+// 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 (
+ "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"
"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"
)
+var version = "dev"
+
+// 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) }
+
+ 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")
+ getVersion := flags.Bool(
+ "version",
+ false,
+ "Print version information and exit.")
+ // Parse args; omit the first arg which is the command name
+ flags.Parse(os.Args[1:])
- pollInterval := flags.Int(
- "poll-interval",
- 10,
- "Interval in seconds to poll for queued containers")
+ // Print version information if requested
+ if *getVersion {
+ fmt.Printf("Version: %s\n", version)
+ os.Exit(0)
+ }
- crunchRunCommand = flags.String(
- "crunch-run-command",
- "/usr/bin/crunch-run",
- "Crunch command to run container")
+ log.Printf("crunch-dispatch-slurm %q started", version)
- // Parse args; omit the first arg which is the command name
- flags.Parse(os.Args[1:])
+ err := readConfig(&theConfig, *configPath)
+ if err != nil {
+ return err
+ }
+
+ 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).")
+ }
+
+ if *dumpConfig {
+ log.Fatal(config.DumpAndExit(theConfig))
+ }
arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
}
arv.Retries = 25
- squeueUpdater.StartMonitor(time.Duration(*pollInterval) * time.Second)
- defer squeueUpdater.Done()
+ sqCheck = &SqueueChecker{Period: time.Duration(theConfig.PollPeriod)}
+ defer sqCheck.Stop()
- dispatcher := dispatch.Dispatcher{
+ dispatcher := &dispatch.Dispatcher{
Arv: arv,
RunContainer: run,
- PollInterval: time.Duration(*pollInterval) * time.Second,
- DoneProcessing: make(chan struct{})}
+ PollPeriod: time.Duration(theConfig.PollPeriod),
+ MinRetryPeriod: time.Duration(theConfig.MinRetryPeriod),
+ }
- err = dispatcher.RunDispatcher()
- if err != nil {
- return err
+ if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
+ log.Printf("Error notifying init daemon: %v", err)
}
- return nil
+ go checkSqueueForOrphans(dispatcher, sqCheck)
+
+ return dispatcher.Run(context.Background())
+}
+
+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.TrackContainer(uuid)
+ if err != nil {
+ log.Printf("checkSqueueForOrphans: TrackContainer(%s): %s", uuid, err)
+ }
+ }
}
// 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))
+func sbatchFunc(container arvados.Container) *exec.Cmd {
+ mem := int64(math.Ceil(float64(container.RuntimeConstraints.RAM+container.RuntimeConstraints.KeepCacheRAM) / float64(1048576)))
+
+ var disk int64
+ for _, m := range container.Mounts {
+ if m.Kind == "tmp" {
+ disk += m.Capacity
+ }
+ }
+ 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, ",")))
+ }
+
+ return exec.Command("sbatch", sbatchArgs...)
}
// scancelCmd
-func scancelFunc(container dispatch.Container) *exec.Cmd {
+func scancelFunc(container arvados.Container) *exec.Cmd {
return exec.Command("scancel", "--name="+container.UUID)
}
var scancelCmd = scancelFunc
// 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
- }
- err := dispatcher.Arv.Update("containers", container.UUID,
- arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": "Queued"}},
- nil)
- if err != nil {
- log.Printf("Error unlocking container %s: %v", container.UUID, err)
- }
- }()
-
- // Create the command and attach to stdin/stdout
+func submit(dispatcher *dispatch.Dispatcher, container arvados.Container, crunchRunCommand []string) error {
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
- }
+ // 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)))
- stderrReader, stderrErr := cmd.StderrPipe()
- if stderrErr != nil {
- submitErr = fmt.Errorf("Error creating stderr pipe %v: %q", container.UUID, stderrErr)
- return
- }
+ var stdout, stderr bytes.Buffer
+ cmd.Stdout = &stdout
+ cmd.Stderr = &stderr
// 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)
- return
- }
-
- stdoutChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stdoutReader)
- stdoutReader.Close()
- stdoutChan <- b
- }()
+ sqCheck.L.Lock()
+ defer sqCheck.L.Unlock()
- stderrChan := make(chan []byte)
- go func() {
- b, _ := ioutil.ReadAll(stderrReader)
- stderrReader.Close()
- stderrChan <- b
- }()
+ log.Printf("exec sbatch %+q", cmd.Args)
+ err := cmd.Run()
- // 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()
+ switch err.(type) {
+ case nil:
+ log.Printf("sbatch succeeded: %q", strings.TrimSpace(stdout.String()))
+ return nil
- err = cmd.Wait()
+ case *exec.ExitError:
+ dispatcher.Unlock(container.UUID)
+ return fmt.Errorf("sbatch %+q failed: %v (stderr: %q)", cmd.Args, err, stderr.Bytes())
- 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
+ default:
+ dispatcher.Unlock(container.UUID)
+ return fmt.Errorf("exec failed: %v", err)
}
+}
- // If everything worked out, got the jobid on stdout
- jobid = strings.TrimSpace(string(stdoutMsg))
+// 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
+ }
+ }
- return
-}
+ 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 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 squeueUpdater.CheckSqueue(container.UUID) {
- // 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)
+ // 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) {
+ }
+ cancel()
+ }(ctr.UUID)
+
+ for {
+ select {
+ 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)
}
-
- var st string
- switch con.State {
- case dispatch.Locked:
- st = dispatch.Queued
+ switch ctr.State {
case dispatch.Running:
- st = dispatch.Cancelled
- default:
- // Container state is Queued, Complete or Cancelled so stop monitoring it.
- return
+ disp.UpdateState(ctr.UUID, dispatch.Cancelled)
+ case dispatch.Locked:
+ disp.Unlock(ctr.UUID)
+ }
+ return
+ 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)
}
-
- 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)
}
}
}
-// 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)
-
- 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 := scancelCmd(container).Run()
- squeueUpdater.SlurmLock.Unlock()
-
- if err != nil {
- log.Printf("Error stopping container %s with scancel: %v",
- container.UUID, err)
- if squeueUpdater.CheckSqueue(container.UUID) {
- log.Printf("Container %s is still in squeue after scancel.",
- container.UUID)
- continue
- }
- }
-
- err = dispatcher.UpdateState(container.UUID, dispatch.Cancelled)
- }
- }
+func scancel(ctr arvados.Container) {
+ sqCheck.L.Lock()
+ cmd := scancelCmd(ctr)
+ msg, err := cmd.CombinedOutput()
+ sqCheck.L.Unlock()
+
+ 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)
+ }
+}
+
+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
}
- monitorDone = true
+ return err
}
projects / arvados.git / blobdiff