmd []string, tok string) (*exec.Cmd, error) {
+ s.runner.ArvMountPoint = s.keepmount
+ return nil, nil
+ }
+ s.keepmount = c.MkDir()
+ err = os.Mkdir(s.keepmount+"/by_id", 0755)
+ c.Assert(err, IsNil)
+ err = os.Mkdir(s.keepmount+"/by_id/"+arvadostest.DockerImage112PDH, 0755)
+ c.Assert(err, IsNil)
+ err = ioutil.WriteFile(s.keepmount+"/by_id/"+arvadostest.DockerImage112PDH+"/"+arvadostest.DockerImage112Filename, []byte("#notarealtarball"), 0644)
+ err = os.Mkdir(s.keepmount+"/by_id/"+fakeInputCollectionPDH, 0755)
+ c.Assert(err, IsNil)
+ err = ioutil.WriteFile(s.keepmount+"/by_id/"+fakeInputCollectionPDH+"/input.json", []byte(`{"input":true}`), 0644)
+ c.Assert(err, IsNil)
+ s.runner.ArvMountPoint = s.keepmount
}
type ArvTestClient struct {
@@ -72,6 +92,38 @@ type KeepTestClient struct {
Content []byte
}
+type stubExecutor struct {
+ imageLoaded bool
+ loaded string
+ loadErr error
+ exitCode int
+ createErr error
+ created containerSpec
+ startErr error
+ waitSleep time.Duration
+ waitErr error
+ stopErr error
+ stopped bool
+ closed bool
+ runFunc func()
+ exit chan int
+}
+
+func (e *stubExecutor) ImageLoaded(imageID string) bool { return e.imageLoaded }
+func (e *stubExecutor) LoadImage(filename string) error { e.loaded = filename; return e.loadErr }
+func (e *stubExecutor) Create(spec containerSpec) error { e.created = spec; return e.createErr }
+func (e *stubExecutor) Start() error { e.exit = make(chan int, 1); go e.runFunc(); return e.startErr }
+func (e *stubExecutor) CgroupID() string { return "cgroupid" }
+func (e *stubExecutor) Stop() error { e.stopped = true; go func() { e.exit <- -1 }(); return e.stopErr }
+func (e *stubExecutor) Close() { e.closed = true }
+func (e *stubExecutor) Wait(context.Context) (int, error) {
+ defer e.created.Stdout.Close()
+ defer e.created.Stderr.Close()
+ return <-e.exit, e.waitErr
+}
+
+const fakeInputCollectionPDH = "ffffffffaaaaaaaa88888888eeeeeeee+1234"
+
var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0 at 569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
var hwImageID = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
@@ -92,129 +144,6 @@ var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
-type TestDockerClient struct {
- imageLoaded string
- logReader io.ReadCloser
- logWriter io.WriteCloser
- fn func(t *TestDockerClient)
- exitCode int
- stop chan bool
- cwd string
- env []string
- api *ArvTestClient
- realTemp string
- calledWait bool
- ctrExited bool
-}
-
-func NewTestDockerClient() *TestDockerClient {
- t := &TestDockerClient{}
- t.logReader, t.logWriter = io.Pipe()
- t.stop = make(chan bool, 1)
- t.cwd = "/"
- return t
-}
-
-type MockConn struct {
- net.Conn
-}
-
-func (m *MockConn) Write(b []byte) (int, error) {
- return len(b), nil
-}
-
-func NewMockConn() *MockConn {
- c := &MockConn{}
- return c
-}
-
-func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
- return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
-}
-
-func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
- if config.WorkingDir != "" {
- t.cwd = config.WorkingDir
- }
- t.env = config.Env
- return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
-}
-
-func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
- if t.exitCode == 3 {
- return errors.New(`Error response from daemon: oci runtime error: container_linux.go:247: starting container process caused "process_linux.go:359: container init caused \"rootfs_linux.go:54: mounting \\\"/tmp/keep453790790/by_id/99999999999999999999999999999999+99999/myGenome\\\" to rootfs \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged\\\" at \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged/keep/99999999999999999999999999999999+99999/myGenome\\\" caused \\\"no such file or directory\\\"\""`)
- }
- if t.exitCode == 4 {
- return errors.New(`panic: standard_init_linux.go:175: exec user process caused "no such file or directory"`)
- }
- if t.exitCode == 5 {
- return errors.New(`Error response from daemon: Cannot start container 41f26cbc43bcc1280f4323efb1830a394ba8660c9d1c2b564ba42bf7f7694845: [8] System error: no such file or directory`)
- }
- if t.exitCode == 6 {
- return errors.New(`Error response from daemon: Cannot start container 58099cd76c834f3dc2a4fb76c8028f049ae6d4fdf0ec373e1f2cfea030670c2d: [8] System error: exec: "foobar": executable file not found in $PATH`)
- }
-
- if container == "abcde" {
- // t.fn gets executed in ContainerWait
- return nil
- }
- return errors.New("Invalid container id")
-}
-
-func (t *TestDockerClient) ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error {
- t.stop <- true
- return nil
-}
-
-func (t *TestDockerClient) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
- t.calledWait = true
- body := make(chan dockercontainer.ContainerWaitOKBody, 1)
- err := make(chan error)
- go func() {
- t.fn(t)
- body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.exitCode)}
- }()
- return body, err
-}
-
-func (t *TestDockerClient) ContainerInspect(ctx context.Context, id string) (c dockertypes.ContainerJSON, err error) {
- c.ContainerJSONBase = &dockertypes.ContainerJSONBase{}
- c.ID = "abcde"
- if t.ctrExited {
- c.State = &dockertypes.ContainerState{Status: "exited", Dead: true}
- } else {
- c.State = &dockertypes.ContainerState{Status: "running", Pid: 1234, Running: true}
- }
- return
-}
-
-func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
- if t.exitCode == 2 {
- return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
- }
-
- if t.imageLoaded == image {
- return dockertypes.ImageInspect{}, nil, nil
- }
- return dockertypes.ImageInspect{}, nil, errors.New("")
-}
-
-func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
- if t.exitCode == 2 {
- return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
- }
- _, err := io.Copy(ioutil.Discard, input)
- if err != nil {
- return dockertypes.ImageLoadResponse{}, err
- }
- t.imageLoaded = hwImageID
- return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
-}
-
-func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
- return nil, nil
-}
-
func (client *ArvTestClient) Create(resourceType string,
parameters arvadosclient.Dict,
output interface{}) error {
@@ -287,7 +216,7 @@ func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
} else {
j = []byte(`{
"command": ["sleep", "1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"}, "/json": {"kind": "json", "content": {"number": 123456789123456789}}},
@@ -438,49 +367,45 @@ func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename s
}
func (s *TestSuite) TestLoadImage(c *C) {
- cr, err := NewContainerRunner(s.client, &ArvTestClient{},
- &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
-
- kc := &KeepTestClient{}
- defer kc.Close()
- cr.ContainerArvClient = &ArvTestClient{}
- cr.ContainerKeepClient = kc
-
- _, err = cr.Docker.ImageRemove(nil, hwImageID, dockertypes.ImageRemoveOptions{})
- c.Check(err, IsNil)
-
- _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageID)
- c.Check(err, NotNil)
-
- cr.Container.ContainerImage = hwPDH
-
- // (1) Test loading image from keep
- c.Check(kc.Called, Equals, false)
- c.Check(cr.ContainerConfig.Image, Equals, "")
-
- err = cr.LoadImage()
-
- c.Check(err, IsNil)
- defer func() {
- cr.Docker.ImageRemove(nil, hwImageID, dockertypes.ImageRemoveOptions{})
- }()
+ s.runner.Container.ContainerImage = arvadostest.DockerImage112PDH
+ s.runner.Container.Mounts = map[string]arvados.Mount{
+ "/out": {Kind: "tmp", Writable: true},
+ }
+ s.runner.Container.OutputPath = "/out"
- c.Check(kc.Called, Equals, true)
- c.Check(cr.ContainerConfig.Image, Equals, hwImageID)
+ _, err := s.runner.SetupMounts()
+ c.Assert(err, IsNil)
- _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageID)
+ imageID, err := s.runner.LoadImage()
c.Check(err, IsNil)
-
- // (2) Test using image that's already loaded
- kc.Called = false
- cr.ContainerConfig.Image = ""
-
- err = cr.LoadImage()
+ c.Check(s.executor.loaded, Matches, ".*"+regexp.QuoteMeta(arvadostest.DockerImage112Filename))
+ c.Check(imageID, Equals, strings.TrimSuffix(arvadostest.DockerImage112Filename, ".tar"))
+
+ s.runner.Container.ContainerImage = arvadostest.DockerImage112PDH
+ s.executor.imageLoaded = false
+ s.executor.loaded = ""
+ s.executor.loadErr = errors.New("bork")
+ imageID, err = s.runner.LoadImage()
+ c.Check(err, ErrorMatches, ".*bork")
+ c.Check(s.executor.loaded, Matches, ".*"+regexp.QuoteMeta(arvadostest.DockerImage112Filename))
+
+ s.runner.Container.ContainerImage = fakeInputCollectionPDH
+ s.executor.imageLoaded = false
+ s.executor.loaded = ""
+ s.executor.loadErr = nil
+ imageID, err = s.runner.LoadImage()
+ c.Check(err, ErrorMatches, "image collection does not include a \\.tar image file")
+ c.Check(s.executor.loaded, Equals, "")
+
+ // if executor reports image is already loaded, LoadImage should not be called
+ s.runner.Container.ContainerImage = arvadostest.DockerImage112PDH
+ s.executor.imageLoaded = true
+ s.executor.loaded = ""
+ s.executor.loadErr = nil
+ imageID, err = s.runner.LoadImage()
c.Check(err, IsNil)
- c.Check(kc.Called, Equals, false)
- c.Check(cr.ContainerConfig.Image, Equals, hwImageID)
-
+ c.Check(s.executor.loaded, Equals, "")
+ c.Check(imageID, Equals, strings.TrimSuffix(arvadostest.DockerImage112Filename, ".tar"))
}
type ArvErrorTestClient struct{}
@@ -555,65 +480,6 @@ func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename
return ErrorReader{}, nil
}
-func (s *TestSuite) TestLoadImageArvError(c *C) {
- // (1) Arvados error
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err := NewContainerRunner(s.client, &ArvErrorTestClient{}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
-
- cr.ContainerArvClient = &ArvErrorTestClient{}
- cr.ContainerKeepClient = &KeepTestClient{}
-
- cr.Container.ContainerImage = hwPDH
-
- err = cr.LoadImage()
- c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
-}
-
-func (s *TestSuite) TestLoadImageKeepError(c *C) {
- // (2) Keep error
- kc := &KeepErrorTestClient{}
- cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
-
- cr.ContainerArvClient = &ArvTestClient{}
- cr.ContainerKeepClient = &KeepErrorTestClient{}
-
- cr.Container.ContainerImage = hwPDH
-
- err = cr.LoadImage()
- c.Assert(err, NotNil)
- c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
-}
-
-func (s *TestSuite) TestLoadImageCollectionError(c *C) {
- // (3) Collection doesn't contain image
- kc := &KeepReadErrorTestClient{}
- cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
- cr.Container.ContainerImage = otherPDH
-
- cr.ContainerArvClient = &ArvTestClient{}
- cr.ContainerKeepClient = &KeepReadErrorTestClient{}
-
- err = cr.LoadImage()
- c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
-}
-
-func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
- // (4) Collection doesn't contain image
- kc := &KeepReadErrorTestClient{}
- cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
- cr.Container.ContainerImage = hwPDH
- cr.ContainerArvClient = &ArvTestClient{}
- cr.ContainerKeepClient = &KeepReadErrorTestClient{}
-
- err = cr.LoadImage()
- c.Check(err, NotNil)
-}
-
type ClosableBuffer struct {
bytes.Buffer
}
@@ -647,35 +513,31 @@ func dockerLog(fd byte, msg string) []byte {
}
func (s *TestSuite) TestRunContainer(c *C) {
- s.docker.fn = func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "Hello world\n"))
- t.logWriter.Close()
+ s.executor.runFunc = func() {
+ fmt.Fprintf(s.executor.created.Stdout, "Hello world\n")
+ s.executor.created.Stdout.Close()
+ s.executor.created.Stderr.Close()
+ s.executor.exit <- 0
}
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
-
- cr.ContainerArvClient = &ArvTestClient{}
- cr.ContainerKeepClient = &KeepTestClient{}
var logs TestLogs
- cr.NewLogWriter = logs.NewTestLoggingWriter
- cr.Container.ContainerImage = hwPDH
- cr.Container.Command = []string{"./hw"}
- err = cr.LoadImage()
- c.Check(err, IsNil)
+ s.runner.NewLogWriter = logs.NewTestLoggingWriter
+ s.runner.Container.ContainerImage = arvadostest.DockerImage112PDH
+ s.runner.Container.Command = []string{"./hw"}
- err = cr.CreateContainer()
- c.Check(err, IsNil)
+ imageID, err := s.runner.LoadImage()
+ c.Assert(err, IsNil)
- err = cr.StartContainer()
- c.Check(err, IsNil)
+ err = s.runner.CreateContainer(imageID, nil)
+ c.Assert(err, IsNil)
- err = cr.WaitFinish()
- c.Check(err, IsNil)
+ err = s.runner.StartContainer()
+ c.Assert(err, IsNil)
+
+ err = s.runner.WaitFinish()
+ c.Assert(err, IsNil)
- c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
+ c.Check(logs.Stdout.String(), Matches, ".*Hello world\n")
c.Check(logs.Stderr.String(), Equals, "")
}
@@ -683,7 +545,7 @@ func (s *TestSuite) TestCommitLogs(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
@@ -705,7 +567,7 @@ func (s *TestSuite) TestUpdateContainerRunning(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
err = cr.UpdateContainerRunning()
@@ -718,7 +580,7 @@ func (s *TestSuite) TestUpdateContainerComplete(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.LogsPDH = new(string)
@@ -740,7 +602,7 @@ func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.cCancelled = true
cr.finalState = "Cancelled"
@@ -755,10 +617,10 @@ func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
// Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
// dress rehearsal of the Run() function, starting from a JSON container record.
-func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
- rec := arvados.Container{}
- err := json.Unmarshal([]byte(record), &rec)
- c.Check(err, IsNil)
+func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func()) (*ArvTestClient, *ContainerRunner, string) {
+ err := json.Unmarshal([]byte(record), &s.api.Container)
+ c.Assert(err, IsNil)
+ initialState := s.api.Container.State
var sm struct {
SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
@@ -766,33 +628,22 @@ func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exi
err = json.Unmarshal([]byte(record), &sm)
c.Check(err, IsNil)
secretMounts, err := json.Marshal(sm)
- c.Logf("%s %q", sm, secretMounts)
- c.Check(err, IsNil)
-
- s.docker.exitCode = exitCode
- s.docker.fn = fn
- s.docker.ImageRemove(nil, hwImageID, dockertypes.ImageRemoveOptions{})
-
- api = &ArvTestClient{Container: rec}
- s.docker.api = api
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
- s.runner = cr
- cr.statInterval = 100 * time.Millisecond
- cr.containerWatchdogInterval = time.Second
- am := &ArvMountCmdLine{}
- cr.RunArvMount = am.ArvMountTest
+ c.Logf("SecretMounts decoded %v json %q", sm, secretMounts)
- realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
- c.Assert(err, IsNil)
- defer os.RemoveAll(realTemp)
+ s.executor.runFunc = func() {
+ fn()
+ s.executor.exit <- exitCode
+ }
- s.docker.realTemp = realTemp
+ s.runner.statInterval = 100 * time.Millisecond
+ s.runner.containerWatchdogInterval = time.Second
+ am := &ArvMountCmdLine{}
+ s.runner.RunArvMount = am.ArvMountTest
+ realTemp := c.MkDir()
tempcount := 0
- cr.MkTempDir = func(_ string, prefix string) (string, error) {
+ s.runner.MkTempDir = func(_, prefix string) (string, error) {
tempcount++
d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
err := os.Mkdir(d, os.ModePerm)
@@ -802,73 +653,80 @@ func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exi
}
return d, err
}
- cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
+ s.runner.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
return &ArvTestClient{secretMounts: secretMounts}, &KeepTestClient{}, nil, nil
}
if extraMounts != nil && len(extraMounts) > 0 {
- err := cr.SetupArvMountPoint("keep")
+ err := s.runner.SetupArvMountPoint("keep")
c.Check(err, IsNil)
for _, m := range extraMounts {
- os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
+ os.MkdirAll(s.runner.ArvMountPoint+"/by_id/"+m, os.ModePerm)
}
}
- err = cr.Run()
- if api.CalledWith("container.state", "Complete") != nil {
+ err = s.runner.Run()
+ if s.api.CalledWith("container.state", "Complete") != nil {
c.Check(err, IsNil)
}
- if exitCode != 2 {
- c.Check(api.WasSetRunning, Equals, true)
+ if s.executor.loadErr == nil && s.executor.createErr == nil && initialState != "Running" {
+ c.Check(s.api.WasSetRunning, Equals, true)
var lastupdate arvadosclient.Dict
- for _, content := range api.Content {
+ for _, content := range s.api.Content {
if content["container"] != nil {
lastupdate = content["container"].(arvadosclient.Dict)
}
}
if lastupdate["log"] == nil {
- c.Errorf("no container update with non-nil log -- updates were: %v", api.Content)
+ c.Errorf("no container update with non-nil log -- updates were: %v", s.api.Content)
}
}
if err != nil {
- for k, v := range api.Logs {
+ for k, v := range s.api.Logs {
c.Log(k)
c.Log(v.String())
}
}
- return
+ return s.api, s.runner, realTemp
}
func (s *TestSuite) TestFullRunHello(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.runner.networkMode = "default"
+ s.fullRunHelper(c, `{
"command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
- "environment": {},
+ "environment": {"foo":"bar","baz":"waz"},
"mounts": {"/tmp": {"kind": "tmp"} },
"output_path": "/tmp",
"priority": 1,
- "runtime_constraints": {},
+ "runtime_constraints": {"vcpus":1,"ram":1000000},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
+}`, nil, 0, func() {
+ c.Check(s.executor.created.Command, DeepEquals, []string{"echo", "hello world"})
+ c.Check(s.executor.created.Image, Equals, "sha256:d8309758b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678")
+ c.Check(s.executor.created.Env, DeepEquals, map[string]string{"foo": "bar", "baz": "waz"})
+ c.Check(s.executor.created.VCPUs, Equals, 1)
+ c.Check(s.executor.created.RAM, Equals, int64(1000000))
+ c.Check(s.executor.created.NetworkMode, Equals, "default")
+ c.Check(s.executor.created.EnableNetwork, Equals, false)
+ fmt.Fprintln(s.executor.created.Stdout, "hello world")
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.Logs["stdout"].String(), Matches, ".*hello world\n")
}
func (s *TestSuite) TestRunAlreadyRunning(c *C) {
var ran bool
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "3"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -877,19 +735,18 @@ func (s *TestSuite) TestRunAlreadyRunning(c *C) {
"runtime_constraints": {},
"scheduling_parameters":{"max_run_time": 1},
"state": "Running"
-}`, nil, 2, func(t *TestDockerClient) {
+}`, nil, 2, func() {
ran = true
})
-
- c.Check(api.CalledWith("container.state", "Cancelled"), IsNil)
- c.Check(api.CalledWith("container.state", "Complete"), IsNil)
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), IsNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), IsNil)
c.Check(ran, Equals, false)
}
func (s *TestSuite) TestRunTimeExceeded(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "3"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -898,38 +755,35 @@ func (s *TestSuite) TestRunTimeExceeded(c *C) {
"runtime_constraints": {},
"scheduling_parameters":{"max_run_time": 1},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
+}`, nil, 0, func() {
time.Sleep(3 * time.Second)
- t.logWriter.Close()
})
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*maximum run time exceeded.*")
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*maximum run time exceeded.*")
}
func (s *TestSuite) TestContainerWaitFails(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "3"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"mounts": {"/tmp": {"kind": "tmp"} },
"output_path": "/tmp",
"priority": 1,
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.ctrExited = true
- time.Sleep(10 * time.Second)
- t.logWriter.Close()
+}`, nil, 0, func() {
+ s.executor.waitErr = errors.New("Container is not running")
})
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Container is not running.*")
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Container is not running.*")
}
func (s *TestSuite) TestCrunchstat(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -937,33 +791,32 @@ func (s *TestSuite) TestCrunchstat(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
- }`, nil, 0, func(t *TestDockerClient) {
+ }`, nil, 0, func() {
time.Sleep(time.Second)
- t.logWriter.Close()
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
// We didn't actually start a container, so crunchstat didn't
// find accounting files and therefore didn't log any stats.
// It should have logged a "can't find accounting files"
// message after one poll interval, though, so we can confirm
// it's alive:
- c.Assert(api.Logs["crunchstat"], NotNil)
- c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
+ c.Assert(s.api.Logs["crunchstat"], NotNil)
+ c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
// The "files never appeared" log assures us that we called
// (*crunchstat.Reporter)Stop(), and that we set it up with
// the correct container ID "abcde":
- c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
+ c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for cgroupid\n`)
}
func (s *TestSuite) TestNodeInfoLog(c *C) {
os.Setenv("SLURMD_NODENAME", "compute2")
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -972,22 +825,21 @@ func (s *TestSuite) TestNodeInfoLog(c *C) {
"runtime_constraints": {},
"state": "Locked"
}`, nil, 0,
- func(t *TestDockerClient) {
+ func() {
time.Sleep(time.Second)
- t.logWriter.Close()
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
- c.Assert(api.Logs["node"], NotNil)
- json := api.Logs["node"].String()
+ c.Assert(s.api.Logs["node"], NotNil)
+ json := s.api.Logs["node"].String()
c.Check(json, Matches, `(?ms).*"uuid": *"zzzzz-7ekkf-2z3mc76g2q73aio".*`)
c.Check(json, Matches, `(?ms).*"total_cpu_cores": *16.*`)
c.Check(json, Not(Matches), `(?ms).*"info":.*`)
- c.Assert(api.Logs["node-info"], NotNil)
- json = api.Logs["node-info"].String()
+ c.Assert(s.api.Logs["node-info"], NotNil)
+ json = s.api.Logs["node-info"].String()
c.Check(json, Matches, `(?ms).*Host Information.*`)
c.Check(json, Matches, `(?ms).*CPU Information.*`)
c.Check(json, Matches, `(?ms).*Memory Information.*`)
@@ -996,9 +848,9 @@ func (s *TestSuite) TestNodeInfoLog(c *C) {
}
func (s *TestSuite) TestContainerRecordLog(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["sleep", "1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1007,22 +859,21 @@ func (s *TestSuite) TestContainerRecordLog(c *C) {
"runtime_constraints": {},
"state": "Locked"
}`, nil, 0,
- func(t *TestDockerClient) {
+ func() {
time.Sleep(time.Second)
- t.logWriter.Close()
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
- c.Assert(api.Logs["container"], NotNil)
- c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
+ c.Assert(s.api.Logs["container"], NotNil)
+ c.Check(s.api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
}
func (s *TestSuite) TestFullRunStderr(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1030,25 +881,24 @@ func (s *TestSuite) TestFullRunStderr(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 1, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello\n"))
- t.logWriter.Write(dockerLog(2, "world\n"))
- t.logWriter.Close()
+}`, nil, 1, func() {
+ fmt.Fprintln(s.executor.created.Stdout, "hello")
+ fmt.Fprintln(s.executor.created.Stderr, "world")
})
- final := api.CalledWith("container.state", "Complete")
+ final := s.api.CalledWith("container.state", "Complete")
c.Assert(final, NotNil)
c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
- c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
+ c.Check(s.api.Logs["stdout"].String(), Matches, ".*hello\n")
+ c.Check(s.api.Logs["stderr"].String(), Matches, ".*world\n")
}
func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["pwd"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1056,21 +906,20 @@ func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
- t.logWriter.Close()
+}`, nil, 0, func() {
+ fmt.Fprintf(s.executor.created.Stdout, "workdir=%q", s.executor.created.WorkingDir)
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Log(api.Logs["stdout"])
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Log(s.api.Logs["stdout"])
+ c.Check(s.api.Logs["stdout"].String(), Matches, `.*workdir=""\n`)
}
func (s *TestSuite) TestFullRunSetCwd(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["pwd"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": "/bin",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1078,41 +927,37 @@ func (s *TestSuite) TestFullRunSetCwd(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
- t.logWriter.Close()
+}`, nil, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.WorkingDir)
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.Logs["stdout"].String(), Matches, ".*/bin\n")
}
func (s *TestSuite) TestStopOnSignal(c *C) {
- s.testStopContainer(c, func(cr *ContainerRunner) {
- go func() {
- for !s.docker.calledWait {
- time.Sleep(time.Millisecond)
- }
- cr.SigChan <- syscall.SIGINT
- }()
- })
+ s.executor.runFunc = func() {
+ s.executor.created.Stdout.Write([]byte("foo\n"))
+ s.runner.SigChan <- syscall.SIGINT
+ }
+ s.testStopContainer(c)
}
func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
- s.testStopContainer(c, func(cr *ContainerRunner) {
- cr.ArvMountExit = make(chan error)
- go func() {
- cr.ArvMountExit <- exec.Command("true").Run()
- close(cr.ArvMountExit)
- }()
- })
+ s.executor.runFunc = func() {
+ s.executor.created.Stdout.Write([]byte("foo\n"))
+ s.runner.ArvMountExit <- nil
+ close(s.runner.ArvMountExit)
+ }
+ s.runner.ArvMountExit = make(chan error)
+ s.testStopContainer(c)
}
-func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
+func (s *TestSuite) testStopContainer(c *C) {
record := `{
"command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1122,31 +967,17 @@ func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
"state": "Locked"
}`
- rec := arvados.Container{}
- err := json.Unmarshal([]byte(record), &rec)
- c.Check(err, IsNil)
-
- s.docker.fn = func(t *TestDockerClient) {
- <-t.stop
- t.logWriter.Write(dockerLog(1, "foo\n"))
- t.logWriter.Close()
- }
- s.docker.ImageRemove(nil, hwImageID, dockertypes.ImageRemoveOptions{})
-
- api := &ArvTestClient{Container: rec}
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ err := json.Unmarshal([]byte(record), &s.api.Container)
c.Assert(err, IsNil)
- cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
- cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
+
+ s.runner.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
+ s.runner.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
return &ArvTestClient{}, &KeepTestClient{}, nil, nil
}
- setup(cr)
done := make(chan error)
go func() {
- done <- cr.Run()
+ done <- s.runner.Run()
}()
select {
case <-time.After(20 * time.Second):
@@ -1155,20 +986,20 @@ func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
case err = <-done:
c.Check(err, IsNil)
}
- for k, v := range api.Logs {
+ for k, v := range s.api.Logs {
c.Log(k)
- c.Log(v.String())
+ c.Log(v.String(), "\n")
}
- c.Check(api.CalledWith("container.log", nil), NotNil)
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
+ c.Check(s.api.CalledWith("container.log", nil), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(s.api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
}
func (s *TestSuite) TestFullRunSetEnv(c *C) {
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1176,14 +1007,13 @@ func (s *TestSuite) TestFullRunSetEnv(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+}`, nil, 0, func() {
+ fmt.Fprintf(s.executor.created.Stdout, "%v", s.executor.created.Env)
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.Logs["stdout"].String(), Matches, `.*map\[FROBIZ:bilbo\]\n`)
}
type ArvMountCmdLine struct {
@@ -1206,27 +1036,17 @@ func stubCert(temp string) string {
}
func (s *TestSuite) TestSetupMounts(c *C) {
- api := &ArvTestClient{}
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- c.Assert(err, IsNil)
+ cr := s.runner
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
cr.ContainerArvClient = &ArvTestClient{}
cr.ContainerKeepClient = &KeepTestClient{}
- realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
- c.Assert(err, IsNil)
- certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
- c.Assert(err, IsNil)
+ realTemp := c.MkDir()
+ certTemp := c.MkDir()
stubCertPath := stubCert(certTemp)
-
cr.parentTemp = realTemp
- defer os.RemoveAll(realTemp)
- defer os.RemoveAll(certTemp)
-
i := 0
cr.MkTempDir = func(_ string, prefix string) (string, error) {
i++
@@ -1255,12 +1075,12 @@ func (s *TestSuite) TestSetupMounts(c *C) {
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.Container.OutputPath = "/tmp"
cr.statInterval = 5 * time.Second
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{"/tmp": {realTemp + "/tmp2", false}})
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1274,12 +1094,12 @@ func (s *TestSuite) TestSetupMounts(c *C) {
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.Container.OutputPath = "/out"
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{"/out": {realTemp + "/tmp2", false}, "/tmp": {realTemp + "/tmp3", false}})
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1293,12 +1113,12 @@ func (s *TestSuite) TestSetupMounts(c *C) {
cr.Container.OutputPath = "/tmp"
cr.Container.RuntimeConstraints.API = true
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{"/tmp": {realTemp + "/tmp2", false}, "/etc/arvados/ca-certificates.crt": {stubCertPath, true}})
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1316,12 +1136,12 @@ func (s *TestSuite) TestSetupMounts(c *C) {
os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{"/keeptmp": {realTemp + "/keep1/tmp0", false}})
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1339,14 +1159,15 @@ func (s *TestSuite) TestSetupMounts(c *C) {
os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- sort.StringSlice(cr.Binds).Sort()
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
- realTemp + "/keep1/tmp0:/keepout"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{
+ "/keepinp": {realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", true},
+ "/keepout": {realTemp + "/keep1/tmp0", false},
+ })
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1365,14 +1186,15 @@ func (s *TestSuite) TestSetupMounts(c *C) {
os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- sort.StringSlice(cr.Binds).Sort()
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
- realTemp + "/keep1/tmp0:/keepout"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{
+ "/keepinp": {realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", true},
+ "/keepout": {realTemp + "/keep1/tmp0", false},
+ })
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1391,10 +1213,11 @@ func (s *TestSuite) TestSetupMounts(c *C) {
cr.Container.Mounts = map[string]arvados.Mount{
"/mnt/test.json": {Kind: "json", Content: test.in},
}
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
- sort.StringSlice(cr.Binds).Sort()
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{
+ "/mnt/test.json": {realTemp + "/json2/mountdata.json", true},
+ })
content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
c.Check(err, IsNil)
c.Check(content, DeepEquals, []byte(test.out))
@@ -1416,13 +1239,14 @@ func (s *TestSuite) TestSetupMounts(c *C) {
cr.Container.Mounts = map[string]arvados.Mount{
"/mnt/test.txt": {Kind: "text", Content: test.in},
}
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
if test.out == "error" {
c.Check(err.Error(), Equals, "content for mount \"/mnt/test.txt\" must be a string")
} else {
c.Check(err, IsNil)
- sort.StringSlice(cr.Binds).Sort()
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/text2/mountdata.text:/mnt/test.txt:ro"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{
+ "/mnt/test.txt": {realTemp + "/text2/mountdata.text", true},
+ })
content, err := ioutil.ReadFile(realTemp + "/text2/mountdata.text")
c.Check(err, IsNil)
c.Check(content, DeepEquals, []byte(test.out))
@@ -1445,12 +1269,15 @@ func (s *TestSuite) TestSetupMounts(c *C) {
os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
"--read-write", "--crunchstat-interval=5",
"--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
+ c.Check(bindmounts, DeepEquals, map[string]bindmount{
+ "/tmp": {realTemp + "/tmp2", false},
+ "/tmp/foo": {realTemp + "/keep1/tmp0", true},
+ })
os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
@@ -1480,7 +1307,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
rf.Write([]byte("bar"))
rf.Close()
- err := cr.SetupMounts()
+ _, err := cr.SetupMounts()
c.Check(err, IsNil)
_, err = os.Stat(cr.HostOutputDir + "/foo")
c.Check(err, IsNil)
@@ -1502,7 +1329,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
}
cr.Container.OutputPath = "/tmp"
- err := cr.SetupMounts()
+ _, err := cr.SetupMounts()
c.Check(err, NotNil)
c.Check(err, ErrorMatches, `only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path.*`)
os.RemoveAll(cr.ArvMountPoint)
@@ -1519,7 +1346,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
"stdin": {Kind: "tmp"},
}
- err := cr.SetupMounts()
+ _, err := cr.SetupMounts()
c.Check(err, NotNil)
c.Check(err, ErrorMatches, `unsupported mount kind 'tmp' for stdin.*`)
os.RemoveAll(cr.ArvMountPoint)
@@ -1550,34 +1377,24 @@ func (s *TestSuite) TestSetupMounts(c *C) {
}
cr.Container.OutputPath = "/tmp"
- err := cr.SetupMounts()
+ bindmounts, err := cr.SetupMounts()
c.Check(err, IsNil)
- // dirMap[mountpoint] == tmpdir
- dirMap := make(map[string]string)
- for _, bind := range cr.Binds {
- tokens := strings.Split(bind, ":")
- dirMap[tokens[1]] = tokens[0]
-
- if cr.Container.Mounts[tokens[1]].Writable {
- c.Check(len(tokens), Equals, 2)
- } else {
- c.Check(len(tokens), Equals, 3)
- c.Check(tokens[2], Equals, "ro")
- }
+ for path, mount := range bindmounts {
+ c.Check(mount.ReadOnly, Equals, !cr.Container.Mounts[path].Writable, Commentf("%s %#v", path, mount))
}
- data, err := ioutil.ReadFile(dirMap["/tip"] + "/dir1/dir2/file with mode 0644")
+ data, err := ioutil.ReadFile(bindmounts["/tip"].HostPath + "/dir1/dir2/file with mode 0644")
c.Check(err, IsNil)
c.Check(string(data), Equals, "\000\001\002\003")
- _, err = ioutil.ReadFile(dirMap["/tip"] + "/file only on testbranch")
+ _, err = ioutil.ReadFile(bindmounts["/tip"].HostPath + "/file only on testbranch")
c.Check(err, FitsTypeOf, &os.PathError{})
c.Check(os.IsNotExist(err), Equals, true)
- data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/dir1/dir2/file with mode 0644")
+ data, err = ioutil.ReadFile(bindmounts["/non-tip"].HostPath + "/dir1/dir2/file with mode 0644")
c.Check(err, IsNil)
c.Check(string(data), Equals, "\000\001\002\003")
- data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/file only on testbranch")
+ data, err = ioutil.ReadFile(bindmounts["/non-tip"].HostPath + "/file only on testbranch")
c.Check(err, IsNil)
c.Check(string(data), Equals, "testfile\n")
@@ -1589,7 +1406,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
func (s *TestSuite) TestStdout(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
@@ -1599,38 +1416,25 @@ func (s *TestSuite) TestStdout(c *C) {
"state": "Locked"
}`
- api, cr, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ s.fullRunHelper(c, helperRecord, nil, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
}
// Used by the TestStdoutWithWrongPath*()
-func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
- rec := arvados.Container{}
- err = json.Unmarshal([]byte(record), &rec)
- c.Check(err, IsNil)
-
- s.docker.fn = fn
- s.docker.ImageRemove(nil, hwImageID, dockertypes.ImageRemoveOptions{})
-
- api = &ArvTestClient{Container: rec}
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func()) (*ArvTestClient, *ContainerRunner, error) {
+ err := json.Unmarshal([]byte(record), &s.api.Container)
c.Assert(err, IsNil)
- am := &ArvMountCmdLine{}
- cr.RunArvMount = am.ArvMountTest
- cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
- return &ArvTestClient{}, &KeepTestClient{}, nil, nil
+ s.executor.runFunc = fn
+ s.runner.RunArvMount = (&ArvMountCmdLine{}).ArvMountTest
+ s.runner.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
+ return s.api, &KeepTestClient{}, nil, nil
}
-
- err = cr.Run()
- return
+ return s.api, s.runner, s.runner.Run()
}
func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
@@ -1638,10 +1442,8 @@ func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
"output_path": "/tmp",
"state": "Locked"
-}`, func(t *TestDockerClient) {})
-
- c.Check(err, NotNil)
- c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
+}`, func() {})
+ c.Check(err, ErrorMatches, ".*Stdout path does not start with OutputPath.*")
}
func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
@@ -1649,10 +1451,8 @@ func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
"output_path": "/tmp",
"state": "Locked"
-}`, func(t *TestDockerClient) {})
-
- c.Check(err, NotNil)
- c.Check(strings.Contains(err.Error(), "unsupported mount kind 'tmp' for stdout"), Equals, true)
+}`, func() {})
+ c.Check(err, ErrorMatches, ".*unsupported mount kind 'tmp' for stdout.*")
}
func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
@@ -1660,18 +1460,14 @@ func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
"output_path": "/tmp",
"state": "Locked"
-}`, func(t *TestDockerClient) {})
-
- c.Check(err, NotNil)
- c.Check(strings.Contains(err.Error(), "unsupported mount kind 'collection' for stdout"), Equals, true)
+}`, func() {})
+ c.Check(err, ErrorMatches, ".*unsupported mount kind 'collection' for stdout.*")
}
func (s *TestSuite) TestFullRunWithAPI(c *C) {
- defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
- os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
- api, _, _ := s.fullRunHelper(c, `{
- "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ s.fullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "true $ARVADOS_API_HOST"],
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": "/bin",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1679,23 +1475,20 @@ func (s *TestSuite) TestFullRunWithAPI(c *C) {
"priority": 1,
"runtime_constraints": {"API": true},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
- t.logWriter.Close()
+}`, nil, 0, func() {
+ c.Check(s.executor.created.Env["ARVADOS_API_HOST"], Equals, os.Getenv("ARVADOS_API_HOST"))
+ s.executor.exit <- 3
})
-
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
- c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 3), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
}
func (s *TestSuite) TestFullRunSetOutput(c *C) {
defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
- api, _, _ := s.fullRunHelper(c, `{
+ s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": "/bin",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -1703,20 +1496,19 @@ func (s *TestSuite) TestFullRunSetOutput(c *C) {
"priority": 1,
"runtime_constraints": {"API": true},
"state": "Locked"
-}`, nil, 0, func(t *TestDockerClient) {
- t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
- t.logWriter.Close()
+}`, nil, 0, func() {
+ s.api.Container.Output = arvadostest.DockerImage112PDH
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.api.CalledWith("container.output", arvadostest.DockerImage112PDH), NotNil)
}
func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1735,20 +1527,19 @@ func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C
extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
- api, cr, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ s.fullRunHelper(c, helperRecord, extraMounts, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
}
func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1771,16 +1562,16 @@ func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
"a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
}
- api, runner, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ api, _, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
- c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
- realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
- realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
- realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
- realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
+ c.Check(s.executor.created.BindMounts, DeepEquals, map[string]bindmount{
+ "/tmp": {realtemp + "/tmp1", false},
+ "/tmp/foo/bar": {s.keepmount + "/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt", true},
+ "/tmp/foo/baz/sub2file2": {s.keepmount + "/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt", true},
+ "/tmp/foo/sub1": {s.keepmount + "/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1", true},
+ "/tmp/foo/sub1file2": {s.keepmount + "/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt", true},
})
c.Check(api.CalledWith("container.exit_code", 0), NotNil)
@@ -1806,7 +1597,7 @@ func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1824,14 +1615,13 @@ func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(
"b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
}
- api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ s.fullRunHelper(c, helperRecord, extraMounts, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- for _, v := range api.Content {
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range s.api.Content {
if v["collection"] != nil {
collection := v["collection"].(arvadosclient.Dict)
if strings.Index(collection["name"].(string), "output") == 0 {
@@ -1848,7 +1638,7 @@ func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(
func (s *TestSuite) TestOutputError(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1859,21 +1649,17 @@ func (s *TestSuite) TestOutputError(c *C) {
"runtime_constraints": {},
"state": "Locked"
}`
-
- extraMounts := []string{}
-
- api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
- t.logWriter.Close()
+ s.fullRunHelper(c, helperRecord, nil, 0, func() {
+ os.Symlink("/etc/hosts", s.runner.HostOutputDir+"/baz")
})
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
}
func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1891,9 +1677,8 @@ func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
"b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
}
- api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
c.Check(api.CalledWith("container.exit_code", 0), NotNil)
@@ -1913,7 +1698,7 @@ func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
@@ -1927,9 +1712,8 @@ func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
"state": "Locked"
}`
- api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
- t.logWriter.Close()
+ api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func() {
+ fmt.Fprintln(s.executor.created.Stdout, s.executor.created.Env["FROBIZ"])
})
c.Check(api.CalledWith("container.exit_code", 0), NotNil)
@@ -1949,7 +1733,7 @@ func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
func (s *TestSuite) TestStderrMount(c *C) {
api, cr, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello;exit 1"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"},
@@ -1959,10 +1743,9 @@ func (s *TestSuite) TestStderrMount(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 1, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello\n"))
- t.logWriter.Write(dockerLog(2, "oops\n"))
- t.logWriter.Close()
+}`, nil, 1, func() {
+ fmt.Fprintln(s.executor.created.Stdout, "hello")
+ fmt.Fprintln(s.executor.created.Stderr, "oops")
})
final := api.CalledWith("container.state", "Complete")
@@ -1974,131 +1757,37 @@ func (s *TestSuite) TestStderrMount(c *C) {
}
func (s *TestSuite) TestNumberRoundTrip(c *C) {
- kc := &KeepTestClient{}
- defer kc.Close()
- cr, err := NewContainerRunner(s.client, &ArvTestClient{callraw: true}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ s.api.callraw = true
+ err := s.runner.fetchContainerRecord()
c.Assert(err, IsNil)
- cr.fetchContainerRecord()
-
- jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
-
+ jsondata, err := json.Marshal(s.runner.Container.Mounts["/json"].Content)
+ c.Logf("%#v", s.runner.Container)
c.Check(err, IsNil)
c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
}
-func (s *TestSuite) TestFullBrokenDocker1(c *C) {
- tf, err := ioutil.TempFile("", "brokenNodeHook-")
- c.Assert(err, IsNil)
- defer os.Remove(tf.Name())
-
- tf.Write([]byte(`#!/bin/sh
-exec echo killme
-`))
- tf.Close()
- os.Chmod(tf.Name(), 0700)
-
- ech := tf.Name()
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
- "command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
- "cwd": ".",
- "environment": {},
- "mounts": {"/tmp": {"kind": "tmp"} },
- "output_path": "/tmp",
- "priority": 1,
- "runtime_constraints": {},
- "state": "Locked"
-}`, nil, 2, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Queued"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
-
-}
-
-func (s *TestSuite) TestFullBrokenDocker2(c *C) {
- ech := ""
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
- "command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
- "cwd": ".",
- "environment": {},
- "mounts": {"/tmp": {"kind": "tmp"} },
- "output_path": "/tmp",
- "priority": 1,
- "runtime_constraints": {},
- "state": "Locked"
-}`, nil, 2, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Queued"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
-}
-
-func (s *TestSuite) TestFullBrokenDocker3(c *C) {
- ech := ""
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
- "command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
- "cwd": ".",
- "environment": {},
- "mounts": {"/tmp": {"kind": "tmp"} },
- "output_path": "/tmp",
- "priority": 1,
- "runtime_constraints": {},
- "state": "Locked"
-}`, nil, 3, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
-}
-
-func (s *TestSuite) TestBadCommand1(c *C) {
- ech := ""
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
- "command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
- "cwd": ".",
- "environment": {},
- "mounts": {"/tmp": {"kind": "tmp"} },
- "output_path": "/tmp",
- "priority": 1,
- "runtime_constraints": {},
- "state": "Locked"
-}`, nil, 4, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
-}
-
-func (s *TestSuite) TestBadCommand2(c *C) {
- ech := ""
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
+func (s *TestSuite) TestFullBrokenDocker(c *C) {
+ nextState := ""
+ for _, setup := range []func(){
+ func() {
+ c.Log("// waitErr = ocl runtime error")
+ s.executor.waitErr = errors.New(`Error response from daemon: oci runtime error: container_linux.go:247: starting container process caused "process_linux.go:359: container init caused \"rootfs_linux.go:54: mounting \\\"/tmp/keep453790790/by_id/99999999999999999999999999999999+99999/myGenome\\\" to rootfs \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged\\\" at \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged/keep/99999999999999999999999999999999+99999/myGenome\\\" caused \\\"no such file or directory\\\"\""`)
+ nextState = "Cancelled"
+ },
+ func() {
+ c.Log("// loadErr = cannot connect")
+ s.executor.loadErr = errors.New("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
+ *brokenNodeHook = c.MkDir() + "/broken-node-hook"
+ err := ioutil.WriteFile(*brokenNodeHook, []byte("#!/bin/sh\nexec echo killme\n"), 0700)
+ c.Assert(err, IsNil)
+ nextState = "Queued"
+ },
+ } {
+ s.SetUpTest(c)
+ setup()
+ s.fullRunHelper(c, `{
"command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -2106,22 +1795,30 @@ func (s *TestSuite) TestBadCommand2(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 5, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+}`, nil, 0, func() {})
+ c.Check(s.api.CalledWith("container.state", nextState), NotNil)
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+ if *brokenNodeHook != "" {
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
+ c.Check(s.api.Logs["crunch-run"].String(), Not(Matches), "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
+ } else {
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
+ }
+ }
}
-func (s *TestSuite) TestBadCommand3(c *C) {
- ech := ""
- brokenNodeHook = &ech
-
- api, _, _ := s.fullRunHelper(c, `{
+func (s *TestSuite) TestBadCommand(c *C) {
+ for _, startError := range []string{
+ `panic: standard_init_linux.go:175: exec user process caused "no such file or directory"`,
+ `Error response from daemon: Cannot start container 41f26cbc43bcc1280f4323efb1830a394ba8660c9d1c2b564ba42bf7f7694845: [8] System error: no such file or directory`,
+ `Error response from daemon: Cannot start container 58099cd76c834f3dc2a4fb76c8028f049ae6d4fdf0ec373e1f2cfea030670c2d: [8] System error: exec: "foobar": executable file not found in $PATH`,
+ } {
+ s.SetUpTest(c)
+ s.executor.startErr = errors.New(startError)
+ s.fullRunHelper(c, `{
"command": ["echo", "hello world"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "`+arvadostest.DockerImage112PDH+`",
"cwd": ".",
"environment": {},
"mounts": {"/tmp": {"kind": "tmp"} },
@@ -2129,20 +1826,16 @@ func (s *TestSuite) TestBadCommand3(c *C) {
"priority": 1,
"runtime_constraints": {},
"state": "Locked"
-}`, nil, 6, func(t *TestDockerClient) {
- t.logWriter.Write(dockerLog(1, "hello world\n"))
- t.logWriter.Close()
- })
-
- c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+}`, nil, 0, func() {})
+ c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+ }
}
func (s *TestSuite) TestSecretTextMountPoint(c *C) {
- // under normal mounts, gets captured in output, oops
helperRecord := `{
"command": ["true"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"mounts": {
"/tmp": {"kind": "tmp"},
@@ -2156,22 +1849,21 @@ func (s *TestSuite) TestSecretTextMountPoint(c *C) {
"state": "Locked"
}`
- api, cr, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
- content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
+ s.fullRunHelper(c, helperRecord, nil, 0, func() {
+ content, err := ioutil.ReadFile(s.runner.HostOutputDir + "/secret.conf")
c.Check(err, IsNil)
- c.Check(content, DeepEquals, []byte("mypassword"))
- t.logWriter.Close()
+ c.Check(string(content), Equals, "mypassword")
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), NotNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ""), IsNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), NotNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ""), IsNil)
// under secret mounts, not captured in output
helperRecord = `{
"command": ["true"],
- "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "container_image": "` + arvadostest.DockerImage112PDH + `",
"cwd": "/bin",
"mounts": {
"/tmp": {"kind": "tmp"}
@@ -2185,17 +1877,17 @@ func (s *TestSuite) TestSecretTextMountPoint(c *C) {
"state": "Locked"
}`
- api, cr, _ = s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
- content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
+ s.SetUpTest(c)
+ s.fullRunHelper(c, helperRecord, nil, 0, func() {
+ content, err := ioutil.ReadFile(s.runner.HostOutputDir + "/secret.conf")
c.Check(err, IsNil)
- c.Check(content, DeepEquals, []byte("mypassword"))
- t.logWriter.Close()
+ c.Check(string(content), Equals, "mypassword")
})
- c.Check(api.CalledWith("container.exit_code", 0), NotNil)
- c.Check(api.CalledWith("container.state", "Complete"), NotNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), IsNil)
- c.Check(cr.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ""), NotNil)
+ c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), IsNil)
+ c.Check(s.runner.ContainerArvClient.(*ArvTestClient).CalledWith("collection.manifest_text", ""), NotNil)
}
type FakeProcess struct {
diff --git a/lib/crunchrun/docker.go b/lib/crunchrun/docker.go
new file mode 100644
index 000000000..32c60e699
--- /dev/null
+++ b/lib/crunchrun/docker.go
@@ -0,0 +1,263 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+package crunchrun
+
+import (
+ "fmt"
+ "io"
+ "io/ioutil"
+ "os"
+ "strings"
+ "time"
+
+ dockertypes "github.com/docker/docker/api/types"
+ dockercontainer "github.com/docker/docker/api/types/container"
+ dockerclient "github.com/docker/docker/client"
+ "golang.org/x/net/context"
+)
+
+// Docker daemon won't let you set a limit less than ~10 MiB
+const minDockerRAM = int64(16 * 1024 * 1024)
+
+type dockerExecutor struct {
+ containerUUID string
+ logf func(string, ...interface{})
+ watchdogInterval time.Duration
+ dockerclient *dockerclient.Client
+ containerID string
+ doneIO chan struct{}
+ errIO error
+}
+
+func newDockerExecutor(containerUUID string, logf func(string, ...interface{}), watchdogInterval time.Duration) (*dockerExecutor, error) {
+ // API version 1.21 corresponds to Docker 1.9, which is
+ // currently the minimum version we want to support.
+ client, err := dockerclient.NewClient(dockerclient.DefaultDockerHost, "1.21", nil, nil)
+ if watchdogInterval < 1 {
+ watchdogInterval = time.Minute
+ }
+ return &dockerExecutor{
+ containerUUID: containerUUID,
+ logf: logf,
+ watchdogInterval: watchdogInterval,
+ dockerclient: client,
+ }, err
+}
+
+func (e *dockerExecutor) ImageLoaded(imageID string) bool {
+ _, _, err := e.dockerclient.ImageInspectWithRaw(context.TODO(), imageID)
+ return err == nil
+}
+
+func (e *dockerExecutor) LoadImage(filename string) error {
+ f, err := os.Open(filename)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ resp, err := e.dockerclient.ImageLoad(context.TODO(), f, true)
+ if err != nil {
+ return fmt.Errorf("While loading container image into Docker: %v", err)
+ }
+ defer resp.Body.Close()
+ buf, _ := ioutil.ReadAll(resp.Body)
+ e.logf("loaded image: response %s", buf)
+ return nil
+}
+
+func (e *dockerExecutor) Create(spec containerSpec) error {
+ e.logf("Creating Docker container")
+ cfg := dockercontainer.Config{
+ Image: spec.Image,
+ Cmd: spec.Command,
+ WorkingDir: spec.WorkingDir,
+ Volumes: map[string]struct{}{},
+ OpenStdin: spec.Stdin != nil,
+ StdinOnce: spec.Stdin != nil,
+ AttachStdin: spec.Stdin != nil,
+ AttachStdout: true,
+ AttachStderr: true,
+ }
+ if cfg.WorkingDir == "." {
+ cfg.WorkingDir = ""
+ }
+ for k, v := range spec.Env {
+ cfg.Env = append(cfg.Env, k+"="+v)
+ }
+ if spec.RAM < minDockerRAM {
+ spec.RAM = minDockerRAM
+ }
+ hostCfg := dockercontainer.HostConfig{
+ LogConfig: dockercontainer.LogConfig{
+ Type: "none",
+ },
+ NetworkMode: dockercontainer.NetworkMode("none"),
+ Resources: dockercontainer.Resources{
+ CgroupParent: spec.CgroupParent,
+ NanoCPUs: int64(spec.VCPUs) * 1000000000,
+ Memory: spec.RAM, // RAM
+ MemorySwap: spec.RAM, // RAM+swap
+ KernelMemory: spec.RAM, // kernel portion
+ },
+ }
+ for path, mount := range spec.BindMounts {
+ bind := mount.HostPath + ":" + path
+ if mount.ReadOnly {
+ bind += ":ro"
+ }
+ hostCfg.Binds = append(hostCfg.Binds, bind)
+ }
+ if spec.EnableNetwork {
+ hostCfg.NetworkMode = dockercontainer.NetworkMode(spec.NetworkMode)
+ }
+
+ created, err := e.dockerclient.ContainerCreate(context.TODO(), &cfg, &hostCfg, nil, e.containerUUID)
+ if err != nil {
+ return fmt.Errorf("While creating container: %v", err)
+ }
+ e.containerID = created.ID
+ return e.startIO(spec.Stdin, spec.Stdout, spec.Stderr)
+}
+
+func (e *dockerExecutor) CgroupID() string {
+ return e.containerID
+}
+
+func (e *dockerExecutor) Start() error {
+ return e.dockerclient.ContainerStart(context.TODO(), e.containerID, dockertypes.ContainerStartOptions{})
+}
+
+func (e *dockerExecutor) Stop() error {
+ err := e.dockerclient.ContainerRemove(context.TODO(), e.containerID, dockertypes.ContainerRemoveOptions{Force: true})
+ if err != nil && strings.Contains(err.Error(), "No such container: "+e.containerID) {
+ err = nil
+ }
+ return err
+}
+
+// Wait for the container to terminate, capture the exit code, and
+// wait for stdout/stderr logging to finish.
+func (e *dockerExecutor) Wait(ctx context.Context) (int, error) {
+ ctx, cancel := context.WithCancel(ctx)
+ defer cancel()
+ watchdogErr := make(chan error, 1)
+ go func() {
+ ticker := time.NewTicker(e.watchdogInterval)
+ defer ticker.Stop()
+ for range ticker.C {
+ dctx, dcancel := context.WithDeadline(ctx, time.Now().Add(e.watchdogInterval))
+ ctr, err := e.dockerclient.ContainerInspect(dctx, e.containerID)
+ dcancel()
+ if ctx.Err() != nil {
+ // Either the container already
+ // exited, or our caller is trying to
+ // kill it.
+ return
+ } else if err != nil {
+ e.logf("Error inspecting container: %s", err)
+ watchdogErr <- err
+ return
+ } else if ctr.State == nil || !(ctr.State.Running || ctr.State.Status == "created") {
+ watchdogErr <- fmt.Errorf("Container is not running: State=%v", ctr.State)
+ return
+ }
+ }
+ }()
+
+ waitOk, waitErr := e.dockerclient.ContainerWait(ctx, e.containerID, dockercontainer.WaitConditionNotRunning)
+ for {
+ select {
+ case waitBody := <-waitOk:
+ e.logf("Container exited with code: %v", waitBody.StatusCode)
+ // wait for stdout/stderr to complete
+ <-e.doneIO
+ return int(waitBody.StatusCode), nil
+
+ case err := <-waitErr:
+ return -1, fmt.Errorf("container wait: %v", err)
+
+ case <-ctx.Done():
+ return -1, ctx.Err()
+
+ case err := <-watchdogErr:
+ return -1, err
+ }
+ }
+}
+
+func (e *dockerExecutor) startIO(stdin io.ReadCloser, stdout, stderr io.WriteCloser) error {
+ resp, err := e.dockerclient.ContainerAttach(context.TODO(), e.containerID, dockertypes.ContainerAttachOptions{
+ Stream: true,
+ Stdin: stdin != nil,
+ Stdout: true,
+ Stderr: true,
+ })
+ if err != nil {
+ return fmt.Errorf("error attaching container stdin/stdout/stderr streams: %v", err)
+ }
+ var errStdin error
+ if stdin != nil {
+ go func() {
+ errStdin = e.handleStdin(stdin, resp.Conn, resp.CloseWrite)
+ }()
+ }
+ e.doneIO = make(chan struct{})
+ go func() {
+ e.errIO = e.handleStdoutStderr(stdout, stderr, resp.Reader)
+ if e.errIO == nil && errStdin != nil {
+ e.errIO = errStdin
+ }
+ close(e.doneIO)
+ }()
+ return nil
+}
+
+func (e *dockerExecutor) handleStdin(stdin io.ReadCloser, conn io.Writer, closeConn func() error) error {
+ defer stdin.Close()
+ defer closeConn()
+ _, err := io.Copy(conn, stdin)
+ if err != nil {
+ return fmt.Errorf("While writing to docker container on stdin: %v", err)
+ }
+ return nil
+}
+
+// Handle docker log protocol; see
+// https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
+func (e *dockerExecutor) handleStdoutStderr(stdout, stderr io.WriteCloser, reader io.Reader) error {
+ header := make([]byte, 8)
+ var err error
+ for err == nil {
+ _, err = io.ReadAtLeast(reader, header, 8)
+ if err != nil {
+ if err == io.EOF {
+ err = nil
+ }
+ break
+ }
+ readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
+ if header[0] == 1 {
+ _, err = io.CopyN(stdout, reader, readsize)
+ } else {
+ // stderr
+ _, err = io.CopyN(stderr, reader, readsize)
+ }
+ }
+ if err != nil {
+ return fmt.Errorf("error copying stdout/stderr from docker: %v", err)
+ }
+ err = stdout.Close()
+ if err != nil {
+ return fmt.Errorf("error writing stdout: close: %v", err)
+ }
+ err = stderr.Close()
+ if err != nil {
+ return fmt.Errorf("error writing stderr: close: %v", err)
+ }
+ return nil
+}
+
+func (e *dockerExecutor) Close() {
+ e.dockerclient.ContainerRemove(context.TODO(), e.containerID, dockertypes.ContainerRemoveOptions{Force: true})
+}
diff --git a/lib/crunchrun/docker_test.go b/lib/crunchrun/docker_test.go
new file mode 100644
index 000000000..28eb59546
--- /dev/null
+++ b/lib/crunchrun/docker_test.go
@@ -0,0 +1,31 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package crunchrun
+
+import (
+ "os/exec"
+ "time"
+
+ . "gopkg.in/check.v1"
+)
+
+var _ = Suite(&dockerSuite{})
+
+type dockerSuite struct {
+ executorSuite
+}
+
+func (s *dockerSuite) SetUpSuite(c *C) {
+ _, err := exec.LookPath("docker")
+ if err != nil {
+ c.Skip("looks like docker is not installed")
+ }
+ s.newExecutor = func(c *C) {
+ exec.Command("docker", "rm", "zzzzz-zzzzz-zzzzzzzzzzzzzzz").Run()
+ var err error
+ s.executor, err = newDockerExecutor("zzzzz-zzzzz-zzzzzzzzzzzzzzz", c.Logf, time.Second/2)
+ c.Assert(err, IsNil)
+ }
+}
diff --git a/lib/crunchrun/executor.go b/lib/crunchrun/executor.go
new file mode 100644
index 000000000..c773febe9
--- /dev/null
+++ b/lib/crunchrun/executor.go
@@ -0,0 +1,63 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+package crunchrun
+
+import (
+ "io"
+
+ "golang.org/x/net/context"
+)
+
+type bindmount struct {
+ HostPath string
+ ReadOnly bool
+}
+
+type containerSpec struct {
+ Image string
+ VCPUs int
+ RAM int64
+ WorkingDir string
+ Env map[string]string
+ BindMounts map[string]bindmount
+ Command []string
+ EnableNetwork bool
+ NetworkMode string // docker network mode, normally "default"
+ CgroupParent string
+ Stdin io.ReadCloser
+ Stdout io.WriteCloser
+ Stderr io.WriteCloser
+}
+
+// containerExecutor is an interface to a container runtime
+// (docker/singularity).
+type containerExecutor interface {
+ // ImageLoaded determines whether the given image is already
+ // available to use without calling ImageLoad.
+ ImageLoaded(imageID string) bool
+
+ // ImageLoad loads the image from the given tarball such that
+ // it can be used to create/start a container.
+ LoadImage(filename string) error
+
+ // Wait for the container process to finish, and return its
+ // exit code. If applicable, also remove the stopped container
+ // before returning.
+ Wait(context.Context) (int, error)
+
+ // Create a container, but don't start it yet.
+ Create(containerSpec) error
+
+ // Start the container
+ Start() error
+
+ // CID the container will belong to
+ CgroupID() string
+
+ // Stop the container immediately
+ Stop() error
+
+ // Release resources (temp dirs, stopped containers)
+ Close()
+}
diff --git a/lib/crunchrun/executor_test.go b/lib/crunchrun/executor_test.go
new file mode 100644
index 000000000..5728a9ccf
--- /dev/null
+++ b/lib/crunchrun/executor_test.go
@@ -0,0 +1,161 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package crunchrun
+
+import (
+ "bytes"
+ "io"
+ "io/ioutil"
+ "net/http"
+ "os"
+ "strings"
+ "time"
+
+ "golang.org/x/net/context"
+ . "gopkg.in/check.v1"
+)
+
+var _ = Suite(&dockerSuite{})
+
+func busyboxDockerImage(c *C) string {
+ fnm := "busybox_uclibc.tar"
+ cachedir := "/var/lib/arvados/tmp"
+ cachefile := cachedir + "/" + fnm
+ if _, err := os.Stat(cachefile); err == nil {
+ return cachefile
+ }
+
+ f, err := ioutil.TempFile(cachedir, "")
+ c.Assert(err, IsNil)
+ defer f.Close()
+ defer os.Remove(f.Name())
+
+ resp, err := http.Get("http://cache.arvados.org/" + fnm)
+ c.Assert(err, IsNil)
+ defer resp.Body.Close()
+ _, err = io.Copy(f, resp.Body)
+ c.Assert(err, IsNil)
+ err = f.Close()
+ c.Assert(err, IsNil)
+ err = os.Rename(f.Name(), cachefile)
+ c.Assert(err, IsNil)
+
+ return cachefile
+}
+
+type nopWriteCloser struct{ io.Writer }
+
+func (nopWriteCloser) Close() error { return nil }
+
+// embedded by dockerSuite and singularitySuite so they can share
+// tests.
+type executorSuite struct {
+ newExecutor func(*C) // embedding struct's SetUpSuite method must set this
+ executor containerExecutor
+ spec containerSpec
+ stdout bytes.Buffer
+ stderr bytes.Buffer
+}
+
+func (s *executorSuite) SetUpTest(c *C) {
+ s.newExecutor(c)
+ s.stdout = bytes.Buffer{}
+ s.stderr = bytes.Buffer{}
+ s.spec = containerSpec{
+ Image: "busybox:uclibc",
+ VCPUs: 1,
+ WorkingDir: "",
+ Env: map[string]string{"PATH": "/bin:/usr/bin"},
+ NetworkMode: "default",
+ Stdout: nopWriteCloser{&s.stdout},
+ Stderr: nopWriteCloser{&s.stderr},
+ }
+ err := s.executor.LoadImage(busyboxDockerImage(c))
+ c.Assert(err, IsNil)
+}
+
+func (s *executorSuite) TearDownTest(c *C) {
+ s.executor.Close()
+}
+
+func (s *executorSuite) TestExecTrivialContainer(c *C) {
+ s.spec.Command = []string{"echo", "ok"}
+ s.checkRun(c, 0)
+ c.Check(s.stdout.String(), Equals, "ok\n")
+ c.Check(s.stderr.String(), Equals, "")
+}
+
+func (s *executorSuite) TestExecStop(c *C) {
+ s.spec.Command = []string{"sh", "-c", "sleep 10; echo ok"}
+ err := s.executor.Create(s.spec)
+ c.Assert(err, IsNil)
+ err = s.executor.Start()
+ c.Assert(err, IsNil)
+ go func() {
+ time.Sleep(time.Second / 10)
+ s.executor.Stop()
+ }()
+ ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(10*time.Second))
+ defer cancel()
+ code, err := s.executor.Wait(ctx)
+ c.Check(code, Not(Equals), 0)
+ c.Check(err, IsNil)
+ c.Check(s.stdout.String(), Equals, "")
+ c.Check(s.stderr.String(), Equals, "")
+}
+
+func (s *executorSuite) TestExecCleanEnv(c *C) {
+ s.spec.Command = []string{"env"}
+ s.checkRun(c, 0)
+ c.Check(s.stderr.String(), Equals, "")
+ got := map[string]string{}
+ for _, kv := range strings.Split(s.stdout.String(), "\n") {
+ if kv == "" {
+ continue
+ }
+ kv := strings.SplitN(kv, "=", 2)
+ switch kv[0] {
+ case "HOSTNAME", "HOME":
+ // docker sets these by itself
+ case "LD_LIBRARY_PATH", "SINGULARITY_NAME", "PWD", "LANG", "SHLVL", "SINGULARITY_INIT", "SINGULARITY_CONTAINER":
+ // singularity sets these by itself (cf. https://sylabs.io/guides/3.5/user-guide/environment_and_metadata.html)
+ case "PROMPT_COMMAND", "PS1", "SINGULARITY_APPNAME":
+ // singularity also sets these by itself (as of v3.5.2)
+ default:
+ got[kv[0]] = kv[1]
+ }
+ }
+ c.Check(got, DeepEquals, s.spec.Env)
+}
+func (s *executorSuite) TestExecEnableNetwork(c *C) {
+ for _, enable := range []bool{false, true} {
+ s.SetUpTest(c)
+ s.spec.Command = []string{"ip", "route"}
+ s.spec.EnableNetwork = enable
+ s.checkRun(c, 0)
+ if enable {
+ c.Check(s.stdout.String(), Matches, "(?ms).*default via.*")
+ } else {
+ c.Check(s.stdout.String(), Equals, "")
+ }
+ }
+}
+
+func (s *executorSuite) TestExecStdoutStderr(c *C) {
+ s.spec.Command = []string{"sh", "-c", "echo foo; echo -n bar >&2; echo baz; echo waz >&2"}
+ s.checkRun(c, 0)
+ c.Check(s.stdout.String(), Equals, "foo\nbaz\n")
+ c.Check(s.stderr.String(), Equals, "barwaz\n")
+}
+
+func (s *executorSuite) checkRun(c *C, expectCode int) {
+ c.Assert(s.executor.Create(s.spec), IsNil)
+ c.Assert(s.executor.Start(), IsNil)
+ ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(10*time.Second))
+ defer cancel()
+ code, err := s.executor.Wait(ctx)
+ c.Assert(err, IsNil)
+ c.Check(code, Equals, expectCode)
+}
diff --git a/lib/crunchrun/logging_test.go b/lib/crunchrun/logging_test.go
index e3fa3af0b..55460af37 100644
--- a/lib/crunchrun/logging_test.go
+++ b/lib/crunchrun/logging_test.go
@@ -45,7 +45,7 @@ func (s *LoggingTestSuite) TestWriteLogs(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
@@ -74,7 +74,7 @@ func (s *LoggingTestSuite) TestWriteLogsLarge(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
cr.CrunchLog.Immediate = nil
@@ -97,7 +97,7 @@ func (s *LoggingTestSuite) TestWriteMultipleLogs(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
ts := &TestTimestamper{}
cr.CrunchLog.Timestamper = ts.Timestamp
@@ -146,7 +146,7 @@ func (s *LoggingTestSuite) TestLogUpdate(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
ts := &TestTimestamper{}
cr.CrunchLog.Timestamper = ts.Timestamp
@@ -197,7 +197,7 @@ func (s *LoggingTestSuite) testWriteLogsWithRateLimit(c *C, throttleParam string
api := &ArvTestClient{}
kc := &KeepTestClient{}
defer kc.Close()
- cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzzzzzzzzzzzz")
+ cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzzzzzzzzzzzz")
c.Assert(err, IsNil)
cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
diff --git a/lib/crunchrun/singularity.go b/lib/crunchrun/singularity.go
new file mode 100644
index 000000000..d783baab9
--- /dev/null
+++ b/lib/crunchrun/singularity.go
@@ -0,0 +1,140 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package crunchrun
+
+import (
+ "io/ioutil"
+ "os"
+ "os/exec"
+ "syscall"
+
+ "golang.org/x/net/context"
+)
+
+type singularityExecutor struct {
+ logf func(string, ...interface{})
+ spec containerSpec
+ tmpdir string
+ child *exec.Cmd
+ imageFilename string // "sif" image
+}
+
+func newSingularityExecutor(logf func(string, ...interface{})) (*singularityExecutor, error) {
+ tmpdir, err := ioutil.TempDir("", "crunch-run-singularity-")
+ if err != nil {
+ return nil, err
+ }
+ return &singularityExecutor{
+ logf: logf,
+ tmpdir: tmpdir,
+ }, nil
+}
+
+func (e *singularityExecutor) ImageLoaded(string) bool {
+ return false
+}
+
+// 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")
+ e.imageFilename = e.tmpdir + "/image.sif"
+ build := exec.Command("singularity", "build", e.imageFilename, "docker-archive://"+imageTarballPath)
+ 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
+ }
+ return nil
+}
+
+func (e *singularityExecutor) Create(spec containerSpec) error {
+ e.spec = spec
+ return nil
+}
+
+func (e *singularityExecutor) Start() error {
+ args := []string{"singularity", "exec", "--containall", "--no-home", "--cleanenv"}
+ if !e.spec.EnableNetwork {
+ args = append(args, "--net", "--network=none")
+ }
+ readonlyflag := map[bool]string{
+ false: "rw",
+ true: "ro",
+ }
+ for path, mount := range e.spec.BindMounts {
+ 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/3.7/user-guide/environment_and_metadata.html
+ // 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)
+ }
+
+ path, err := exec.LookPath(args[0])
+ if err != nil {
+ return err
+ }
+ child := &exec.Cmd{
+ Path: path,
+ Args: args,
+ Env: env,
+ Stdin: e.spec.Stdin,
+ Stdout: e.spec.Stdout,
+ Stderr: e.spec.Stderr,
+ }
+ err = child.Start()
+ if err != nil {
+ return err
+ }
+ e.child = child
+ return nil
+}
+
+func (e *singularityExecutor) CgroupID() string {
+ return ""
+}
+
+func (e *singularityExecutor) Stop() error {
+ if err := e.child.Process.Signal(syscall.Signal(0)); err != nil {
+ // process already exited
+ return nil
+ }
+ return e.child.Process.Signal(syscall.SIGKILL)
+}
+
+func (e *singularityExecutor) Wait(context.Context) (int, error) {
+ err := e.child.Wait()
+ if err, ok := err.(*exec.ExitError); ok {
+ return err.ProcessState.ExitCode(), nil
+ }
+ if err != nil {
+ return 0, err
+ }
+ return e.child.ProcessState.ExitCode(), nil
+}
+
+func (e *singularityExecutor) Close() {
+ err := os.RemoveAll(e.tmpdir)
+ if err != nil {
+ e.logf("error removing temp dir: %s", err)
+ }
+}
diff --git a/lib/crunchrun/singularity_test.go b/lib/crunchrun/singularity_test.go
new file mode 100644
index 000000000..a1263da32
--- /dev/null
+++ b/lib/crunchrun/singularity_test.go
@@ -0,0 +1,29 @@
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package crunchrun
+
+import (
+ "os/exec"
+
+ . "gopkg.in/check.v1"
+)
+
+var _ = Suite(&singularitySuite{})
+
+type singularitySuite struct {
+ executorSuite
+}
+
+func (s *singularitySuite) SetUpSuite(c *C) {
+ _, err := exec.LookPath("singularity")
+ if err != nil {
+ c.Skip("looks like singularity is not installed")
+ }
+ s.newExecutor = func(c *C) {
+ var err error
+ s.executor, err = newSingularityExecutor(c.Logf)
+ c.Assert(err, IsNil)
+ }
+}
diff --git a/lib/dispatchcloud/dispatcher_test.go b/lib/dispatchcloud/dispatcher_test.go
index 8752ee054..829a05363 100644
--- a/lib/dispatchcloud/dispatcher_test.go
+++ b/lib/dispatchcloud/dispatcher_test.go
@@ -56,6 +56,7 @@ func (s *DispatcherSuite) SetUpTest(c *check.C) {
CrunchRunArgumentsList: []string{"--foo", "--extra='args'"},
DispatchPrivateKey: string(dispatchprivraw),
StaleLockTimeout: arvados.Duration(5 * time.Millisecond),
+ RuntimeEngine: "stub",
CloudVMs: arvados.CloudVMsConfig{
Driver: "test",
SyncInterval: arvados.Duration(10 * time.Millisecond),
@@ -163,7 +164,7 @@ func (s *DispatcherSuite) TestDispatchToStubDriver(c *check.C) {
stubvm.CrunchRunDetachDelay = time.Duration(rand.Int63n(int64(10 * time.Millisecond)))
stubvm.ExecuteContainer = executeContainer
stubvm.CrashRunningContainer = finishContainer
- stubvm.ExtraCrunchRunArgs = "'--foo' '--extra='\\''args'\\'''"
+ stubvm.ExtraCrunchRunArgs = "'--runtime-engine=stub' '--foo' '--extra='\\''args'\\'''"
switch n % 7 {
case 0:
stubvm.Broken = time.Now().Add(time.Duration(rand.Int63n(90)) * time.Millisecond)
diff --git a/lib/dispatchcloud/worker/pool.go b/lib/dispatchcloud/worker/pool.go
index 7289179fd..a5924cf99 100644
--- a/lib/dispatchcloud/worker/pool.go
+++ b/lib/dispatchcloud/worker/pool.go
@@ -122,7 +122,7 @@ func NewPool(logger logrus.FieldLogger, arvClient *arvados.Client, reg *promethe
installPublicKey: installPublicKey,
tagKeyPrefix: cluster.Containers.CloudVMs.TagKeyPrefix,
runnerCmdDefault: cluster.Containers.CrunchRunCommand,
- runnerArgs: cluster.Containers.CrunchRunArgumentsList,
+ runnerArgs: append([]string{"--runtime-engine=" + cluster.Containers.RuntimeEngine}, cluster.Containers.CrunchRunArgumentsList...),
stop: make(chan bool),
}
wp.registerMetrics(reg)
diff --git a/lib/install/deps.go b/lib/install/deps.go
index 8df3fba53..255e56aaf 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -181,6 +181,11 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
"wget",
"xvfb",
)
+ if dev || test {
+ pkgs = append(pkgs,
+ "squashfs-tools", // for singularity
+ )
+ }
switch {
case osv.Debian && osv.Major >= 10:
pkgs = append(pkgs, "libcurl4")
@@ -315,6 +320,28 @@ rm ${zip}
}
}
+ singularityversion := "3.5.2"
+ if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
+ logger.Print("singularity " + singularityversion + " already installed")
+ } else if dev || test {
+ err = inst.runBash(`
+S=`+singularityversion+`
+tmp=/var/lib/arvados/tmp/singularity
+trap "rm -r ${tmp}" ERR EXIT
+cd /var/lib/arvados/tmp
+git clone https://github.com/sylabs/singularity
+cd singularity
+git checkout v${S}
+./mconfig --prefix=/var/lib/arvados
+make -C ./builddir
+make -C ./builddir install
+rm -r ${tmp}
+`, stdout, stderr)
+ if err != nil {
+ return 1
+ }
+ }
+
// The entry in /etc/locale.gen is "en_US.UTF-8"; once
// it's installed, locale -a reports it as
// "en_US.utf8".
diff --git a/sdk/go/arvados/config.go b/sdk/go/arvados/config.go
index 2c6db42d1..2ff432321 100644
--- a/sdk/go/arvados/config.go
+++ b/sdk/go/arvados/config.go
@@ -414,6 +414,7 @@ type ContainersConfig struct {
StaleLockTimeout Duration
SupportedDockerImageFormats StringSet
UsePreemptibleInstances bool
+ RuntimeEngine string
JobsAPI struct {
Enable string
diff --git a/sdk/go/arvadostest/fixtures.go b/sdk/go/arvadostest/fixtures.go
index aeb5a47e6..16e209816 100644
--- a/sdk/go/arvadostest/fixtures.go
+++ b/sdk/go/arvadostest/fixtures.go
@@ -96,6 +96,9 @@ const (
LogCollectionUUID = "zzzzz-4zz18-logcollection01"
LogCollectionUUID2 = "zzzzz-4zz18-logcollection02"
+
+ DockerImage112PDH = "d740a57097711e08eb9b2a93518f20ab+174"
+ DockerImage112Filename = "sha256:d8309758b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678.tar"
)
// PathologicalManifest : A valid manifest designed to test
-----------------------------------------------------------------------
hooks/post-receive
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