package main
+// Dispatcher service for Crunch that submits containers to the slurm queue.
+
import (
- "bufio"
"flag"
"fmt"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/dispatch"
"io/ioutil"
"log"
"math"
"os"
"os/exec"
- "os/signal"
- "strconv"
- "sync"
- "syscall"
+ "strings"
"time"
)
}
var (
- arv arvadosclient.ArvadosClient
- runningCmds map[string]*exec.Cmd
- runningCmdsMutex sync.Mutex
- waitGroup sync.WaitGroup
- doneProcessing chan bool
- sigChan chan os.Signal
+ crunchRunCommand *string
+ squeueUpdater Squeue
)
func doMain() error {
10,
"Interval in seconds to poll for queued containers")
- priorityPollInterval := flags.Int(
- "container-priority-poll-interval",
- 60,
- "Interval in seconds to check priority of a dispatched container")
-
- crunchRunCommand := flags.String(
+ crunchRunCommand = flags.String(
"crunch-run-command",
"/usr/bin/crunch-run",
"Crunch command to run container")
- finishCommand := flags.String(
- "finish-command",
- "/usr/bin/crunch-finish-slurm.sh",
- "Command to run from strigger when job is finished")
-
// Parse args; omit the first arg which is the command name
flags.Parse(os.Args[1:])
- var err error
- arv, err = arvadosclient.MakeArvadosClient()
+ arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
+ log.Printf("Error making Arvados client: %v", err)
return err
}
+ arv.Retries = 25
- // Channel to terminate
- doneProcessing = make(chan bool)
-
- // Graceful shutdown
- sigChan = make(chan os.Signal, 1)
- signal.Notify(sigChan, syscall.SIGINT, syscall.SIGTERM, syscall.SIGQUIT)
- go func(sig <-chan os.Signal) {
- for sig := range sig {
- log.Printf("Caught signal: %v", sig)
- doneProcessing <- true
- }
- }(sigChan)
-
- // Run all queued containers
- runQueuedContainers(*pollInterval, *priorityPollInterval, *crunchRunCommand, *finishCommand)
-
- // Wait for all running crunch jobs to complete / terminate
- waitGroup.Wait()
-
- return nil
-}
-
-type apiClientAuthorization struct {
- UUID string `json:"uuid"`
- APIToken string `json:"api_token"`
-}
-
-type apiClientAuthorizationList struct {
- Items []apiClientAuthorization `json:"items"`
-}
-
-// Poll for queued containers using pollInterval.
-// Invoke dispatchSlurm for each ticker cycle, which will run all the queued containers.
-//
-// Any errors encountered are logged but the program would continue to run (not exit).
-// This is because, once one or more crunch jobs are running,
-// we would need to wait for them complete.
-func runQueuedContainers(pollInterval, priorityPollInterval int, crunchRunCommand, finishCommand string) {
- var auth apiClientAuthorization
- err := arv.Call("GET", "api_client_authorizations", "", "current", nil, &auth)
- if err != nil {
- log.Printf("Error getting my token UUID: %v", err)
- return
- }
-
- ticker := time.NewTicker(time.Duration(pollInterval) * time.Second)
- for {
- select {
- case <-ticker.C:
- dispatchSlurm(auth, time.Duration(priorityPollInterval)*time.Second, crunchRunCommand, finishCommand)
- case <-doneProcessing:
- ticker.Stop()
- return
- }
- }
-}
-
-// Container data
-type Container struct {
- UUID string `json:"uuid"`
- State string `json:"state"`
- Priority int `json:"priority"`
- RuntimeConstraints map[string]int64 `json:"runtime_constraints"`
- LockedByUUID string `json:"locked_by_uuid"`
-}
-
-// ContainerList is a list of the containers from api
-type ContainerList struct {
- Items []Container `json:"items"`
-}
+ squeueUpdater.StartMonitor(time.Duration(*pollInterval) * time.Second)
+ defer squeueUpdater.Done()
-// Get the list of queued containers from API server and invoke run
-// for each container.
-func dispatchSlurm(auth apiClientAuthorization, pollInterval time.Duration, crunchRunCommand, finishCommand string) {
- params := arvadosclient.Dict{
- "filters": [][]interface{}{{"state", "in", []string{"Queued", "Locked"}}},
- }
+ dispatcher := dispatch.Dispatcher{
+ Arv: arv,
+ RunContainer: run,
+ PollInterval: time.Duration(*pollInterval) * time.Second,
+ DoneProcessing: make(chan struct{})}
- var containers ContainerList
- err := arv.List("containers", params, &containers)
+ err = dispatcher.RunDispatcher()
if err != nil {
- log.Printf("Error getting list of queued containers: %q", err)
- return
+ return err
}
- for _, container := range containers.Items {
- if container.State == "Locked" {
- if container.LockedByUUID != auth.UUID {
- // Locked by a different dispatcher
- continue
- } else if checkMine(container.UUID) {
- // I already have a goroutine running
- // for this container: it just hasn't
- // gotten past Locked state yet.
- continue
- }
- log.Printf("WARNING: found container %s already locked by my token %s, but I didn't submit it. "+
- "Assuming it was left behind by a previous dispatch process, and waiting for it to finish.",
- container.UUID, auth.UUID)
- setMine(container.UUID, true)
- go func() {
- waitContainer(container, pollInterval)
- setMine(container.UUID, false)
- }()
- }
- go run(container, crunchRunCommand, finishCommand, pollInterval)
- }
+ return nil
}
// sbatchCmd
-func sbatchFunc(container Container) *exec.Cmd {
+func sbatchFunc(container dispatch.Container) *exec.Cmd {
memPerCPU := math.Ceil((float64(container.RuntimeConstraints["ram"])) / (float64(container.RuntimeConstraints["vcpus"] * 1048576)))
return exec.Command("sbatch", "--share", "--parsable",
- "--job-name="+container.UUID,
- "--mem-per-cpu="+strconv.Itoa(int(memPerCPU)),
- "--cpus-per-task="+strconv.Itoa(int(container.RuntimeConstraints["vcpus"])))
+ fmt.Sprintf("--job-name=%s", container.UUID),
+ fmt.Sprintf("--mem-per-cpu=%d", int(memPerCPU)),
+ fmt.Sprintf("--cpus-per-task=%d", int(container.RuntimeConstraints["vcpus"])),
+ fmt.Sprintf("--priority=%d", container.Priority))
}
+// Wrap these so that they can be overridden by tests
var sbatchCmd = sbatchFunc
-// striggerCmd
-func striggerFunc(jobid, containerUUID, finishCommand, apiHost, apiToken, apiInsecure string) *exec.Cmd {
- return exec.Command("strigger", "--set", "--jobid="+jobid, "--fini",
- fmt.Sprintf("--program=%s %s %s %s %s", finishCommand, apiHost, apiToken, apiInsecure, containerUUID))
-}
-
-var striggerCmd = striggerFunc
-
// Submit job to slurm using sbatch.
-func submit(container Container, crunchRunCommand string) (jobid string, submitErr error) {
+func submit(dispatcher *dispatch.Dispatcher,
+ container dispatch.Container, crunchRunCommand string) (jobid string, submitErr error) {
submitErr = nil
defer func() {
// OK, no cleanup needed
return
}
- err := arv.Update("containers", container.UUID,
+ err := dispatcher.Arv.Update("containers", container.UUID,
arvadosclient.Dict{
"container": arvadosclient.Dict{"state": "Queued"}},
nil)
return
}
+ // Mutex between squeue sync and running sbatch or scancel.
+ squeueUpdater.SlurmLock.Lock()
+ defer squeueUpdater.SlurmLock.Unlock()
+
err := cmd.Start()
if err != nil {
submitErr = fmt.Errorf("Error starting %v: %v", cmd.Args, err)
b, _ := ioutil.ReadAll(stdoutReader)
stdoutReader.Close()
stdoutChan <- b
- close(stdoutChan)
}()
stderrChan := make(chan []byte)
b, _ := ioutil.ReadAll(stderrReader)
stderrReader.Close()
stderrChan <- b
- close(stderrChan)
}()
// Send a tiny script on stdin to execute the crunch-run command
stdoutMsg := <-stdoutChan
stderrmsg := <-stderrChan
+ close(stdoutChan)
+ close(stderrChan)
+
if err != nil {
submitErr = fmt.Errorf("Container submission failed %v: %v %v", cmd.Args, err, stderrmsg)
return
}
// If everything worked out, got the jobid on stdout
- jobid = string(stdoutMsg)
+ jobid = strings.TrimSpace(string(stdoutMsg))
return
}
-// finalizeRecordOnFinish uses 'strigger' command to register a script that will run on
-// the slurm controller when the job finishes.
-func finalizeRecordOnFinish(jobid, containerUUID, finishCommand, apiHost, apiToken, apiInsecure string) {
- cmd := striggerCmd(jobid, containerUUID, finishCommand, apiHost, apiToken, apiInsecure)
- cmd.Stdout = os.Stdout
- cmd.Stderr = os.Stderr
- err := cmd.Run()
- if err != nil {
- log.Printf("While setting up strigger: %v", err)
- // BUG: we drop the error here and forget about it. A
- // human has to notice the container is stuck in
- // Running state, and fix it manually.
- }
-}
-
-// Run a queued container: [1] Set container state to locked. [2]
-// Execute crunch-run as a slurm batch job. [3] waitContainer().
-func run(container Container, crunchRunCommand, finishCommand string, pollInterval time.Duration) {
- setMine(container.UUID, true)
- defer setMine(container.UUID, false)
-
- // Update container status to Locked. This will fail if
- // another dispatcher (token) has already locked it. It will
- // succeed if *this* dispatcher has already locked it.
- err := arv.Update("containers", container.UUID,
- arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": "Locked"}},
- nil)
- if err != nil {
- log.Printf("Error updating container state to 'Locked' for %v: %q", container.UUID, err)
- return
- }
-
- log.Printf("About to submit queued container %v", container.UUID)
+// If the container is marked as Locked, check if it is already in the slurm
+// queue. If not, submit it.
+//
+// If the container is marked as Running, check if it is in the slurm queue.
+// If not, mark it as Cancelled.
+func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container dispatch.Container, monitorDone *bool) {
+ submitted := false
+ for !*monitorDone {
+ if inQ, err := squeueUpdater.CheckSqueue(container.UUID); err != nil {
+ // Most recent run of squeue had an error, so do nothing.
+ continue
+ } else if inQ {
+ // Found in the queue, so continue monitoring
+ submitted = true
+ } else if container.State == dispatch.Locked && !submitted {
+ // Not in queue but in Locked state and we haven't
+ // submitted it yet, so submit it.
+
+ log.Printf("About to submit queued container %v", container.UUID)
+
+ if _, err := submit(dispatcher, container, *crunchRunCommand); err != nil {
+ log.Printf("Error submitting container %s to slurm: %v",
+ container.UUID, err)
+ // maybe sbatch is broken, put it back to queued
+ dispatcher.UpdateState(container.UUID, dispatch.Queued)
+ }
+ submitted = true
+ } else {
+ // Not in queue and we are not going to submit it.
+ // Refresh the container state. If it is
+ // Complete/Cancelled, do nothing, if it is Locked then
+ // release it back to the Queue, if it is Running then
+ // clean up the record.
+
+ var con dispatch.Container
+ err := dispatcher.Arv.Get("containers", container.UUID, nil, &con)
+ if err != nil {
+ log.Printf("Error getting final container state: %v", err)
+ }
- jobid, err := submit(container, crunchRunCommand)
- if err != nil {
- log.Printf("Error submitting container %s to slurm: %v", container.UUID, err)
- return
- }
+ var st string
+ switch con.State {
+ case dispatch.Locked:
+ st = dispatch.Queued
+ case dispatch.Running:
+ st = dispatch.Cancelled
+ default:
+ // Container state is Queued, Complete or Cancelled so stop monitoring it.
+ return
+ }
- insecure := "0"
- if arv.ApiInsecure {
- insecure = "1"
- }
- finalizeRecordOnFinish(jobid, container.UUID, finishCommand, arv.ApiServer, arv.ApiToken, insecure)
-
- // Update container status to Running. This will fail if
- // another dispatcher (token) has already locked it. It will
- // succeed if *this* dispatcher has already locked it.
- err = arv.Update("containers", container.UUID,
- arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": "Running"}},
- nil)
- if err != nil {
- log.Printf("Error updating container state to 'Running' for %v: %q", container.UUID, err)
+ log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.",
+ container.UUID, con.State, st)
+ dispatcher.UpdateState(container.UUID, st)
+ }
}
- log.Printf("Submitted container %v to slurm", container.UUID)
- waitContainer(container, pollInterval)
}
-// Wait for a container to finish. Cancel the slurm job if the
-// container priority changes to zero before it ends.
-func waitContainer(container Container, pollInterval time.Duration) {
+// Run or monitor a container.
+//
+// Monitor status updates. If the priority changes to zero, cancel the
+// container using scancel.
+func run(dispatcher *dispatch.Dispatcher,
+ container dispatch.Container,
+ status chan dispatch.Container) {
+
log.Printf("Monitoring container %v started", container.UUID)
defer log.Printf("Monitoring container %v finished", container.UUID)
- pollTicker := time.NewTicker(pollInterval)
- defer pollTicker.Stop()
- for _ = range pollTicker.C {
- var updated Container
- err := arv.Get("containers", container.UUID, nil, &updated)
- if err != nil {
- log.Printf("Error getting container %s: %q", container.UUID, err)
- continue
- }
- if updated.State == "Complete" || updated.State == "Cancelled" {
- return
- }
- if updated.Priority != 0 {
- continue
- }
-
- // Priority is zero, but state is Running or Locked
- log.Printf("Canceling container %s", container.UUID)
-
- err = exec.Command("scancel", "--name="+container.UUID).Run()
- if err != nil {
- log.Printf("Error stopping container %s with scancel: %v", container.UUID, err)
- if inQ, err := checkSqueue(container.UUID); err != nil {
- log.Printf("Error running squeue: %v", err)
- continue
- } else if inQ {
- log.Printf("Container %s is still in squeue; will retry", container.UUID)
- continue
+ monitorDone := false
+ go monitorSubmitOrCancel(dispatcher, container, &monitorDone)
+
+ for container = range status {
+ if container.State == dispatch.Locked || container.State == dispatch.Running {
+ if container.Priority == 0 {
+ log.Printf("Canceling container %s", container.UUID)
+
+ // Mutex between squeue sync and running sbatch or scancel.
+ squeueUpdater.SlurmLock.Lock()
+ err := exec.Command("scancel", "--name="+container.UUID).Run()
+ squeueUpdater.SlurmLock.Unlock()
+
+ if err != nil {
+ log.Printf("Error stopping container %s with scancel: %v",
+ container.UUID, err)
+ if inQ, err := squeueUpdater.CheckSqueue(container.UUID); err != nil {
+ continue
+ } else if inQ {
+ log.Printf("Container %s is still in squeue after scancel.",
+ container.UUID)
+ continue
+ }
+ }
+
+ err = dispatcher.UpdateState(container.UUID, dispatch.Cancelled)
}
}
-
- err = arv.Update("containers", container.UUID,
- arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": "Cancelled"}},
- nil)
- if err != nil {
- log.Printf("Error updating state for container %s: %s", container.UUID, err)
- continue
- }
-
- return
- }
-}
-
-func checkSqueue(uuid string) (bool, error) {
- cmd := exec.Command("squeue", "--format=%j")
- sq, err := cmd.StdoutPipe()
- if err != nil {
- return false, err
- }
- cmd.Start()
- defer cmd.Wait()
- scanner := bufio.NewScanner(sq)
- found := false
- for scanner.Scan() {
- if scanner.Text() == uuid {
- found = true
- }
- }
- if err := scanner.Err(); err != nil {
- return false, err
}
- return found, nil
-}
-
-var mineMutex sync.RWMutex
-var mineMap = make(map[string]bool)
-
-// Goroutine-safely add/remove uuid to the set of "my" containers,
-// i.e., ones for which this process has a goroutine running.
-func setMine(uuid string, t bool) {
- mineMutex.Lock()
- if t {
- mineMap[uuid] = true
- } else {
- delete(mineMap, uuid)
- }
- mineMutex.Unlock()
-}
-
-// Check whether there is already a goroutine running for this
-// container.
-func checkMine(uuid string) bool {
- mineMutex.RLocker().Lock()
- defer mineMutex.RLocker().Unlock()
- return mineMap[uuid]
+ monitorDone = true
}
projects / arvados.git / blobdiff