X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/861cff5ffc2eb2739573b8991fca1cfdc388377f..c3d4f8a585202ec58df5506934b698039c200b68:/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 8fbc0fa8b6..1c080f36ac 100644 --- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go +++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go @@ -1,300 +1,296 @@ package main +// Dispatcher service for Crunch that submits containers to the slurm queue. + import ( + "bytes" "flag" "fmt" - "git.curoverse.com/arvados.git/sdk/go/arvadosclient" - "io/ioutil" "log" + "math" "os" "os/exec" - "os/signal" - "sync" - "syscall" + "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.Fatalf("%q", err) + log.Fatal(err) } } var ( - arv arvadosclient.ArvadosClient - runningCmds map[string]*exec.Cmd - runningCmdsMutex sync.Mutex - waitGroup sync.WaitGroup - doneProcessing chan bool - sigChan chan os.Signal + 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") - - priorityPollInterval := flags.Int( - "container-priority-poll-interval", - 60, - "Interval in seconds to check priority of a dispatched container") - - 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") + 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:]) - var err error - arv, err = arvadosclient.MakeArvadosClient() + err := readConfig(&theConfig, *configPath) if err != nil { return err } - // 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() + if theConfig.CrunchRunCommand == nil { + theConfig.CrunchRunCommand = []string{"crunch-run"} + } - return nil -} + if theConfig.PollPeriod == 0 { + theConfig.PollPeriod = arvados.Duration(10 * time.Second) + } -// 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) { - ticker := time.NewTicker(time.Duration(pollInterval) * time.Second) - - for { - select { - case <-ticker.C: - dispatchSlurm(priorityPollInterval, crunchRunCommand, finishCommand) - case <-doneProcessing: - ticker.Stop() - return + 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).") } -} - -// Container data -type Container struct { - UUID string `json:"uuid"` - State string `json:"state"` - Priority int `json:"priority"` -} -// ContainerList is a list of the containers from api -type ContainerList struct { - Items []Container `json:"items"` -} - -// Get the list of queued containers from API server and invoke run for each container. -func dispatchSlurm(priorityPollInterval int, crunchRunCommand, finishCommand string) { - params := arvadosclient.Dict{ - "filters": [][]string{[]string{"state", "=", "Queued"}}, + if *dumpConfig { + log.Fatal(config.DumpAndExit(theConfig)) } - var containers ContainerList - err := arv.List("containers", params, &containers) + arv, err := arvadosclient.MakeArvadosClient() if err != nil { - log.Printf("Error getting list of queued containers: %q", err) - return + 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), } - for i := 0; i < len(containers.Items); i++ { - log.Printf("About to submit queued container %v", containers.Items[i].UUID) - // Run the container - go run(containers.Items[i], crunchRunCommand, finishCommand, priorityPollInterval) + if _, err := daemon.SdNotify(false, "READY=1"); err != nil { + log.Printf("Error notifying init daemon: %v", err) } + + return dispatcher.Run() } // sbatchCmd -func sbatchFunc(uuid string) *exec.Cmd { - return exec.Command("sbatch", "--job-name="+uuid, "--share", "--parsable") -} +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, ","))) + } -var sbatchCmd = sbatchFunc + return exec.Command("sbatch", sbatchArgs...) +} -// 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)) +// scancelCmd +func scancelFunc(container arvados.Container) *exec.Cmd { + return exec.Command("scancel", "--name="+container.UUID) } -var striggerCmd = striggerFunc +// Wrap these so that they can be overridden by tests +var sbatchCmd = sbatchFunc +var scancelCmd = scancelFunc // Submit job to slurm using sbatch. -func submit(container Container, crunchRunCommand string) (jobid string, submitErr error) { - submitErr = nil - - // Mark record as complete if anything errors out. +func submit(dispatcher *dispatch.Dispatcher, + container arvados.Container, crunchRunCommand []string) (submitErr error) { defer func() { - if submitErr != nil { - // This really should be an "Error" state, see #8018 - updateErr := arv.Update("containers", container.UUID, - arvadosclient.Dict{ - "container": arvadosclient.Dict{"state": "Complete"}}, - nil) - if updateErr != nil { - log.Printf("Error updating container state to 'Complete' for %v: %q", container.UUID, updateErr) - } + // 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.Unlock(container.UUID) + if err != nil { + log.Printf("Error unlocking container %s: %v", container.UUID, err) } }() - // Create the command and attach to stdin/stdout - cmd := sbatchCmd(container.UUID) - 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 - } - - stderrReader, stderrErr := cmd.StderrPipe() - if stderrErr != nil { - submitErr = fmt.Errorf("Error creating stderr pipe %v: %q", container.UUID, stderrErr) - return - } - - 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) - stdoutChan <- b - close(stdoutChan) - }() - - stderrChan := make(chan []byte) - go func() { - b, _ := ioutil.ReadAll(stderrReader) - stderrChan <- b - close(stderrChan) - }() - - // 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() - - err = cmd.Wait() + cmd := sbatchCmd(container) - stdoutMsg := <-stdoutChan - stderrmsg := <-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 = string(stdoutMsg) + // Mutex between squeue sync and running sbatch or scancel. + sqCheck.L.Lock() + defer sqCheck.L.Unlock() - 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 + log.Printf("exec sbatch %+q", cmd.Args) err := cmd.Run() - if err != nil { - log.Printf("While setting up strigger: %v", err) + 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) + default: + return fmt.Errorf("exec failed: %v", err) } } -// Run a queued container. -// Set container state to locked (TBD) -// Submit job to slurm to execute crunch-run command for the container -// If the container priority becomes zero while crunch job is still running, cancel the job. -func run(container Container, crunchRunCommand, finishCommand string, priorityPollInterval int) { - - jobid, err := submit(container, crunchRunCommand) - if err != nil { - log.Printf("Error queuing container run: %v", err) - return - } +// 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) + } - insecure := "0" - if arv.ApiInsecure { - insecure = "1" - } - finalizeRecordOnFinish(jobid, container.UUID, finishCommand, arv.ApiServer, arv.ApiToken, insecure) - - // Update container status to Running, this is a temporary workaround - // to avoid resubmitting queued containers because record locking isn't - // implemented yet. - 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) + 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 + } + } } +} - log.Printf("Submitted container run for %v", container.UUID) - - containerUUID := container.UUID +// 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() - // A goroutine to terminate the runner if container priority becomes zero - priorityTicker := time.NewTicker(time.Duration(priorityPollInterval) * time.Second) - go func() { - for _ = range priorityTicker.C { - var container Container - err := arv.Get("containers", containerUUID, nil, &container) if err != nil { - log.Printf("Error getting container info for %v: %q", container.UUID, err) - } else { - if container.Priority == 0 { - log.Printf("Canceling container %v", container.UUID) - priorityTicker.Stop() - cancelcmd := exec.Command("scancel", "--name="+container.UUID) - cancelcmd.Run() - } - if container.State == "Complete" { - priorityTicker.Stop() + 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 }