X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/48c0b2f90d232d1508f1a6c8214c1b8e33c78795..fd4d26e448b1f9f45f84c0ff9ec10db54471d880:/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 8c3f5c99fc..c1009a5d8e 100644 --- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go +++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.go @@ -1,307 +1,382 @@ +// 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" - "io/ioutil" "log" "math" "os" - "os/exec" - "os/signal" - "strconv" - "sync" - "syscall" + "regexp" + "strings" "time" + + "git.curoverse.com/arvados.git/lib/dispatchcloud" + "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" ) -func main() { - err := doMain() - if err != nil { - log.Fatalf("%q", err) - } -} +const initialNiceValue int64 = 10000 var ( - arv arvadosclient.ArvadosClient - runningCmds map[string]*exec.Cmd - runningCmdsMutex sync.Mutex - waitGroup sync.WaitGroup - doneProcessing chan bool - sigChan chan os.Signal + version = "dev" + defaultConfigPath = "/etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml" ) -func doMain() error { - flags := flag.NewFlagSet("crunch-dispatch-slurm", flag.ExitOnError) +type Dispatcher struct { + *dispatch.Dispatcher + cluster *arvados.Cluster + sqCheck *SqueueChecker + slurm Slurm - pollInterval := flags.Int( - "poll-interval", - 10, - "Interval in seconds to poll for queued containers") + Client arvados.Client - priorityPollInterval := flags.Int( - "container-priority-poll-interval", - 60, - "Interval in seconds to check priority of a dispatched container") + SbatchArguments []string + PollPeriod arvados.Duration + PrioritySpread int64 - crunchRunCommand := flags.String( - "crunch-run-command", - "/usr/bin/crunch-run", - "Crunch command to run container") + // 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 - finishCommand := flags.String( - "finish-command", - "/usr/bin/crunch-finish-slurm.sh", - "Command to run from strigger when job is finished") + // Extra RAM to reserve (in Bytes) for SLURM job, in addition + // to the amount specified in the container's RuntimeConstraints + ReserveExtraRAM int64 - // Parse args; omit the first arg which is the command name - flags.Parse(os.Args[1:]) + // Minimum time between two attempts to run the same container + MinRetryPeriod arvados.Duration - var err error - arv, err = arvadosclient.MakeArvadosClient() + // Batch size for container queries + BatchSize int64 +} + +func main() { + disp := &Dispatcher{} + err := disp.Run(os.Args[0], os.Args[1:]) if err != nil { + log.Fatal(err) + } +} + +func (disp *Dispatcher) Run(prog string, args []string) error { + if err := disp.configure(prog, args); err != nil { return err } + disp.setup() + return disp.run() +} - // Channel to terminate - doneProcessing = make(chan bool) +// configure() loads config files. Tests skip this. +func (disp *Dispatcher) configure(prog string, args []string) error { + flags := flag.NewFlagSet(prog, 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(args) - // 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) + // Print version information if requested + if *getVersion { + fmt.Printf("crunch-dispatch-slurm %s\n", version) + return nil + } - // Run all queued containers - runQueuedContainers(*pollInterval, *priorityPollInterval, *crunchRunCommand, *finishCommand) + log.Printf("crunch-dispatch-slurm %s started", version) - // Wait for all running crunch jobs to complete / terminate - waitGroup.Wait() + err := disp.readConfig(*configPath) + if err != nil { + return err + } - return nil -} + if disp.CrunchRunCommand == nil { + disp.CrunchRunCommand = []string{"crunch-run"} + } -// 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) + if disp.PollPeriod == 0 { + disp.PollPeriod = arvados.Duration(10 * time.Second) + } - for { - select { - case <-ticker.C: - dispatchSlurm(priorityPollInterval, crunchRunCommand, finishCommand) - case <-doneProcessing: - ticker.Stop() - return + if disp.Client.APIHost != "" || disp.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", disp.Client.APIHost) + os.Setenv("ARVADOS_API_TOKEN", disp.Client.AuthToken) + os.Setenv("ARVADOS_API_HOST_INSECURE", "") + if disp.Client.Insecure { + os.Setenv("ARVADOS_API_HOST_INSECURE", "1") } + os.Setenv("ARVADOS_KEEP_SERVICES", strings.Join(disp.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"` - RuntimeConstraints map[string]int64 `json:"runtime_constraints"` -} - -// ContainerList is a list of the containers from api -type ContainerList struct { - Items []Container `json:"items"` -} + if *dumpConfig { + return config.DumpAndExit(disp) + } -// 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"}}, + siteConfig, err := arvados.GetConfig(arvados.DefaultConfigFile) + if os.IsNotExist(err) { + log.Printf("warning: no cluster config (%s), proceeding with no node types defined", err) + } else if err != nil { + return fmt.Errorf("error loading config: %s", err) + } else if disp.cluster, err = siteConfig.GetCluster(""); err != nil { + return fmt.Errorf("config error: %s", err) } - var containers ContainerList - err := arv.List("containers", params, &containers) + return nil +} + +// setup() initializes private fields after configure(). +func (disp *Dispatcher) setup() { + arv, err := arvadosclient.MakeArvadosClient() if err != nil { - log.Printf("Error getting list of queued containers: %q", err) - return + log.Fatalf("Error making Arvados client: %v", err) } + arv.Retries = 25 - 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) + disp.slurm = &slurmCLI{} + disp.sqCheck = &SqueueChecker{ + Period: time.Duration(disp.PollPeriod), + PrioritySpread: disp.PrioritySpread, + Slurm: disp.slurm, + } + disp.Dispatcher = &dispatch.Dispatcher{ + Arv: arv, + BatchSize: disp.BatchSize, + RunContainer: disp.runContainer, + PollPeriod: time.Duration(disp.PollPeriod), + MinRetryPeriod: time.Duration(disp.MinRetryPeriod), } } -// sbatchCmd -func sbatchFunc(container Container) *exec.Cmd { - memPerCPU := math.Ceil(float64(container.RuntimeConstraints["ram"]) / float64(container.RuntimeConstraints["vcpus"]*1048576)) - return exec.Command("sbatch", "--share", "--parsable", - "--job-name="+container.UUID, - "--mem-per-cpu="+strconv.Itoa(int(memPerCPU)), - "--cpus-per-task="+strconv.Itoa(int(container.RuntimeConstraints["vcpus"]))) -} +func (disp *Dispatcher) run() error { + defer disp.sqCheck.Stop() -var sbatchCmd = sbatchFunc + if disp.cluster != nil && len(disp.cluster.InstanceTypes) > 0 { + go dispatchcloud.SlurmNodeTypeFeatureKludge(disp.cluster) + } -// 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)) + if _, err := daemon.SdNotify(false, "READY=1"); err != nil { + log.Printf("Error notifying init daemon: %v", err) + } + go disp.checkSqueueForOrphans() + return disp.Dispatcher.Run(context.Background()) } -var striggerCmd = striggerFunc - -// 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. - 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) - } +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 (disp *Dispatcher) checkSqueueForOrphans() { + for _, uuid := range disp.sqCheck.All() { + if !containerUuidPattern.MatchString(uuid) { + continue + } + err := disp.TrackContainer(uuid) + if err != nil { + 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 - } +func (disp *Dispatcher) slurmConstraintArgs(container arvados.Container) []string { + mem := int64(math.Ceil(float64(container.RuntimeConstraints.RAM+container.RuntimeConstraints.KeepCacheRAM+disp.ReserveExtraRAM) / 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))) + return []string{ + fmt.Sprintf("--mem=%d", mem), + fmt.Sprintf("--cpus-per-task=%d", container.RuntimeConstraints.VCPUs), + fmt.Sprintf("--tmp=%d", disk), } +} - 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() - - stdoutMsg := <-stdoutChan - stderrmsg := <-stderrChan - - if err != nil { - submitErr = fmt.Errorf("Container submission failed %v: %v %v", cmd.Args, err, stderrmsg) - return +func (disp *Dispatcher) sbatchArgs(container arvados.Container) ([]string, error) { + var args []string + args = append(args, disp.SbatchArguments...) + args = append(args, "--job-name="+container.UUID, fmt.Sprintf("--nice=%d", initialNiceValue)) + + if disp.cluster == nil { + // no instance types configured + args = append(args, disp.slurmConstraintArgs(container)...) + } else if it, err := dispatchcloud.ChooseInstanceType(disp.cluster, &container); err == dispatchcloud.ErrInstanceTypesNotConfigured { + // ditto + args = append(args, disp.slurmConstraintArgs(container)...) + } else if err != nil { + return nil, err + } else { + // use instancetype constraint instead of slurm mem/cpu/tmp specs + args = append(args, "--constraint=instancetype="+it.Name) } - // If everything worked out, got the jobid on stdout - jobid = string(stdoutMsg) + if len(container.SchedulingParameters.Partitions) > 0 { + args = append(args, "--partition="+strings.Join(container.SchedulingParameters.Partitions, ",")) + } - return + return args, nil } -// 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 - err := cmd.Run() +func (disp *Dispatcher) submit(container arvados.Container, crunchRunCommand []string) error { + // append() here avoids modifying crunchRunCommand's + // underlying array, which is shared with other goroutines. + crArgs := append([]string(nil), crunchRunCommand...) + crArgs = append(crArgs, container.UUID) + crScript := strings.NewReader(execScript(crArgs)) + + disp.sqCheck.L.Lock() + defer disp.sqCheck.L.Unlock() + + sbArgs, err := disp.sbatchArgs(container) if err != nil { - log.Printf("While setting up strigger: %v", err) + return err } + log.Printf("running sbatch %+q", sbArgs) + return disp.slurm.Batch(crScript, sbArgs) } -// 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) { +// 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 (disp *Dispatcher) runContainer(_ *dispatch.Dispatcher, ctr arvados.Container, status <-chan arvados.Container) { + ctx, cancel := context.WithCancel(context.Background()) + defer cancel() + + if ctr.State == dispatch.Locked && !disp.sqCheck.HasUUID(ctr.UUID) { + log.Printf("Submitting container %s to slurm", ctr.UUID) + if err := disp.submit(ctr, disp.CrunchRunCommand); err != nil { + var text string + if err, ok := err.(dispatchcloud.ConstraintsNotSatisfiableError); ok { + var logBuf bytes.Buffer + fmt.Fprintf(&logBuf, "cannot run container %s: %s\n", ctr.UUID, err) + if len(err.AvailableTypes) == 0 { + fmt.Fprint(&logBuf, "No instance types are configured.\n") + } else { + fmt.Fprint(&logBuf, "Available instance types:\n") + for _, t := range err.AvailableTypes { + fmt.Fprintf(&logBuf, + "Type %q: %d VCPUs, %d RAM, %d Scratch, %f Price\n", + t.Name, t.VCPUs, t.RAM, t.Scratch, t.Price, + ) + } + } + text = logBuf.String() + disp.UpdateState(ctr.UUID, dispatch.Cancelled) + } else { + text = fmt.Sprintf("Error submitting container %s to slurm: %s", ctr.UUID, err) + } + log.Print(text) - jobid, err := submit(container, crunchRunCommand) - if err != nil { - log.Printf("Error queuing container run: %v", err) - return - } + 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) - 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) + disp.Unlock(ctr.UUID) + return + } } - log.Printf("Submitted container run for %v", container.UUID) + log.Printf("Start monitoring container %v in state %q", ctr.UUID, ctr.State) + defer log.Printf("Done monitoring container %s", ctr.UUID) - containerUUID := container.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 && disp.sqCheck.HasUUID(uuid) { + } + cancel() + }(ctr.UUID) - // 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) + 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) + } + switch ctr.State { + case dispatch.Running: + disp.UpdateState(ctr.UUID, dispatch.Cancelled) + case dispatch.Locked: + disp.Unlock(ctr.UUID) + } + return + case updated, ok := <-status: + if !ok { + log.Printf("container %s is done: cancel slurm job", ctr.UUID) + disp.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) + disp.scancel(ctr) } 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() + p := int64(updated.Priority) + if p <= 1000 { + // API is providing + // user-assigned priority. If + // ctrs have equal priority, + // run the older one first. + p = int64(p)<<50 - (updated.CreatedAt.UnixNano() >> 14) } + disp.sqCheck.SetPriority(ctr.UUID, p) } } - }() + } +} +func (disp *Dispatcher) scancel(ctr arvados.Container) { + disp.sqCheck.L.Lock() + err := disp.slurm.Cancel(ctr.UUID) + disp.sqCheck.L.Unlock() + if err != nil { + log.Printf("scancel: %s", err) + time.Sleep(time.Second) + } else if disp.sqCheck.HasUUID(ctr.UUID) { + log.Printf("container %s is still in squeue after scancel", ctr.UUID) + time.Sleep(time.Second) + } +} + +func (disp *Dispatcher) readConfig(path string) error { + err := config.LoadFile(disp, path) + if err != nil && os.IsNotExist(err) && path == defaultConfigPath { + log.Printf("Config not specified. Continue with default configuration.") + err = nil + } + return err }