"errors"
"flag"
"fmt"
- "git.curoverse.com/arvados.git/lib/crunchstat"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/keepclient"
- "git.curoverse.com/arvados.git/sdk/go/manifest"
- "github.com/curoverse/dockerclient"
"io"
"io/ioutil"
"log"
"sync"
"syscall"
"time"
+
+ "git.curoverse.com/arvados.git/lib/crunchstat"
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
+ "git.curoverse.com/arvados.git/sdk/go/manifest"
+ "github.com/curoverse/dockerclient"
)
// IArvadosClient is the minimal Arvados API methods used by crunch-run.
// 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.
SigChan chan os.Signal
ArvMountExit chan error
finalState string
- trashLifetime time.Duration
statLogger io.WriteCloser
statReporter *crunchstat.Reporter
signal.Notify(runner.SigChan, syscall.SIGINT)
signal.Notify(runner.SigChan, syscall.SIGQUIT)
- go func(sig <-chan os.Signal) {
- for range sig {
- if !runner.Cancelled {
- runner.CancelLock.Lock()
- runner.Cancelled = true
- if runner.ContainerID != "" {
- runner.Docker.StopContainer(runner.ContainerID, 10)
- }
- runner.CancelLock.Unlock()
- }
- }
+ go func(sig chan os.Signal) {
+ <-sig
+ runner.stop()
+ signal.Stop(sig)
}(runner.SigChan)
}
+// stop the underlying Docker container.
+func (runner *ContainerRunner) stop() {
+ runner.CancelLock.Lock()
+ defer runner.CancelLock.Unlock()
+ if runner.Cancelled {
+ return
+ }
+ runner.Cancelled = true
+ if runner.ContainerID != "" {
+ err := runner.Docker.StopContainer(runner.ContainerID, 10)
+ if err != nil {
+ log.Printf("StopContainer failed: %s", err)
+ }
+ }
+}
+
// 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.
return c, nil
}
-var tmpBackedOutputDir = false
+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)
}
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")
}
runner.CleanupTempDir = append(runner.CleanupTempDir, runner.HostOutputDir)
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", runner.HostOutputDir, bind))
- tmpBackedOutputDir = true
case mnt.Kind == "tmp":
runner.Binds = append(runner.Binds, bind)
func (runner *ContainerRunner) WaitFinish() error {
runner.CrunchLog.Print("Waiting for container to finish")
- result := runner.Docker.Wait(runner.ContainerID)
- wr := <-result
- if wr.Error != nil {
- return fmt.Errorf("While waiting for container to finish: %v", wr.Error)
+ waitDocker := runner.Docker.Wait(runner.ContainerID)
+ waitMount := runner.ArvMountExit
+ for waitDocker != nil {
+ select {
+ case err := <-waitMount:
+ runner.CrunchLog.Printf("arv-mount exited before container finished: %v", err)
+ waitMount = nil
+ runner.stop()
+ case wr := <-waitDocker:
+ if wr.Error != nil {
+ return fmt.Errorf("While waiting for container to finish: %v", wr.Error)
+ }
+ runner.ExitCode = &wr.ExitCode
+ waitDocker = nil
+ }
}
- runner.ExitCode = &wr.ExitCode
// wait for stdout/stderr to complete
<-runner.loggingDone
_, err = os.Stat(collectionMetafile)
if err != nil {
// Regular directory
- cw := CollectionWriter{runner.Kc, nil, sync.Mutex{}}
+ cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
if err != nil {
return fmt.Errorf("While uploading output files: %v", err)
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{
+ "ensure_unique_name": true,
"collection": arvadosclient.Dict{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "output for " + runner.Container.UUID,
"manifest_text": manifestText}},
&response)
return nil
}
-func (runner *ContainerRunner) loadDiscoveryVars() {
- tl, err := runner.ArvClient.Discovery("defaultTrashLifetime")
- if err != nil {
- log.Fatalf("getting defaultTrashLifetime from discovery document: %s", err)
+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
+ }
+
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ 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())
}
- runner.trashLifetime = time.Duration(tl.(float64)) * time.Second
+ return extracted.Text, nil
}
func (runner *ContainerRunner) CleanupDirs() {
var response arvados.Collection
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
+ "ensure_unique_name": true,
"collection": arvadosclient.Dict{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "logs for " + runner.Container.UUID,
"manifest_text": mt}},
&response)
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
cr.MkTempDir = ioutil.TempDir
- cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
+ cr.LogCollection = &CollectionWriter{0, kc, nil, nil, sync.Mutex{}}
cr.Container.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
- cr.loadDiscoveryVars()
return cr
}
projects / arvados.git / blobdiff