package main
import (
+ "encoding/json"
"errors"
"flag"
+ "fmt"
"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"
"os"
+ "os/exec"
"os/signal"
"strings"
"sync"
}
// Mount describes the mount points to create inside the container.
-type Mount struct{}
+type Mount struct {
+ Kind string `json:"kind"`
+ Writable bool `json:"writable"`
+ PortableDataHash string `json:"portable_data_hash"`
+ UUID string `json:"uuid"`
+ DeviceType string `json:"device_type"`
+}
// Collection record returned by the API server.
-type Collection struct {
- ManifestText string `json:"manifest_text"`
+type CollectionRecord struct {
+ ManifestText string `json:"manifest_text"`
+ PortableDataHash string `json:"portable_data_hash"`
}
// ContainerRecord is the container record returned by the API server.
Priority int `json:"priority"`
RuntimeConstraints map[string]interface{} `json:"runtime_constraints"`
State string `json:"state"`
+ Output string `json:"output"`
}
// NewLogWriter is a factory function to create a new log writer.
Stderr *ThrottledLogger
LogCollection *CollectionWriter
LogsPDH *string
+ ArvMount *exec.Cmd
+ ArvMountPoint string
+ HostOutputDir string
+ Binds []string
+ OutputPDH *string
CancelLock sync.Mutex
Cancelled bool
SigChan chan os.Signal
runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.ContainerRecord.ContainerImage)
- var collection Collection
+ var collection CollectionRecord
err = runner.ArvClient.Get("collections", runner.ContainerRecord.ContainerImage, nil, &collection)
if err != nil {
- return err
+ return fmt.Errorf("While getting container image collection: %v", 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 errors.New("First file in the collection does not end in .tar")
+ return fmt.Errorf("First file in the container image collection does not end in .tar")
}
imageID = img[:len(img)-4]
}
var readCloser io.ReadCloser
readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
if err != nil {
- return err
+ return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
}
err = runner.Docker.LoadImage(readCloser)
if err != nil {
- return err
+ return fmt.Errorf("While loading container image into Docker: %v", err)
}
} else {
runner.CrunchLog.Print("Docker image is available")
return nil
}
+func (runner *ContainerRunner) SetupMounts() (err error) {
+ runner.ArvMountPoint, err = ioutil.TempDir("", "keep")
+ if err != nil {
+ return fmt.Errorf("While creating keep mount temp dir: %v", err)
+ }
+
+ pdhOnly := true
+ tmpcount := 0
+ arvMountCmd := []string{"--foreground"}
+ collectionPaths := []string{}
+
+ for bind, mnt := range runner.ContainerRecord.Mounts {
+ if mnt.Kind == "collection" {
+ var src string
+ if mnt.UUID != "" && mnt.PortableDataHash != "" {
+ return 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.")
+ }
+ pdhOnly = false
+ src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
+ } else if mnt.PortableDataHash != "" {
+ if mnt.Writable {
+ return fmt.Errorf("Can never write to a collection specified by portable data hash")
+ }
+ src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
+ } else {
+ src = fmt.Sprintf("%s/tmp%i", runner.ArvMountPoint, tmpcount)
+ arvMountCmd = append(arvMountCmd, "--mount-tmp")
+ arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%i", tmpcount))
+ tmpcount += 1
+ }
+ if mnt.Writable {
+ if bind == runner.ContainerRecord.OutputPath {
+ runner.HostOutputDir = src
+ }
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
+ } else {
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
+ }
+ collectionPaths = append(collectionPaths, src)
+ } else if mnt.Kind == "tmp" {
+ if bind == runner.ContainerRecord.OutputPath {
+ runner.HostOutputDir, err = ioutil.TempDir("", "")
+ if err != nil {
+ return fmt.Errorf("While creating mount temp dir: %v", err)
+ }
+
+ runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", runner.HostOutputDir, bind))
+ } else {
+ runner.Binds = append(runner.Binds, bind)
+ }
+ } else {
+ return fmt.Errorf("Unknown mount kind '%s'", mnt.Kind)
+ }
+ }
+
+ if runner.HostOutputDir == "" {
+ return fmt.Errorf("Output path does not correspond to a writable mount point")
+ }
+
+ if pdhOnly {
+ arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
+ } else {
+ arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
+ }
+ arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
+
+ runner.ArvMount = exec.Command("arv-mount", arvMountCmd...)
+ err = runner.ArvMount.Start()
+ if err != nil {
+ runner.ArvMount = nil
+ return 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
+}
+
// StartContainer creates the container and runs it.
func (runner *ContainerRunner) StartContainer() (err error) {
runner.CrunchLog.Print("Creating Docker container")
for k, v := range runner.ContainerRecord.Environment {
runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
}
+ runner.ContainerConfig.NetworkDisabled = true
runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
if err != nil {
- return
+ return fmt.Errorf("While creating container: %v", err)
}
- hostConfig := &dockerclient.HostConfig{}
+ hostConfig := &dockerclient.HostConfig{Binds: runner.Binds}
runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
err = runner.Docker.StartContainer(runner.ContainerID, hostConfig)
if err != nil {
- return
+ return fmt.Errorf("While starting container: %v", err)
}
return nil
var stderrReader, stdoutReader io.Reader
stderrReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stderr: true})
if err != nil {
- return
+ return fmt.Errorf("While getting container standard error: %v", err)
}
stdoutReader, err = runner.Docker.ContainerLogs(runner.ContainerID, &dockerclient.LogOptions{Follow: true, Stdout: true})
if err != nil {
- return
+ return fmt.Errorf("While getting container standard output: %v", err)
}
runner.loggingDone = make(chan bool)
result := runner.Docker.Wait(runner.ContainerID)
wr := <-result
if wr.Error != nil {
- return wr.Error
+ return fmt.Errorf("While waiting for container to finish: %v", wr.Error)
}
runner.ExitCode = &wr.ExitCode
return nil
}
+// HandleOutput sets the output and unmounts the FUSE mount.
+func (runner *ContainerRunner) CaptureOutput() error {
+ if runner.ArvMount != nil {
+ defer func() {
+ umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
+ umount.Run()
+ }()
+ }
+
+ if runner.finalState != "Complete" {
+ return nil
+ }
+
+ if runner.HostOutputDir == "" {
+ return nil
+ }
+
+ _, err := os.Stat(runner.HostOutputDir)
+ if err != nil {
+ return fmt.Errorf("While checking host output path: %v", err)
+ }
+
+ var manifestText string
+
+ collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
+ _, err = os.Stat(collectionMetafile)
+ if err != nil {
+ // Regular directory
+ cw := CollectionWriter{runner.Kc, nil, sync.Mutex{}}
+ manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
+ if err != nil {
+ return fmt.Errorf("While uploading output files: %v", err)
+ }
+ } else {
+ // FUSE mount directory
+ file, openerr := os.Open(collectionMetafile)
+ if openerr != nil {
+ return fmt.Errorf("While opening FUSE metafile: %v", err)
+ }
+ defer file.Close()
+
+ rec := CollectionRecord{}
+ err = json.NewDecoder(file).Decode(&rec)
+ if err != nil {
+ return fmt.Errorf("While reading FUSE metafile: %v", err)
+ }
+ manifestText = rec.ManifestText
+ }
+
+ var response CollectionRecord
+ err = runner.ArvClient.Create("collections",
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "manifest_text": manifestText}},
+ &response)
+ if err != nil {
+ return fmt.Errorf("While creating output collection: %v", err)
+ }
+
+ runner.OutputPDH = new(string)
+ *runner.OutputPDH = response.PortableDataHash
+
+ return nil
+}
+
// CommitLogs posts the collection containing the final container logs.
func (runner *ContainerRunner) CommitLogs() error {
runner.CrunchLog.Print(runner.finalState)
mt, err := runner.LogCollection.ManifestText()
if err != nil {
- return err
+ return fmt.Errorf("While creating log manifest: %v", err)
}
- response := make(map[string]string)
+ var response CollectionRecord
err = runner.ArvClient.Create("collections",
- arvadosclient.Dict{"name": "logs for " + runner.ContainerRecord.UUID,
- "manifest_text": mt},
- response)
+ arvadosclient.Dict{
+ "collection": arvadosclient.Dict{
+ "name": "logs for " + runner.ContainerRecord.UUID,
+ "manifest_text": mt}},
+ &response)
if err != nil {
- return err
+ return fmt.Errorf("While creating log collection: %v", err)
}
runner.LogsPDH = new(string)
- *runner.LogsPDH = response["portable_data_hash"]
+ *runner.LogsPDH = response.PortableDataHash
return nil
}
// UpdateContainerRecordRunning updates the container state to "Running"
func (runner *ContainerRunner) UpdateContainerRecordRunning() error {
- update := arvadosclient.Dict{"state": "Running"}
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, update, nil)
+ return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID,
+ arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
}
// UpdateContainerRecordComplete updates the container record state on API
if runner.ExitCode != nil {
update["exit_code"] = *runner.ExitCode
}
+ if runner.OutputPDH != nil {
+ update["output"] = runner.OutputPDH
+ }
update["state"] = runner.finalState
- return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, update, nil)
+ return runner.ArvClient.Update("containers", runner.ContainerRecord.UUID, arvadosclient.Dict{"container": update}, nil)
}
// NewArvLogWriter creates an ArvLogWriter
}
// Run the full container lifecycle.
-func (runner *ContainerRunner) Run(containerUUID string) (err error) {
- runner.CrunchLog.Printf("Executing container '%s'", containerUUID)
+func (runner *ContainerRunner) Run() (err error) {
+ runner.CrunchLog.Printf("Executing container '%s'", runner.ContainerRecord.UUID)
var runerr, waiterr error
runner.finalState = "Complete"
}
- // (6) write logs
+ // (7) capture output
+ outputerr := runner.CaptureOutput()
+ if outputerr != nil {
+ runner.CrunchLog.Print(outputerr)
+ }
+
+ // (8) write logs
logerr := runner.CommitLogs()
if logerr != nil {
runner.CrunchLog.Print(logerr)
}
- // (7) update container record with results
+ // (9) update container record with results
updateerr := runner.UpdateContainerRecordComplete()
if updateerr != nil {
runner.CrunchLog.Print(updateerr)
}
}()
- err = runner.ArvClient.Get("containers", containerUUID, nil, &runner.ContainerRecord)
+ err = runner.ArvClient.Get("containers", runner.ContainerRecord.UUID, nil, &runner.ContainerRecord)
if err != nil {
- return
+ return fmt.Errorf("While getting container record: %v", err)
}
- // (0) setup signal handling
+ // (1) setup signal handling
err = runner.SetupSignals()
if err != nil {
- return
+ return fmt.Errorf("While setting up signal handling: %v", err)
}
- // (1) check for and/or load image
+ // (2) check for and/or load image
err = runner.LoadImage()
if err != nil {
- return
+ return fmt.Errorf("While loading container image: %v", err)
+ }
+
+ // (3) set up FUSE mount and binds
+ err = runner.SetupMounts()
+ if err != nil {
+ return fmt.Errorf("While setting up mounts: %v", err)
}
- // (2) start container
+ // (3) create and start container
err = runner.StartContainer()
if err != nil {
if err == ErrCancelled {
return
}
- // (3) update container record state
+ // (4) update container record state
err = runner.UpdateContainerRecordRunning()
if err != nil {
runner.CrunchLog.Print(err)
}
- // (4) attach container logs
+ // (5) attach container logs
runerr = runner.AttachLogs()
if runerr != nil {
runner.CrunchLog.Print(runerr)
}
- // (5) wait for container to finish
+ // (6) wait for container to finish
waiterr = runner.WaitFinish()
return
// NewContainerRunner creates a new container runner.
func NewContainerRunner(api IArvadosClient,
kc IKeepClient,
- docker ThinDockerClient) *ContainerRunner {
+ docker ThinDockerClient,
+ containerUUID string) *ContainerRunner {
cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
cr.NewLogWriter = cr.NewArvLogWriter
- cr.LogCollection = &CollectionWriter{kc, nil}
+ cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
+ cr.ContainerRecord.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
return cr
}
log.Fatal(err)
}
- cr := NewContainerRunner(api, kc, docker)
+ cr := NewContainerRunner(api, kc, docker, flag.Arg(0))
- err = cr.Run(flag.Arg(0))
+ err = cr.Run()
if err != nil {
log.Fatal(err)
}
projects / arvados.git / blobdiff