"os/signal"
"path"
"path/filepath"
+ "sort"
"strings"
"sync"
"syscall"
type IArvadosClient interface {
Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
- Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error)
- Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) (err error)
+ Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
+ Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
+ Discovery(key string) (interface{}, error)
}
// ErrCancelled is the error returned when the container is cancelled.
// IKeepClient is the minimal Keep API methods used by crunch-run.
type IKeepClient interface {
PutHB(hash string, buf []byte) (string, int, error)
- ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error)
+ ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error)
}
// NewLogWriter is a factory function to create a new log writer.
statReporter *crunchstat.Reporter
statInterval time.Duration
cgroupRoot string
- cgroupParent string
+ // What we expect the container's cgroup parent to be.
+ expectCgroupParent string
+ // What we tell docker to use as the container's cgroup
+ // parent. Note: Ideally we would use the same field for both
+ // expectCgroupParent and setCgroupParent, and just make it
+ // default to "docker". However, when using docker < 1.10 with
+ // systemd, specifying a non-empty cgroup parent (even the
+ // default value "docker") hits a docker bug
+ // (https://github.com/docker/docker/issues/17126). Using two
+ // separate fields makes it possible to use the "expect cgroup
+ // parent to be X" feature even on sites where the "specify
+ // cgroup parent" feature breaks.
+ setCgroupParent string
}
// SetupSignals sets up signal handling to gracefully terminate the underlying
return c, nil
}
+func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
+ if runner.ArvMountPoint == "" {
+ runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
+ }
+ return
+}
+
func (runner *ContainerRunner) SetupMounts() (err error) {
- runner.ArvMountPoint, err = runner.MkTempDir("", "keep")
+ err = runner.SetupArvMountPoint("keep")
if err != nil {
return fmt.Errorf("While creating keep mount temp dir: %v", err)
}
pdhOnly := true
tmpcount := 0
arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
+
+ if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
+ arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
+ }
+
collectionPaths := []string{}
runner.Binds = nil
+ needCertMount := true
- for bind, mnt := range runner.Container.Mounts {
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
if bind == "stdout" {
// Is it a "file" mount kind?
if mnt.Kind != "file" {
}
}
+ if bind == "/etc/arvados/ca-certificates.crt" {
+ needCertMount = false
+ }
+
+ if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
+ if mnt.Kind != "collection" {
+ return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind)
+ }
+ }
+
switch {
case mnt.Kind == "collection":
var src string
if mnt.Writable {
return fmt.Errorf("Can never write to a collection specified by portable data hash")
}
+ idx := strings.Index(mnt.PortableDataHash, "/")
+ if idx > 0 {
+ mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
+ mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
+ runner.Container.Mounts[bind] = mnt
+ }
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
+ if mnt.Path != "" && mnt.Path != "." {
+ if strings.HasPrefix(mnt.Path, "./") {
+ mnt.Path = mnt.Path[2:]
+ } else if strings.HasPrefix(mnt.Path, "/") {
+ mnt.Path = mnt.Path[1:]
+ }
+ src += "/" + mnt.Path
+ }
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp")
if mnt.Writable {
if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
+ } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
+ return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind)
}
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
} else {
return fmt.Errorf("Output path does not correspond to a writable mount point")
}
+ if wantAPI := runner.Container.RuntimeConstraints.API; needCertMount && wantAPI != nil && *wantAPI {
+ 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))
+ break
+ }
+ }
+ }
+
if pdhOnly {
arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
} else {
runner.statReporter = &crunchstat.Reporter{
CID: runner.ContainerID,
Logger: log.New(runner.statLogger, "", 0),
- CgroupParent: runner.cgroupParent,
+ CgroupParent: runner.expectCgroupParent,
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
}
return fmt.Errorf("While creating container: %v", err)
}
- runner.HostConfig = dockerclient.HostConfig{Binds: runner.Binds,
- LogConfig: dockerclient.LogConfig{Type: "none"}}
+ runner.HostConfig = dockerclient.HostConfig{
+ Binds: runner.Binds,
+ CgroupParent: runner.setCgroupParent,
+ LogConfig: dockerclient.LogConfig{
+ Type: "none",
+ },
+ }
return runner.AttachStreams()
}
return nil
}
+ if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
+ // Output may have been set directly by the container, so
+ // refresh the container record to check.
+ err := runner.ArvClient.Get("containers", runner.Container.UUID,
+ nil, &runner.Container)
+ if err != nil {
+ return err
+ }
+ if runner.Container.Output != "" {
+ // Container output is already set.
+ runner.OutputPDH = &runner.Container.Output
+ return nil
+ }
+ }
+
if runner.HostOutputDir == "" {
return nil
}
manifestText = rec.ManifestText
}
+ // Pre-populate output from the configured mount points
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
+
+ bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
+
+ if bindSuffix == bind || len(bindSuffix) <= 0 {
+ // either does not start with OutputPath or is OutputPath itself
+ continue
+ }
+
+ if mnt.ExcludeFromOutput == true {
+ continue
+ }
+
+ // append to manifest_text
+ m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
+ if err != nil {
+ return err
+ }
+
+ manifestText = manifestText + m
+ }
+
+ // Save output
var response arvados.Collection
+ manifest := manifest.Manifest{Text: manifestText}
+ manifestText = manifest.Extract(".", ".").Text
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
"collection": arvadosclient.Dict{
+ "is_trashed": true,
+ "name": "output for " + runner.Container.UUID,
"manifest_text": manifestText}},
&response)
if err != nil {
return fmt.Errorf("While creating output collection: %v", err)
}
+ runner.OutputPDH = &response.PortableDataHash
+ return nil
+}
+
+var outputCollections = make(map[string]arvados.Collection)
+
+// Fetch the collection for the mnt.PortableDataHash
+// Return the manifest_text fragment corresponding to the specified mnt.Path
+// after making any required updates.
+// Ex:
+// If mnt.Path is not specified,
+// return the entire manifest_text after replacing any "." with bindSuffix
+// If mnt.Path corresponds to one stream,
+// return the manifest_text for that stream after replacing that stream name with bindSuffix
+// Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
+// for that stream after replacing stream name with bindSuffix minus the last word
+// and the file name with last word of the bindSuffix
+// Allowed path examples:
+// "path":"/"
+// "path":"/subdir1"
+// "path":"/subdir1/subdir2"
+// "path":"/subdir/filename" etc
+func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
+ collection := outputCollections[mnt.PortableDataHash]
+ if collection.PortableDataHash == "" {
+ err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
+ if err != nil {
+ return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
+ }
+ outputCollections[mnt.PortableDataHash] = collection
+ }
- runner.OutputPDH = new(string)
- *runner.OutputPDH = response.PortableDataHash
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ return "", nil
+ }
- return nil
+ mft := manifest.Manifest{Text: collection.ManifestText}
+ extracted := mft.Extract(mnt.Path, bindSuffix)
+ if extracted.Err != nil {
+ return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
+ }
+ return extracted.Text, nil
}
func (runner *ContainerRunner) CleanupDirs() {
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
"collection": arvadosclient.Dict{
+ "is_trashed": true,
"name": "logs for " + runner.Container.UUID,
"manifest_text": mt}},
&response)
if err != nil {
return fmt.Errorf("While creating log collection: %v", err)
}
-
runner.LogsPDH = &response.PortableDataHash
-
return nil
}
func (runner *ContainerRunner) UpdateContainerFinal() error {
update := arvadosclient.Dict{}
update["state"] = runner.finalState
+ if runner.LogsPDH != nil {
+ update["log"] = *runner.LogsPDH
+ }
if runner.finalState == "Complete" {
- if runner.LogsPDH != nil {
- update["log"] = *runner.LogsPDH
- }
if runner.ExitCode != nil {
update["exit_code"] = *runner.ExitCode
}
checkErr(err)
if runner.finalState == "Queued" {
+ runner.CrunchLog.Close()
runner.UpdateContainerFinal()
return
}
// check for and/or load image
err = runner.LoadImage()
if err != nil {
+ runner.finalState = "Cancelled"
err = fmt.Errorf("While loading container image: %v", err)
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
}
func main() {
statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
- cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup")
+ cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
+ cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
+ caCertsPath := flag.String("ca-certs", "", "Path to TLS root certificates")
flag.Parse()
containerId := flag.Arg(0)
+ if *caCertsPath != "" {
+ arvadosclient.CertFiles = []string{*caCertsPath}
+ }
+
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Fatalf("%s: %v", containerId, err)
api.Retries = 8
var kc *keepclient.KeepClient
- kc, err = keepclient.MakeKeepClient(&api)
+ kc, err = keepclient.MakeKeepClient(api)
if err != nil {
log.Fatalf("%s: %v", containerId, err)
}
cr := NewContainerRunner(api, kc, docker, containerId)
cr.statInterval = *statInterval
cr.cgroupRoot = *cgroupRoot
- cr.cgroupParent = *cgroupParent
+ cr.expectCgroupParent = *cgroupParent
+ if *cgroupParentSubsystem != "" {
+ p := findCgroup(*cgroupParentSubsystem)
+ cr.setCgroupParent = p
+ cr.expectCgroupParent = p
+ }
err = cr.Run()
if err != nil {