+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package main
// Dispatcher service for Crunch that submits containers to the slurm queue.
import (
- "bufio"
+ "bytes"
+ "context"
"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"
+ "regexp"
"strings"
- "sync"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/config"
+ "git.curoverse.com/arvados.git/sdk/go/dispatch"
+ "github.com/coreos/go-systemd/daemon"
)
-type Squeue struct {
- sync.Mutex
- squeueContents []string
- SqueueDone chan struct{}
+// Config used by crunch-dispatch-slurm
+type Config struct {
+ Client arvados.Client
+
+ SbatchArguments []string
+ PollPeriod arvados.Duration
+
+ // crunch-run command to invoke. The container UUID will be
+ // appended. If nil, []string{"crunch-run"} will be used.
+ //
+ // Example: []string{"crunch-run", "--cgroup-parent-subsystem=memory"}
+ CrunchRunCommand []string
+
+ // Minimum time between two attempts to run the same container
+ MinRetryPeriod arvados.Duration
}
func main() {
err := doMain()
if err != nil {
- log.Fatalf("%q", err)
+ log.Fatal(err)
}
}
var (
- crunchRunCommand *string
- squeueUpdater Squeue
+ theConfig Config
+ sqCheck = &SqueueChecker{}
)
+const defaultConfigPath = "/etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml"
+
func doMain() error {
flags := flag.NewFlagSet("crunch-dispatch-slurm", flag.ExitOnError)
+ flags.Usage = func() { usage(flags) }
- pollInterval := flags.Int(
- "poll-interval",
- 10,
- "Interval in seconds to poll for queued containers")
-
- crunchRunCommand = flags.String(
- "crunch-run-command",
- "/usr/bin/crunch-run",
- "Crunch command to run container")
+ configPath := flags.String(
+ "config",
+ defaultConfigPath,
+ "`path` to JSON or YAML configuration file")
+ dumpConfig := flag.Bool(
+ "dump-config",
+ false,
+ "write current configuration to stdout and exit")
// Parse args; omit the first arg which is the command name
flags.Parse(os.Args[1:])
- arv, err := arvadosclient.MakeArvadosClient()
+ err := readConfig(&theConfig, *configPath)
if err != nil {
- log.Printf("Error making Arvados client: %v", err)
return err
}
- arv.Retries = 25
- dispatcher := dispatch.Dispatcher{
- Arv: arv,
- RunContainer: run,
- PollInterval: time.Duration(*pollInterval) * time.Second,
- DoneProcessing: make(chan struct{})}
+ if theConfig.CrunchRunCommand == nil {
+ theConfig.CrunchRunCommand = []string{"crunch-run"}
+ }
+
+ if theConfig.PollPeriod == 0 {
+ theConfig.PollPeriod = arvados.Duration(10 * time.Second)
+ }
+
+ if theConfig.Client.APIHost != "" || theConfig.Client.AuthToken != "" {
+ // Copy real configs into env vars so [a]
+ // MakeArvadosClient() uses them, and [b] they get
+ // propagated to crunch-run via SLURM.
+ os.Setenv("ARVADOS_API_HOST", theConfig.Client.APIHost)
+ os.Setenv("ARVADOS_API_TOKEN", theConfig.Client.AuthToken)
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "")
+ if theConfig.Client.Insecure {
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "1")
+ }
+ os.Setenv("ARVADOS_KEEP_SERVICES", strings.Join(theConfig.Client.KeepServiceURIs, " "))
+ os.Setenv("ARVADOS_EXTERNAL_CLIENT", "")
+ } else {
+ log.Printf("warning: Client credentials missing from config, so falling back on environment variables (deprecated).")
+ }
- squeueUpdater.SqueueDone = make(chan struct{})
- go squeueUpdater.SyncSqueue(time.Duration(*pollInterval) * time.Second)
+ if *dumpConfig {
+ log.Fatal(config.DumpAndExit(theConfig))
+ }
- err = dispatcher.RunDispatcher()
+ arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
+ log.Printf("Error making Arvados client: %v", err)
return err
}
+ arv.Retries = 25
- squeueUpdater.SqueueDone <- struct{}{}
- close(squeueUpdater.SqueueDone)
+ sqCheck = &SqueueChecker{Period: time.Duration(theConfig.PollPeriod)}
+ defer sqCheck.Stop()
- return nil
-}
+ dispatcher := &dispatch.Dispatcher{
+ Arv: arv,
+ RunContainer: run,
+ PollPeriod: time.Duration(theConfig.PollPeriod),
+ MinRetryPeriod: time.Duration(theConfig.MinRetryPeriod),
+ }
-// sbatchCmd
-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",
- 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))
-}
+ if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
+ log.Printf("Error notifying init daemon: %v", err)
+ }
-// squeueFunc
-func squeueFunc() *exec.Cmd {
- return exec.Command("squeue", "--format=%j")
-}
+ go checkSqueueForOrphans(dispatcher, sqCheck)
-// Wrap these so that they can be overridden by tests
-var sbatchCmd = sbatchFunc
-var squeueCmd = squeueFunc
+ return dispatcher.Run(context.Background())
+}
-// Submit job to slurm using sbatch.
-func submit(dispatcher *dispatch.Dispatcher,
- container dispatch.Container, crunchRunCommand string) (jobid string, submitErr error) {
- submitErr = nil
-
- defer func() {
- // If we didn't get as far as submitting a slurm job,
- // unlock the container and return it to the queue.
- if submitErr == nil {
- // OK, no cleanup needed
- return
+var containerUuidPattern = regexp.MustCompile(`^[a-z0-9]{5}-dz642-[a-z0-9]{15}$`)
+
+// Check the next squeue report, and invoke TrackContainer for all the
+// containers in the report. This gives us a chance to cancel slurm
+// jobs started by a previous dispatch process that never released
+// their slurm allocations even though their container states are
+// Cancelled or Complete. See https://dev.arvados.org/issues/10979
+func checkSqueueForOrphans(dispatcher *dispatch.Dispatcher, sqCheck *SqueueChecker) {
+ for _, uuid := range sqCheck.All() {
+ if !containerUuidPattern.MatchString(uuid) {
+ continue
}
- err := dispatcher.Arv.Update("containers", container.UUID,
- arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": "Queued"}},
- nil)
+ err := dispatcher.TrackContainer(uuid)
if err != nil {
- log.Printf("Error unlocking container %s: %v", container.UUID, err)
+ log.Printf("checkSqueueForOrphans: TrackContainer(%s): %s", uuid, err)
}
- }()
-
- // Create the command and attach to stdin/stdout
- cmd := sbatchCmd(container)
- stdinWriter, stdinerr := cmd.StdinPipe()
- if stdinerr != nil {
- submitErr = fmt.Errorf("Error creating stdin pipe %v: %q", container.UUID, stdinerr)
- return
}
+}
- stdoutReader, stdoutErr := cmd.StdoutPipe()
- if stdoutErr != nil {
- submitErr = fmt.Errorf("Error creating stdout pipe %v: %q", container.UUID, stdoutErr)
- return
- }
+// sbatchCmd
+func sbatchFunc(container arvados.Container) *exec.Cmd {
+ mem := int64(math.Ceil(float64(container.RuntimeConstraints.RAM+container.RuntimeConstraints.KeepCacheRAM) / float64(1048576)))
- stderrReader, stderrErr := cmd.StderrPipe()
- if stderrErr != nil {
- submitErr = fmt.Errorf("Error creating stderr pipe %v: %q", container.UUID, stderrErr)
- return
+ var disk int64
+ for _, m := range container.Mounts {
+ if m.Kind == "tmp" {
+ disk += m.Capacity
+ }
}
-
- err := cmd.Start()
- if err != nil {
- submitErr = fmt.Errorf("Error starting %v: %v", cmd.Args, err)
- return
+ disk = int64(math.Ceil(float64(disk) / float64(1048576)))
+
+ var sbatchArgs []string
+ sbatchArgs = append(sbatchArgs, theConfig.SbatchArguments...)
+ sbatchArgs = append(sbatchArgs, fmt.Sprintf("--job-name=%s", container.UUID))
+ sbatchArgs = append(sbatchArgs, fmt.Sprintf("--mem=%d", mem))
+ sbatchArgs = append(sbatchArgs, fmt.Sprintf("--cpus-per-task=%d", container.RuntimeConstraints.VCPUs))
+ sbatchArgs = append(sbatchArgs, fmt.Sprintf("--tmp=%d", disk))
+ if len(container.SchedulingParameters.Partitions) > 0 {
+ sbatchArgs = append(sbatchArgs, fmt.Sprintf("--partition=%s", strings.Join(container.SchedulingParameters.Partitions, ",")))
}
- stdoutChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stdoutReader)
- stdoutReader.Close()
- stdoutChan <- b
- }()
-
- stderrChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stderrReader)
- stderrReader.Close()
- stderrChan <- b
- }()
+ return exec.Command("sbatch", sbatchArgs...)
+}
- // Send a tiny script on stdin to execute the crunch-run command
- // slurm actually enforces that this must be a #! script
- fmt.Fprintf(stdinWriter, "#!/bin/sh\nexec '%s' '%s'\n", crunchRunCommand, container.UUID)
- stdinWriter.Close()
+// scancelCmd
+func scancelFunc(container arvados.Container) *exec.Cmd {
+ return exec.Command("scancel", "--name="+container.UUID)
+}
- err = cmd.Wait()
+// Wrap these so that they can be overridden by tests
+var sbatchCmd = sbatchFunc
+var scancelCmd = scancelFunc
- stdoutMsg := <-stdoutChan
- stderrmsg := <-stderrChan
+// Submit job to slurm using sbatch.
+func submit(dispatcher *dispatch.Dispatcher, container arvados.Container, crunchRunCommand []string) error {
+ cmd := sbatchCmd(container)
- close(stdoutChan)
- close(stderrChan)
+ // Send a tiny script on stdin to execute the crunch-run
+ // command (slurm requires this to be a #! script)
+ cmd.Stdin = strings.NewReader(execScript(append(crunchRunCommand, container.UUID)))
- if err != nil {
- submitErr = fmt.Errorf("Container submission failed %v: %v %v", cmd.Args, err, stderrmsg)
- return
- }
+ var stdout, stderr bytes.Buffer
+ cmd.Stdout = &stdout
+ cmd.Stderr = &stderr
- // If everything worked out, got the jobid on stdout
- jobid = strings.TrimSpace(string(stdoutMsg))
+ // Mutex between squeue sync and running sbatch or scancel.
+ sqCheck.L.Lock()
+ defer sqCheck.L.Unlock()
- return
-}
+ log.Printf("exec sbatch %+q", cmd.Args)
+ err := cmd.Run()
-func (squeue *Squeue) runSqueue() ([]string, error) {
- var newSqueueContents []string
+ switch err.(type) {
+ case nil:
+ log.Printf("sbatch succeeded: %q", strings.TrimSpace(stdout.String()))
+ return nil
- cmd := squeueCmd()
- sq, err := cmd.StdoutPipe()
- if err != nil {
- return nil, err
- }
- cmd.Start()
- scanner := bufio.NewScanner(sq)
- for scanner.Scan() {
- newSqueueContents = append(newSqueueContents, scanner.Text())
- }
- if err := scanner.Err(); err != nil {
- cmd.Wait()
- return nil, err
- }
+ case *exec.ExitError:
+ dispatcher.Unlock(container.UUID)
+ return fmt.Errorf("sbatch %+q failed: %v (stderr: %q)", cmd.Args, err, stderr.Bytes())
- err = cmd.Wait()
- if err != nil {
- return nil, err
+ default:
+ dispatcher.Unlock(container.UUID)
+ return fmt.Errorf("exec failed: %v", err)
}
-
- return newSqueueContents, nil
}
-func (squeue *Squeue) CheckSqueue(uuid string, check bool) (bool, error) {
- if check {
- n, err := squeue.runSqueue()
- if err != nil {
- return false, err
+// Submit a container to the slurm queue (or resume monitoring if it's
+// already in the queue). Cancel the slurm job if the container's
+// priority changes to zero or its state indicates it's no longer
+// running.
+func run(disp *dispatch.Dispatcher, ctr arvados.Container, status <-chan arvados.Container) {
+ ctx, cancel := context.WithCancel(context.Background())
+ defer cancel()
+
+ if ctr.State == dispatch.Locked && !sqCheck.HasUUID(ctr.UUID) {
+ log.Printf("Submitting container %s to slurm", ctr.UUID)
+ if err := submit(disp, ctr, theConfig.CrunchRunCommand); err != nil {
+ text := fmt.Sprintf("Error submitting container %s to slurm: %s", ctr.UUID, err)
+ log.Print(text)
+
+ lr := arvadosclient.Dict{"log": arvadosclient.Dict{
+ "object_uuid": ctr.UUID,
+ "event_type": "dispatch",
+ "properties": map[string]string{"text": text}}}
+ disp.Arv.Create("logs", lr, nil)
+
+ disp.Unlock(ctr.UUID)
+ return
}
- squeue.Lock()
- squeue.squeueContents = n
- squeue.Unlock()
}
- if uuid != "" {
- squeue.Lock()
- defer squeue.Unlock()
- for _, k := range squeue.squeueContents {
- if k == uuid {
- return true, nil
- }
+ log.Printf("Start monitoring container %v in state %q", ctr.UUID, ctr.State)
+ defer log.Printf("Done monitoring container %s", ctr.UUID)
+
+ // If the container disappears from the slurm queue, there is
+ // no point in waiting for further dispatch updates: just
+ // clean up and return.
+ go func(uuid string) {
+ for ctx.Err() == nil && sqCheck.HasUUID(uuid) {
}
- }
- return false, nil
-}
+ cancel()
+ }(ctr.UUID)
-func (squeue *Squeue) SyncSqueue(pollInterval time.Duration) {
- // TODO: considering using "squeue -i" instead of polling squeue.
- ticker := time.NewTicker(pollInterval)
for {
select {
- case <-squeueUpdater.SqueueDone:
+ case <-ctx.Done():
+ // Disappeared from squeue
+ if err := disp.Arv.Get("containers", ctr.UUID, nil, &ctr); err != nil {
+ log.Printf("Error getting final container state for %s: %s", ctr.UUID, err)
+ }
+ switch ctr.State {
+ case dispatch.Running:
+ disp.UpdateState(ctr.UUID, dispatch.Cancelled)
+ case dispatch.Locked:
+ disp.Unlock(ctr.UUID)
+ }
return
- case <-ticker.C:
- squeue.CheckSqueue("", true)
+ case updated, ok := <-status:
+ if !ok {
+ log.Printf("Dispatcher says container %s is done: cancel slurm job", ctr.UUID)
+ scancel(ctr)
+ } else if updated.Priority == 0 {
+ log.Printf("Container %s has state %q, priority %d: cancel slurm job", ctr.UUID, updated.State, updated.Priority)
+ scancel(ctr)
+ }
}
}
}
-// Run or monitor a container.
-//
-// 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.
-//
-// 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) {
-
- uuid := container.UUID
-
- if container.State == dispatch.Locked {
- if inQ, err := squeueUpdater.CheckSqueue(container.UUID, true); err != nil {
- // maybe squeue is broken, put it back in the queue
- log.Printf("Error running squeue: %v", err)
- dispatcher.UpdateState(container.UUID, dispatch.Queued)
- } else if !inQ {
- 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)
- }
- }
- }
+func scancel(ctr arvados.Container) {
+ sqCheck.L.Lock()
+ cmd := scancelCmd(ctr)
+ msg, err := cmd.CombinedOutput()
+ sqCheck.L.Unlock()
- log.Printf("Monitoring container %v started", uuid)
-
- // periodically check squeue
- doneSqueue := make(chan struct{})
- go func() {
- squeueUpdater.CheckSqueue(container.UUID, true)
- ticker := time.NewTicker(dispatcher.PollInterval)
- for {
- select {
- case <-ticker.C:
- if inQ, err := squeueUpdater.CheckSqueue(container.UUID, false); err != nil {
- log.Printf("Error running squeue: %v", err)
- // don't cancel, just leave it the way it is
- } else if !inQ {
- var con dispatch.Container
- err := dispatcher.Arv.Get("containers", uuid, nil, &con)
- if err != nil {
- log.Printf("Error getting final container state: %v", err)
- }
-
- var st string
- switch con.State {
- case dispatch.Locked:
- st = dispatch.Queued
- case dispatch.Running:
- st = dispatch.Cancelled
- default:
- st = ""
- }
-
- if st != "" {
- log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.",
- uuid, con.State, st)
- dispatcher.UpdateState(uuid, st)
- }
- }
- case <-doneSqueue:
- close(doneSqueue)
- ticker.Stop()
- return
- }
- }
- }()
-
- for container = range status {
- if container.State == dispatch.Locked || container.State == dispatch.Running {
- if container.Priority == 0 {
- 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 := squeueUpdater.CheckSqueue(container.UUID, true); err != nil {
- log.Printf("Error running squeue: %v", err)
- continue
- } else if inQ {
- log.Printf("Container %s is still in squeue after scancel.",
- container.UUID)
- continue
- }
- }
-
- err = dispatcher.UpdateState(container.UUID, dispatch.Cancelled)
- }
- }
+ if err != nil {
+ log.Printf("%q %q: %s %q", cmd.Path, cmd.Args, err, msg)
+ time.Sleep(time.Second)
+ } else if sqCheck.HasUUID(ctr.UUID) {
+ log.Printf("container %s is still in squeue after scancel", ctr.UUID)
+ time.Sleep(time.Second)
}
+}
- doneSqueue <- struct{}{}
-
- log.Printf("Monitoring container %v finished", uuid)
+func readConfig(dst interface{}, path string) error {
+ err := config.LoadFile(dst, path)
+ if err != nil && os.IsNotExist(err) && path == defaultConfigPath {
+ log.Printf("Config not specified. Continue with default configuration.")
+ err = nil
+ }
+ return err
}