X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2efdb0e205abe63c5ca777fc4dacca65192e5dd3..cae94f22b760c6c6899fc4d23db15d389535ff0a:/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go diff --git a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go index f718fbcdce..b33dc64e7b 100644 --- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go +++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go @@ -3,10 +3,14 @@ package main // Dispatcher service for Crunch that submits containers to the slurm queue. import ( + "encoding/json" "flag" "fmt" + "git.curoverse.com/arvados.git/sdk/go/arvados" "git.curoverse.com/arvados.git/sdk/go/arvadosclient" "git.curoverse.com/arvados.git/sdk/go/dispatch" + "github.com/coreos/go-systemd/daemon" + "io" "io/ioutil" "log" "math" @@ -16,6 +20,20 @@ import ( "time" ) +// 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 +} + func main() { err := doMain() if err != nil { @@ -24,26 +42,54 @@ func main() { } var ( - crunchRunCommand *string - squeueUpdater Squeue + config Config + squeueUpdater Squeue ) +const defaultConfigPath = "/etc/arvados/crunch-dispatch-slurm/config.json" + 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 configuration file") // Parse args; omit the first arg which is the command name flags.Parse(os.Args[1:]) + err := readConfig(&config, *configPath) + if err != nil { + log.Printf("Error reading configuration: %v", err) + return err + } + + if config.CrunchRunCommand == nil { + config.CrunchRunCommand = []string{"crunch-run"} + } + + if config.PollPeriod == 0 { + config.PollPeriod = arvados.Duration(10 * time.Second) + } + + if config.Client.APIHost != "" || config.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", config.Client.APIHost) + os.Setenv("ARVADOS_API_TOKEN", config.Client.AuthToken) + os.Setenv("ARVADOS_API_INSECURE", "") + if config.Client.Insecure { + os.Setenv("ARVADOS_API_INSECURE", "1") + } + os.Setenv("ARVADOS_KEEP_SERVICES", "") + os.Setenv("ARVADOS_EXTERNAL_CLIENT", "") + } else { + log.Printf("warning: Client credentials missing from config, so falling back on environment variables (deprecated).") + } + arv, err := arvadosclient.MakeArvadosClient() if err != nil { log.Printf("Error making Arvados client: %v", err) @@ -51,15 +97,19 @@ func doMain() error { } arv.Retries = 25 - squeueUpdater.StartMonitor(time.Duration(*pollInterval) * time.Second) + squeueUpdater.StartMonitor(time.Duration(config.PollPeriod)) defer squeueUpdater.Done() dispatcher := dispatch.Dispatcher{ Arv: arv, RunContainer: run, - PollInterval: time.Duration(*pollInterval) * time.Second, + PollInterval: time.Duration(config.PollPeriod), DoneProcessing: make(chan struct{})} + if _, err := daemon.SdNotify("READY=1"); err != nil { + log.Printf("Error notifying init daemon: %v", err) + } + err = dispatcher.RunDispatcher() if err != nil { return err @@ -69,17 +119,21 @@ func doMain() error { } // 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 { + memPerCPU := math.Ceil(float64(container.RuntimeConstraints.RAM) / (float64(container.RuntimeConstraints.VCPUs) * 1048576)) + + var sbatchArgs []string + sbatchArgs = append(sbatchArgs, "--share") + sbatchArgs = append(sbatchArgs, config.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)) + + 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) } @@ -89,9 +143,7 @@ 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 - + 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. @@ -99,10 +151,7 @@ func submit(dispatcher *dispatch.Dispatcher, // OK, no cleanup needed return } - err := dispatcher.Arv.Update("containers", container.UUID, - arvadosclient.Dict{ - "container": arvadosclient.Dict{"state": "Queued"}}, - nil) + err := dispatcher.Unlock(container.UUID) if err != nil { log.Printf("Error unlocking container %s: %v", container.UUID, err) } @@ -154,7 +203,7 @@ func submit(dispatcher *dispatch.Dispatcher, // 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) + io.WriteString(stdinWriter, execScript(append(crunchRunCommand, container.UUID))) stdinWriter.Close() err = cmd.Wait() @@ -166,13 +215,11 @@ func submit(dispatcher *dispatch.Dispatcher, close(stderrChan) if err != nil { - submitErr = fmt.Errorf("Container submission failed %v: %v %v", cmd.Args, err, stderrmsg) + submitErr = fmt.Errorf("Container submission failed: %v: %v (stderr: %q)", cmd.Args, err, stderrmsg) return } - // If everything worked out, got the jobid on stdout - jobid = strings.TrimSpace(string(stdoutMsg)) - + log.Printf("sbatch succeeded: %s", strings.TrimSpace(string(stdoutMsg))) return } @@ -181,7 +228,7 @@ func submit(dispatcher *dispatch.Dispatcher, // // 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) { +func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container arvados.Container, monitorDone *bool) { submitted := false for !*monitorDone { if squeueUpdater.CheckSqueue(container.UUID) { @@ -193,11 +240,11 @@ func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container dispatch.C log.Printf("About to submit queued container %v", container.UUID) - if _, err := submit(dispatcher, container, *crunchRunCommand); err != nil { + if err := submit(dispatcher, container, config.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) + dispatcher.Unlock(container.UUID) } submitted = true } else { @@ -207,26 +254,26 @@ func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container dispatch.C // release it back to the Queue, if it is Running then // clean up the record. - var con dispatch.Container + 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) } - var st string switch con.State { case dispatch.Locked: - st = dispatch.Queued + 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 + 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 } - - 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) } } } @@ -236,8 +283,8 @@ func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container dispatch.C // 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) { + container arvados.Container, + status chan arvados.Container) { log.Printf("Monitoring container %v started", container.UUID) defer log.Printf("Monitoring container %v finished", container.UUID) @@ -271,3 +318,18 @@ func run(dispatcher *dispatch.Dispatcher, } monitorDone = true } + +func readConfig(dst interface{}, path string) error { + if buf, err := ioutil.ReadFile(path); err != nil && os.IsNotExist(err) { + if path == defaultConfigPath { + log.Printf("Config not specified. Continue with default configuration.") + } else { + return fmt.Errorf("Config file not found %q: %v", path, err) + } + } else if err != nil { + return fmt.Errorf("Error reading config %q: %v", path, err) + } else if err = json.Unmarshal(buf, dst); err != nil { + return fmt.Errorf("Error decoding config %q: %v", path, err) + } + return nil +}