package main // Dispatcher service for Crunch that submits containers to the slurm queue. import ( "bytes" "flag" "fmt" "log" "math" "os" "os/exec" "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" ) // 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.Fatal(err) } } var ( 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") // 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 { log.Printf("Error making Arvados client: %v", err) return err } arv.Retries = 25 sqCheck = SqueueChecker{Period: time.Duration(theConfig.PollPeriod)} defer sqCheck.Stop() dispatcher := dispatch.Dispatcher{ Arv: arv, RunContainer: run, PollPeriod: time.Duration(theConfig.PollPeriod), MinRetryPeriod: time.Duration(theConfig.MinRetryPeriod), } if _, err := daemon.SdNotify(false, "READY=1"); err != nil { log.Printf("Error notifying init daemon: %v", err) } return dispatcher.Run() } // sbatchCmd func sbatchFunc(container arvados.Container) *exec.Cmd { memPerCPU := math.Ceil(float64(container.RuntimeConstraints.RAM) / (float64(container.RuntimeConstraints.VCPUs) * 1048576)) var sbatchArgs []string sbatchArgs = append(sbatchArgs, "--share") sbatchArgs = append(sbatchArgs, theConfig.SbatchArguments...) sbatchArgs = append(sbatchArgs, fmt.Sprintf("--job-name=%s", container.UUID)) sbatchArgs = append(sbatchArgs, fmt.Sprintf("--mem-per-cpu=%d", int(memPerCPU))) sbatchArgs = append(sbatchArgs, fmt.Sprintf("--cpus-per-task=%d", container.RuntimeConstraints.VCPUs)) if container.SchedulingParameters.Partitions != nil { sbatchArgs = append(sbatchArgs, fmt.Sprintf("--partition=%s", strings.Join(container.SchedulingParameters.Partitions, ","))) } return exec.Command("sbatch", sbatchArgs...) } // scancelCmd func scancelFunc(container arvados.Container) *exec.Cmd { return exec.Command("scancel", "--name="+container.UUID) } // Wrap these so that they can be overridden by tests var sbatchCmd = sbatchFunc var scancelCmd = scancelFunc // Submit job to slurm using sbatch. func submit(dispatcher *dispatch.Dispatcher, container arvados.Container, crunchRunCommand []string) (submitErr error) { 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 } dispatcher.Unlock(container.UUID) }() cmd := sbatchCmd(container) // 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))) var stdout, stderr bytes.Buffer cmd.Stdout = &stdout cmd.Stderr = &stderr // Mutex between squeue sync and running sbatch or scancel. sqCheck.L.Lock() defer sqCheck.L.Unlock() log.Printf("exec sbatch %+q", cmd.Args) err := cmd.Run() switch err.(type) { case nil: log.Printf("sbatch succeeded: %q", strings.TrimSpace(stdout.String())) return nil case *exec.ExitError: return fmt.Errorf("sbatch %+q failed: %v (stderr: %q)", cmd.Args, err, stderr.Bytes()) default: return fmt.Errorf("exec failed: %v", err) } } // 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 arvados.Container, monitorDone *bool) { submitted := false for !*monitorDone { if sqCheck.HasUUID(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, theConfig.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.Unlock(container.UUID) } 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 arvados.Container err := dispatcher.Arv.Get("containers", container.UUID, nil, &con) if err != nil { log.Printf("Error getting final container state: %v", err) } switch con.State { case dispatch.Locked: log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.", container.UUID, con.State, dispatch.Queued) dispatcher.Unlock(container.UUID) case dispatch.Running: st := dispatch.Cancelled 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) default: // Container state is Queued, Complete or Cancelled so stop monitoring it. return } } } } // 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 arvados.Container, status chan arvados.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.Priority == 0 && (container.State == dispatch.Locked || container.State == dispatch.Running) { log.Printf("Canceling container %s", container.UUID) // Mutex between squeue sync and running sbatch or scancel. sqCheck.L.Lock() cmd := scancelCmd(container) msg, err := cmd.CombinedOutput() sqCheck.L.Unlock() if err != nil { log.Printf("Error stopping container %s with %v %v: %v %v", container.UUID, cmd.Path, cmd.Args, err, string(msg)) if sqCheck.HasUUID(container.UUID) { log.Printf("Container %s is still in squeue after scancel.", container.UUID) continue } } // Ignore errors; if necessary, we'll try again next time dispatcher.UpdateState(container.UUID, dispatch.Cancelled) } } monitorDone = true } 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 }